Contacts of the helix formed by residues 164 - 182 (chain A) in PDB entry 4TLG
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 TRP 164 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LYS* 3.7 61.3 - - + +
112A LEU* 3.9 16.6 - - + -
113A LEU* 4.3 9.2 - - + -
161A LYS 3.5 15.2 + - - +
162A HIS 3.3 1.0 - - - -
163A LEU* 1.3 74.4 - - - +
165A LYS* 1.3 68.3 + - - +
166A PRO* 3.6 30.7 - - + +
167A ALA* 2.9 36.6 + - + +
168A VAL 3.0 9.7 + - - -
273A GLN* 3.5 20.6 - - - -
274A VAL* 4.1 18.2 - - + -
350A ASP* 2.8 38.7 + - + -
503A EDO 3.7 20.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU 3.1 6.4 + - - -
164A TRP* 1.3 72.9 - - - +
166A PRO* 1.3 73.0 - - + +
168A VAL* 3.2 4.3 + - + +
169A GLU* 3.0 46.4 + - + +
277A GLN 5.4 1.1 - - - -
304A ARG* 3.6 30.7 - - - +
306A GLN* 3.5 28.5 - - - +
380A THR* 4.9 7.5 - - + +
382A GLU* 3.0 31.0 + - - +
503A EDO 4.7 0.6 + - - -
511A EDO 3.6 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 3.8 7.0 - - + +
117A LYS* 5.8 1.9 - - - +
164A TRP* 3.6 38.1 - - + +
165A LYS* 1.3 93.7 - - + +
167A ALA* 1.3 61.1 + - - +
169A GLU* 3.5 8.1 + - - +
170A VAL* 3.4 21.0 + - - +
274A VAL* 3.7 24.5 - - + -
276A LEU* 3.9 8.3 - - + -
306A GLN* 5.0 0.7 - - - +
350A ASP* 5.4 0.2 - - - +
511A EDO 3.7 24.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PRO* 3.7 34.9 - - + +
112A LEU* 3.8 10.3 - - + -
162A HIS 4.2 4.7 - - - +
164A TRP* 2.9 31.2 + - + +
166A PRO* 1.3 70.8 - - - +
168A VAL* 1.3 66.3 + - - +
170A VAL* 3.0 22.0 + - - +
171A TYR 3.4 3.6 + - - -
518A 11A 3.8 13.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A HIS 3.8 10.1 - - - +
163A LEU* 3.6 23.8 - - - +
164A TRP 3.0 12.8 + - - +
165A LYS* 3.7 7.2 - - + +
167A ALA* 1.3 76.3 - - - +
169A GLU* 1.3 57.6 + - + +
171A TYR* 3.1 4.2 + - - +
172A GLN* 2.9 51.1 + - + +
204A LEU* 4.0 27.8 - - + -
205A VAL* 4.7 6.3 - - + -
304A ARG* 4.0 10.8 - - - +
518A 11A 4.1 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 5.5 6.5 - - + -
165A LYS* 3.0 35.4 + - + +
166A PRO* 3.7 7.2 - - - +
167A ALA 3.2 0.2 - - - -
168A VAL* 1.3 78.5 - - + +
170A VAL* 1.3 55.2 + - - +
172A GLN* 3.7 18.2 - - - +
173A GLN* 3.0 32.9 + - - +
277A GLN* 5.4 3.6 + - - -
511A EDO 2.7 41.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PRO* 6.2 0.7 - - + -
112A LEU* 3.9 29.2 - - + -
117A LYS* 4.2 16.5 - - + +
120A MET* 4.6 20.2 - - + -
121A ILE* 3.5 21.7 - - + +
124A ARG* 4.4 12.8 - - - +
166A PRO 3.4 14.3 + - - +
167A ALA* 3.0 11.0 + - - +
169A GLU* 1.3 75.0 - - - +
171A TYR* 1.3 75.3 + - + +
173A GLN* 4.8 0.7 - - - -
174A PHE* 2.9 26.9 + - - +
518A 11A 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASN* 3.3 26.9 + - - -
103A ILE* 3.5 26.7 - - + +
106A LEU* 4.8 3.5 - - + +
120A MET* 6.1 0.2 - - + -
123A LYS* 5.9 0.3 + - - -
124A ARG* 3.2 45.3 + - + +
153A PHE* 5.2 2.7 - + - -
167A ALA 3.4 1.6 + - - -
168A VAL 3.1 7.0 + - - +
170A VAL* 1.3 84.8 - - + +
172A GLN* 1.3 60.1 + - - +
174A PHE* 3.4 15.4 + + + +
175A PHE* 2.9 61.1 + + - -
205A VAL* 4.3 10.8 - - + -
518A 11A 3.0 43.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A VAL* 2.9 33.4 + - + +
169A GLU* 3.7 24.4 - - - +
171A TYR* 1.3 76.2 - - - +
173A GLN* 1.3 60.8 + - - +
175A PHE* 3.3 2.0 + - - -
176A SER* 3.0 25.1 + - - -
204A LEU* 2.9 27.8 + - - +
205A VAL* 4.3 5.8 - - + -
208A PHE* 3.4 53.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS* 3.4 41.1 + - - +
121A ILE* 4.3 12.1 - - + +
169A GLU 3.0 17.4 + - - +
170A VAL 3.9 3.6 - - - +
172A GLN* 1.3 76.2 - - - +
174A PHE* 1.3 58.5 + - - +
176A SER* 3.2 8.3 + - - -
177A ILE* 2.9 47.6 + - + +
208A PHE* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASN* 6.0 2.2 - - - -
121A ILE* 4.0 15.9 - - + +
124A ARG* 3.5 48.9 - - + -
125A ILE* 4.3 5.4 - - + -
128A CYS* 3.9 23.8 - - - -
151A MET* 6.1 7.0 - - + -
170A VAL 2.9 19.2 + - - +
171A TYR* 3.7 25.6 - + + +
173A GLN* 1.3 76.3 - - - +
175A PHE* 1.3 69.5 + + - +
177A ILE* 3.2 12.3 + - + +
178A LEU* 2.9 51.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A PHE* 4.8 13.2 - + - -
171A TYR* 2.9 51.3 + + - +
172A GLN* 3.3 4.0 + - - +
174A PHE* 1.3 82.2 - + - +
176A SER* 1.3 61.9 + - - +
178A LEU* 3.3 24.3 + - + +
179A GLU* 3.1 29.8 + - - +
186A LEU* 6.2 0.2 - - + -
189A LEU* 4.6 13.9 - - + -
205A VAL* 4.2 19.3 - - + -
208A PHE* 3.7 21.5 - - + +
209A MET* 3.7 40.6 - - + -
213A THR* 5.3 1.6 - - + -
518A 11A 4.6 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLN 3.0 7.0 + - - -
173A GLN* 3.5 11.8 - - - -
174A PHE 3.2 0.2 - - - -
175A PHE* 1.3 76.6 - - - +
177A ILE* 1.3 63.3 + - - +
179A GLU* 3.4 4.3 + - - +
180A ALA* 3.1 24.3 + - - +
208A PHE* 3.4 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE* 4.2 24.7 - - + -
121A ILE* 3.6 29.2 - - + -
125A ILE* 4.2 15.3 - - + -
173A GLN* 2.9 37.5 + - + +
174A PHE* 3.2 13.7 + - + +
176A SER* 1.3 77.9 - - - +
178A LEU* 1.3 56.5 + - - +
180A ALA* 4.7 1.1 - - - -
181A ASN* 2.9 55.5 + - + +
182A TYR* 4.8 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A CYS* 3.8 21.3 - - - -
151A MET* 6.0 2.2 - - - -
174A PHE* 2.9 33.8 + - + +
175A PHE* 3.5 30.1 - - + +
176A SER 3.3 0.2 - - - -
177A ILE* 1.3 75.8 - - - +
179A GLU* 1.3 62.2 + - - +
182A TYR* 2.8 51.2 + - + +
185A THR* 4.6 1.6 - - - +
186A LEU* 4.2 13.9 - - + -
213A THR* 5.6 1.8 - - + -
501A EDO 4.0 23.3 - - - -
513A EDO 3.7 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A MET* 3.3 18.1 - - - +
175A PHE* 3.1 17.9 + - - +
176A SER* 4.0 4.3 - - - +
178A LEU* 1.3 79.4 - - + +
180A ALA* 1.3 61.8 + - - +
181A ASN 3.6 0.2 + - - -
183A PRO* 3.9 11.8 - - - +
208A PHE 3.9 9.9 - - - +
209A MET* 3.7 4.8 - - + +
210A SER* 3.0 40.7 + - - +
213A THR* 2.6 29.4 + - - +
501A EDO 2.8 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TRP* 3.5 18.0 - - - -
45A ARG* 5.7 2.7 - - - +
55A MET* 3.8 17.1 - - + +
59A HIS* 4.5 2.9 + - - +
176A SER 3.1 18.2 + - - +
177A ILE* 4.7 0.7 - - - -
179A GLU* 1.3 78.4 - - - +
181A ASN* 1.3 71.4 + - - +
183A PRO* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TRP* 3.4 6.3 - - - -
58A ARG 5.0 0.5 - - - -
59A HIS* 2.9 37.6 + - + +
62A PHE* 3.3 27.5 - - + +
177A ILE* 2.9 39.9 + - - +
180A ALA* 1.3 89.4 - - - +
182A TYR* 1.3 68.3 + - + +
183A PRO* 3.3 5.8 - - - -
502A EDO 2.7 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A HIS* 4.5 2.5 - + - -
62A PHE* 5.5 0.4 - + - -
68A LEU* 3.6 10.0 - - + +
125A ILE* 3.5 24.1 - - + +
128A CYS* 3.8 33.4 - - + -
129A GLU* 2.6 33.2 + - - +
132A LEU* 3.7 21.5 - - + -
174A PHE* 6.2 0.4 - + - -
177A ILE* 4.3 14.6 - - + -
178A LEU* 2.8 25.0 + - + +
181A ASN* 1.3 96.2 - - + +
183A PRO* 1.4 63.5 - - - +
185A THR* 2.7 31.8 + - + +
501A EDO 3.2 9.0 - - - -
502A EDO 3.6 18.6 - - - -
513A EDO 4.0 2.7 - - - -
----------------------------------------------------------
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