Contacts of the helix formed by residues 155 - 178 (chain A) in PDB entry 3EUP
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 155 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ASP 3.4 4.5 + - - +
154A THR* 1.3 70.8 - - - +
156A VAL* 1.3 61.8 + - - +
157A THR* 3.5 7.6 + - - -
158A LYS* 3.2 43.8 + - + +
159A ILE* 2.4 37.4 + - + +
185B TYR* 4.6 9.2 - - - -
188B GLU* 4.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 3.6 39.3 - - + +
141A ILE* 3.8 29.4 - - + +
142A LYS* 4.5 23.3 - - + +
145A ILE* 4.1 15.7 - - + -
154A THR* 3.1 17.0 + - + +
155A ASP* 1.3 72.2 + - - +
157A THR* 1.3 58.6 + - - +
159A ILE* 3.4 3.3 + - - +
160A ALA* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS* 2.9 33.6 + - - +
138A VAL* 4.5 2.7 - - - +
155A ASP* 3.4 6.3 + - - -
156A VAL* 1.3 78.8 - - - +
158A LYS* 1.3 63.0 + - - +
160A ALA* 3.3 2.1 + - - +
161A PHE* 3.0 29.9 + - + -
182B TYR* 6.1 0.4 - - + -
185B TYR* 3.5 36.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASP* 3.2 39.2 + - - +
157A THR* 1.3 80.9 - - - +
159A ILE* 1.3 62.0 + - + +
161A PHE* 4.0 1.2 - - - +
162A SER* 2.7 36.7 + - - -
185B TYR* 3.9 26.1 - - + +
188B GLU* 3.3 39.9 + - + +
189B SER* 3.7 16.4 - - - +
192B ASP* 2.6 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 5.8 0.2 - - + -
141A ILE* 4.0 18.6 - - + -
154A THR* 3.5 15.9 - - + -
155A ASP* 2.4 53.5 + - + +
156A VAL* 3.8 4.0 - - - +
158A LYS* 1.3 82.4 - - + +
160A ALA* 1.3 61.2 + - - +
162A SER* 3.3 5.8 + - - -
163A MET* 2.9 43.5 + - + +
193A LEU* 4.1 20.6 - - + +
194A ILE* 5.1 4.0 - - + -
197A ILE* 3.8 32.5 - - + -
189B SER* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS* 4.0 10.3 - - + +
137A LEU* 3.4 36.3 - - + +
138A VAL* 3.7 23.6 - - + -
141A ILE* 4.2 6.1 - - + -
156A VAL 3.0 17.7 + - - +
157A THR 3.3 4.0 + - - +
159A ILE* 1.3 77.5 - - - +
161A PHE* 1.3 61.8 + - - +
163A MET* 4.5 0.7 - - - -
164A ILE* 3.3 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ILE* 4.4 5.8 - - + -
131A LEU* 3.8 20.0 - - + -
134A LYS* 3.6 41.1 - - + -
157A THR* 3.0 28.7 + - + +
158A LYS 4.2 2.0 - - - +
160A ALA* 1.3 75.4 - - - +
162A SER* 1.3 57.4 + - - +
164A ILE* 3.3 8.7 + - + +
165A ALA* 3.0 23.4 + - - +
173B ILE* 3.5 31.1 - - + +
182B TYR* 3.4 55.9 - + + +
185B TYR* 3.5 22.2 - + + -
186B VAL* 4.0 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LYS 2.7 20.6 + - - -
159A ILE* 3.3 4.7 + - - -
161A PHE* 1.3 74.6 - - - +
163A MET* 1.3 59.4 - - - +
165A ALA* 3.3 7.4 + - - +
166A LEU* 2.9 32.6 + - - +
193A LEU* 3.8 17.3 - - - -
166B LEU* 4.2 4.6 - - - +
185B TYR 3.9 5.7 + - - -
186B VAL* 4.2 4.5 - - - -
189B SER* 2.5 38.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 3.3 57.9 - - + +
89A TYR* 3.9 8.3 - - + -
133A TRP* 5.6 0.4 - - - -
137A LEU* 3.7 26.7 - - + -
141A ILE* 4.5 5.2 - - - -
159A ILE* 2.9 38.1 + - + +
160A ALA 3.6 4.9 - - - +
162A SER* 1.3 73.1 - - - +
164A ILE* 1.3 61.3 + - - +
166A LEU* 3.1 2.9 + - - +
167A VAL* 2.9 36.5 + - + +
190A LEU* 3.8 22.2 - - + +
193A LEU* 4.0 10.3 - - + +
194A ILE* 4.2 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ILE* 3.7 34.5 - - + +
133A TRP* 3.8 33.7 - - + -
134A LYS* 3.7 40.2 - - + +
137A LEU* 3.8 11.0 - - + -
160A ALA 3.4 15.7 - - - +
161A PHE* 3.3 13.4 + - + +
162A SER 3.3 0.4 - - - -
163A MET* 1.3 75.0 - - - +
165A ALA* 1.3 62.9 + - - +
167A VAL* 3.3 1.2 + - - -
168A GLU* 3.0 29.8 + - + +
173B ILE* 3.9 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PHE 3.0 11.2 + - - +
162A SER 3.5 7.9 - - - +
164A ILE* 1.3 77.1 - - - +
166A LEU* 1.3 57.8 + - - +
168A GLU* 4.9 0.7 - - - -
169A GLY 2.8 25.3 + - - -
165B ALA 3.5 11.0 - - - +
166B LEU* 4.3 5.4 - - + +
169B GLY* 3.7 25.3 - - - -
173B ILE* 4.0 2.4 - - + +
186B VAL* 3.4 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A SER* 2.9 20.2 + - - +
163A MET 3.1 4.9 + - - +
165A ALA* 1.3 78.1 - - - +
167A VAL* 1.3 57.2 + - - +
170A ALA* 2.9 24.4 + - - +
186A VAL* 3.1 35.3 - - + +
187A PHE* 5.8 0.7 - - - -
189A SER* 4.1 14.1 - - - +
190A LEU* 3.8 37.7 - - + +
193A LEU* 4.1 20.4 - - + -
162B SER* 4.3 8.3 - - - +
165B ALA* 4.3 2.9 - - + -
166B LEU* 3.7 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TYR* 3.7 45.5 - - + -
93A TYR* 6.2 0.7 - - + -
101A PHE* 5.9 2.7 - - + -
133A TRP* 4.1 14.4 - - + -
163A MET* 2.9 21.6 + - + +
164A ILE 3.9 2.9 - - - +
166A LEU* 1.3 75.1 - - - +
168A GLU* 1.3 77.8 + - - +
170A ALA* 3.2 8.0 + - - +
171A ILE* 3.0 33.0 + - + +
187A PHE* 4.5 9.9 - - + -
190A LEU* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PHE* 5.7 0.5 - - - -
106A CYS* 2.9 34.8 - - - +
108A LEU* 3.6 12.2 - - + +
109A LEU* 3.7 15.5 - - + +
133A TRP* 3.5 30.7 - - + -
164A ILE* 3.0 22.9 + - + +
165A ALA* 4.2 2.7 - - - +
167A VAL* 1.3 83.0 - - - +
169A GLY* 1.3 56.7 + - - +
171A ILE* 3.4 12.0 + - - +
172A LEU* 3.1 26.6 + - - +
169B GLY* 5.1 2.7 - - - -
172B LEU* 3.4 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ALA 2.8 18.6 + - - -
168A GLU* 1.3 74.1 - - - +
170A ALA* 1.3 63.0 + - - +
172A LEU* 3.3 8.5 + - - +
173A ILE* 3.1 28.9 + - - +
165B ALA* 3.7 26.6 - - - -
168B GLU* 5.1 3.1 - - - -
169B GLY* 4.7 5.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU 2.9 20.2 + - - +
167A VAL 3.5 5.2 - - - +
169A GLY* 1.3 75.3 - - - +
171A ILE* 1.3 61.6 + - - +
173A ILE* 3.3 2.7 + - - +
174A HIS 3.0 18.7 + - - -
183A SER* 3.3 15.6 - - - +
186A VAL* 3.7 26.2 - - + +
187A PHE* 3.6 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A TYR* 3.7 55.2 - - + +
101A PHE* 3.9 22.2 - - + -
106A CYS* 4.1 13.0 - - + +
109A LEU* 3.7 18.8 - - + -
167A VAL* 3.0 21.2 + - + +
168A GLU* 3.7 27.8 - - - +
170A ALA* 1.3 73.5 - - - +
172A LEU* 1.3 52.4 + - - +
174A HIS* 3.2 2.8 + - - +
175A ARG* 2.8 45.1 + - + +
187A PHE* 5.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 4.3 7.6 - - + +
168A GLU 3.1 13.2 + - - +
169A GLY* 3.5 10.8 - - - +
170A ALA 3.3 0.2 - - - -
171A ILE* 1.3 76.2 - - - +
173A ILE* 1.3 58.2 + - + +
175A ARG* 3.2 3.8 + - - -
176A ALA* 2.9 27.7 + - - +
108B LEU* 5.3 2.7 - - + -
109B LEU* 3.7 32.5 - - + +
112B THR* 3.6 35.8 - - + +
113B ILE* 4.2 10.5 - - + -
130B ILE* 5.0 11.0 - - + -
168B GLU* 3.5 41.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLY 3.1 15.3 + - - +
170A ALA* 3.6 5.8 - - - +
172A LEU* 1.3 73.6 - - + +
174A HIS* 1.3 66.9 + - - +
176A ALA* 4.6 0.2 - - - -
177A THR* 2.7 36.5 + - + +
182A TYR* 3.8 29.8 - - + -
183A SER* 4.1 7.4 - - - +
186A VAL* 3.9 15.5 - - + -
130B ILE* 3.7 25.8 - - + -
161B PHE* 3.6 39.5 - - + +
164B ILE* 3.9 14.1 - - + -
165B ALA* 4.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A TYR* 2.7 40.8 - + + +
170A ALA 3.0 11.0 + - - +
171A ILE 3.2 6.0 + - - +
173A ILE* 1.3 78.9 - - - +
175A ARG* 1.3 63.2 + - + +
177A THR* 4.0 4.0 - - - -
178A LYS* 2.7 48.4 + - - -
179A ASN 3.8 2.5 + - - -
180A ARG* 3.5 54.1 + - + +
183A SER* 3.4 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A TYR* 3.3 24.2 + - - +
102A PRO 5.1 1.2 + - - -
104A GLY* 3.1 28.4 + - - +
105A GLY* 3.7 16.9 - - - +
106A CYS 5.5 0.2 - - - +
109A LEU* 6.0 0.9 - - + -
110A ASN* 5.7 0.9 - - - -
171A ILE* 2.8 33.5 + - + +
172A LEU* 3.2 5.3 + - - +
174A HIS* 1.3 79.3 + - + +
176A ALA* 1.3 60.1 + - - +
178A LYS* 4.3 4.7 + - - +
112B THR* 3.8 9.2 - - + -
113B ILE* 5.8 2.9 - - + -
116B ASP* 2.9 37.9 - - + +
117B ASP* 2.3 39.9 + - - -
123B ARG* 3.5 15.4 - - - -
203B SO4 4.5 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 2.9 16.8 + - + +
173A ILE 4.0 2.9 - - - +
175A ARG* 1.3 76.9 - - - +
177A THR* 1.3 55.6 + - + +
112B THR* 3.6 24.6 - - - +
123B ARG* 2.8 33.8 + - - +
126B ALA* 4.2 4.7 - - - -
127B GLY* 3.2 24.7 + - - +
130B ILE* 4.2 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ILE* 2.7 27.7 + - + +
176A ALA* 1.3 81.8 - - + +
178A LYS* 1.3 70.4 + - - +
179A ASN* 3.2 18.1 + - - +
182A TYR* 3.5 32.2 - - + -
123B ARG* 4.0 7.9 + - - +
127B GLY* 4.3 7.9 - - - +
130B ILE* 4.1 25.8 - - + -
131B LEU* 4.3 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A HIS* 2.7 35.4 + - - -
175A ARG 4.6 3.6 - - - +
177A THR* 1.3 74.8 - - - +
179A ASN* 1.3 55.9 + - - +
180A ARG 4.1 0.7 + - - -
116B ASP 6.1 1.1 - - - -
120B ASP* 4.1 16.6 + - - -
123B ARG* 3.6 38.8 - - - +
124B LYS* 5.5 1.0 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il