Contacts of the helix formed by residues 153 - 173 (chain A) in PDB entry 3EVA
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 SER 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 4.7 0.2 - - - -
151A SER* 3.0 7.6 + - - -
152A SER* 1.3 81.3 + - - +
154A SER* 1.3 58.4 + - - +
155A VAL* 3.3 12.1 + - - +
156A THR* 3.1 31.0 + - - -
157A GLU* 2.9 30.0 + - - +
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Residues in contact with SER 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLU* 4.7 10.1 + - - +
13A LYS* 4.0 17.5 - - - +
152A SER 3.8 3.6 + - - -
153A SER* 1.3 69.4 + - - +
155A VAL* 1.3 66.1 + - - +
157A GLU* 3.3 2.6 + - - +
158A GLY 2.9 24.4 + - - -
187A TYR* 3.8 25.1 - - - -
188A MET* 3.3 26.7 - - - +
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A SER* 3.2 9.3 + - - +
154A SER* 1.3 83.9 + - - +
156A THR* 1.3 58.1 + - - +
158A GLY* 3.2 2.8 + - - -
159A GLU* 2.9 51.3 + - + +
188A MET* 4.0 12.3 - - + +
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Residues in contact with THR 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A SER* 3.4 23.7 + - - +
153A SER* 3.1 16.8 + - - -
155A VAL* 1.3 77.1 - - - +
157A GLU* 1.3 64.7 + - - +
159A GLU* 3.2 17.0 + - - +
160A ARG* 2.9 55.8 + - + +
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Residues in contact with GLU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TRP* 4.6 3.7 - - - -
13A LYS* 3.4 13.0 + - - +
150A SER* 3.4 13.3 + - - -
151A SER* 3.0 39.4 + - - +
153A SER 2.9 18.8 + - - +
154A SER 3.3 5.6 + - - +
156A THR* 1.3 76.1 - - - +
158A GLY* 1.3 58.1 + - - +
160A ARG* 3.4 2.9 + - - +
161A THR* 2.7 34.1 + - - -
184A LEU* 4.0 26.3 - - + +
185A ALA* 3.7 13.3 - - + +
187A TYR* 2.7 33.0 + - - +
215A SER 5.8 0.2 - - - +
216A THR* 5.5 2.3 + - - -
217A HIS 5.6 1.2 + - - -
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Residues in contact with GLY 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A SER 2.9 14.9 + - - -
155A VAL 3.6 3.6 - - - -
157A GLU* 1.3 77.6 - - - +
159A GLU* 1.3 60.9 + - - +
161A THR* 3.2 1.8 + - - -
162A VAL* 2.9 32.2 + - - +
185A ALA* 4.5 0.2 - - - -
188A MET* 3.9 25.5 - - - +
191A VAL* 4.4 5.8 - - - -
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Residues in contact with GLU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL* 2.9 37.0 + - + +
156A THR* 3.2 19.1 + - - +
158A GLY* 1.3 74.3 - - - +
160A ARG* 1.3 62.8 + - + +
162A VAL* 2.9 26.4 - - - +
163A ARG* 3.0 12.5 + - - +
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Residues in contact with ARG 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLY* 5.6 2.7 - - - -
149A GLU* 2.9 63.9 + - - +
150A SER 3.2 16.8 + - - -
151A SER* 3.6 8.9 + - - -
156A THR* 2.9 41.9 + - + +
157A GLU 3.8 3.6 - - - +
159A GLU* 1.3 77.0 - - + +
161A THR* 1.3 62.2 + - - +
163A ARG* 3.4 7.3 + - - +
164A VAL* 3.1 28.7 + - + +
184A LEU* 4.3 8.5 - - + -
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Residues in contact with THR 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLU 2.7 21.3 + - - -
158A GLY 3.7 3.6 - - - -
160A ARG* 1.3 74.7 - - - +
162A VAL* 1.3 65.4 + - - +
164A VAL* 3.2 8.1 + - + +
165A LEU* 3.0 27.0 + - + +
182A LYS 5.6 0.2 - - - +
183A VAL* 3.6 33.7 - - + -
184A LEU* 3.3 14.2 - - - +
185A ALA* 2.9 21.4 + - - +
191A VAL* 3.7 24.0 - - + -
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Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A GLY 2.9 19.8 + - - +
159A GLU* 2.9 30.7 - - - +
161A THR* 1.3 77.2 - - - +
163A ARG* 1.3 57.7 + - - +
165A LEU* 3.7 7.5 - - + +
166A ASP* 2.8 31.3 + - - +
190A ASP* 4.4 20.0 - - + +
191A VAL* 3.8 22.2 - - + +
194A LYS* 5.5 6.8 - - + +
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Residues in contact with ARG 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ASP* 4.7 6.7 + - - -
133A HIS* 3.5 51.2 + - + +
134A ARG* 6.0 3.8 - - - +
159A GLU 3.0 18.1 + - - +
160A ARG* 3.6 8.3 - - - +
162A VAL* 1.3 80.1 - - + +
164A VAL* 1.3 62.2 + - - +
166A ASP* 3.3 7.6 + - + +
167A THR* 3.0 25.5 + - - +
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Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE* 6.3 1.1 - - + -
133A HIS* 4.2 14.8 - - + +
145A CYS* 4.2 11.4 - - - -
147A ILE* 3.8 36.1 - - + +
148A GLY* 4.9 2.7 - - - +
160A ARG* 3.1 15.9 + - + +
161A THR* 3.6 9.9 - - + +
163A ARG* 1.3 77.1 - - - +
165A LEU* 1.3 59.2 + - + +
167A THR* 3.2 3.0 + - - -
168A VAL* 2.8 47.2 + - + +
181A VAL* 4.2 6.7 - - + -
182A LYS 4.0 20.0 - - - +
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A THR* 3.0 26.3 + - + +
162A VAL* 3.9 5.6 - - - +
164A VAL* 1.3 77.5 - - + +
166A ASP* 1.3 57.9 + - - +
168A VAL* 3.9 5.2 - - + +
169A GLU* 2.9 30.5 + - - +
181A VAL* 4.6 16.4 - - + -
182A LYS 5.2 0.4 - - - +
183A VAL* 4.3 19.5 - - + -
191A VAL* 4.1 20.9 - - + -
194A LYS* 4.0 33.7 - - + -
195A LEU* 4.0 20.9 - - + -
198A LEU* 4.1 18.6 - - + +
221A TYR* 5.0 5.4 - - + -
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Residues in contact with ASP 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A VAL 2.8 19.3 + - - +
163A ARG* 3.4 9.6 - - + +
165A LEU* 1.3 78.9 - - - +
167A THR* 1.3 66.0 + - - +
169A GLU* 3.5 16.2 + - - +
170A LYS* 3.7 14.9 - - - +
194A LYS* 5.0 12.6 + - - +
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Residues in contact with THR 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU* 5.2 0.7 - - + -
132A ILE* 3.7 37.7 - - + +
133A HIS* 2.8 35.0 + - - +
163A ARG* 3.0 11.6 + - - +
164A VAL 3.7 3.6 - - - -
166A ASP* 1.3 77.6 + - - +
168A VAL* 1.3 69.3 + - + +
170A LYS* 3.0 29.4 + - - +
171A TRP* 3.2 22.4 - - + +
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU* 4.9 7.6 - - + -
132A ILE* 6.3 0.4 - - + -
143A LEU* 4.1 7.4 - - + -
145A CYS* 4.1 16.6 - - + -
164A VAL* 2.8 30.9 + - + +
165A LEU* 3.9 9.0 - - + +
167A THR* 1.3 73.0 - - + +
169A GLU* 1.3 62.1 + - - +
171A TRP* 3.0 11.5 + - - +
172A LEU* 2.9 41.6 + - + +
181A VAL* 3.8 41.5 - - + -
198A LEU* 6.2 1.3 - - + -
221A TYR* 5.6 1.8 - - + -
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Residues in contact with GLU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU 2.9 18.1 + - - +
166A ASP* 3.7 9.2 - - - +
167A THR 3.2 0.4 - - - -
168A VAL* 1.3 76.5 - - - +
170A LYS* 1.3 62.7 + - + +
172A LEU* 3.9 10.3 - - - +
173A ALA* 3.0 23.2 + - - +
194A LYS* 2.7 30.6 + - - -
197A LEU* 4.1 7.3 - - - +
198A LEU* 4.0 22.3 - - + +
201A ARG* 2.9 34.9 + - - +
202A PHE* 4.2 2.9 - - + -
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Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A HIS 3.4 25.7 + - - -
134A ARG* 5.2 1.0 - - - +
135A LEU 4.5 8.7 + - - -
137A PRO* 3.9 24.8 - - + +
166A ASP* 3.7 14.8 - - - +
167A THR* 3.0 30.1 + - - +
169A GLU* 1.3 77.9 - - + +
171A TRP* 1.3 65.0 + - - +
173A ALA* 3.5 15.1 + - - +
174A CYS* 3.7 12.8 - - - -
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Residues in contact with TRP 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE* 3.7 26.7 - - + -
80A LEU* 4.0 23.8 - - + +
103A PHE* 5.0 1.1 - + - -
132A ILE 4.3 2.1 + - - -
135A LEU* 3.7 45.4 + - + -
136A GLU 3.8 3.1 - - - -
137A PRO* 3.6 28.4 - - + +
138A VAL* 3.2 40.8 - - + +
140A CYS* 5.4 0.9 - - - -
143A LEU* 3.4 35.4 - - + -
167A THR* 3.2 34.9 - - + +
168A VAL* 3.0 4.1 + - - +
170A LYS* 1.3 77.9 - - + +
172A LEU* 1.3 66.3 + - - +
174A CYS* 3.1 20.1 + - - +
176A VAL* 3.7 9.1 - - + +
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Residues in contact with LEU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 3.7 16.6 - - + -
168A VAL* 2.9 35.6 + - + +
169A GLU* 3.9 2.7 - - - +
171A TRP* 1.3 75.9 - - - +
173A ALA* 1.3 57.0 + - - +
174A CYS 3.0 0.4 - - - -
175A GLY* 2.9 21.5 + - - -
176A VAL* 3.3 32.7 + - + +
179A PHE* 3.8 18.8 - - + -
181A VAL* 5.7 0.2 - - + -
198A LEU* 4.9 3.4 - - + -
202A PHE* 3.5 49.5 - - + -
221A TYR* 4.0 22.7 - - + -
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Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A GLU* 3.0 19.1 + - + +
170A LYS* 3.6 9.4 - - - +
171A TRP 3.1 0.2 - - - -
172A LEU* 1.3 75.9 - - - +
174A CYS* 1.3 61.2 + - - +
175A GLY* 3.1 2.1 + - - -
201A ARG* 4.2 22.4 - - - +
202A PHE* 3.9 10.9 - - + -
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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
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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) + - + + + + + -
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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