Contacts of the helix formed by residues 152 - 168 (chain B) in PDB entry 3SEA
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 GLU 152 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B GLN* 4.4 1.8 - - - -
121B LYS* 2.9 29.6 + - - -
122B ASP* 4.1 18.0 - - - +
149B SER* 2.8 20.3 + - - +
150B ALA 3.2 0.2 - - - -
151B LYS* 1.3 84.8 - - + +
153B ASN* 1.3 67.4 + - - +
154B GLN 3.3 2.2 - - - +
155B THR* 2.9 33.4 + - + +
156B ALA* 3.3 2.6 + - - +
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Residues in contact with ASN 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLN* 3.0 48.8 + - - +
26B PHE* 4.8 2.2 + - - +
29B GLY* 3.9 9.4 - - - +
151B LYS 3.9 3.0 + - - -
152B GLU* 1.3 71.7 - - - +
154B GLN* 1.3 67.1 + - - +
156B ALA* 3.0 5.5 + - - +
157B VAL* 3.0 37.7 + - - +
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Residues in contact with GLN 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B GLU 3.3 1.0 - - - -
153B ASN* 1.3 84.5 + - - +
155B THR* 1.3 61.2 + - + +
157B VAL* 3.5 21.0 + - - +
158B ASP* 2.8 65.2 + - - +
161B ARG* 4.3 3.2 - - - +
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Residues in contact with THR 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B LYS* 3.8 16.4 - - - +
146B LEU* 4.9 1.2 - - - +
147B GLU 4.6 2.9 - - - +
148B SER* 3.6 9.9 - - - -
149B SER 2.9 37.4 + - - -
152B GLU* 2.9 33.2 + - + +
154B GLN* 1.3 78.5 - - + +
156B ALA* 1.3 60.6 + - - +
158B ASP* 3.4 9.4 + - - +
159B VAL* 3.1 27.8 + - - +
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Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU* 3.5 43.5 - - + +
25B GLN* 3.8 19.3 - - + -
26B PHE* 3.9 8.3 - - + +
149B SER 5.0 0.2 - - - +
152B GLU 3.3 1.3 + - - +
153B ASN 3.0 8.6 + - - +
155B THR* 1.3 78.9 + - - +
157B VAL* 1.3 64.7 + - - +
159B VAL* 3.1 10.7 + - - +
160B PHE* 3.3 21.5 - - + -
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 3.8 23.5 - - + +
47B ILE* 4.7 16.0 - - + +
153B ASN* 3.0 34.9 + - - +
154B GLN* 3.7 28.3 - - - +
156B ALA* 1.3 76.6 - - - +
158B ASP* 1.3 60.0 + - - +
160B PHE* 3.3 1.6 + - - +
161B ARG* 2.9 34.4 + - + +
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Residues in contact with ASP 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLU* 4.4 16.1 - - - +
146B LEU* 4.0 16.1 - - + +
154B GLN* 2.8 45.8 + - - +
155B THR* 3.6 9.5 - - - +
156B ALA 3.1 0.4 - - - -
157B VAL* 1.3 77.3 - - - +
159B VAL* 1.3 58.2 + - - +
161B ARG* 2.7 34.0 + - - +
162B ARG* 2.9 31.5 + - - +
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Residues in contact with VAL 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU* 4.2 10.3 - - + -
82B ILE* 3.8 35.9 - - + -
115B MET* 3.1 29.9 - - - +
117B VAL* 4.0 11.2 - - + -
146B LEU* 3.4 24.9 - - + -
148B SER* 4.0 13.9 - - - -
155B THR 3.1 16.4 + - - +
156B ALA* 3.1 9.5 + - - +
158B ASP* 1.3 78.1 - - - +
160B PHE* 1.3 72.3 + - + +
163B ILE* 3.2 7.3 + - - +
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Residues in contact with PHE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ILE* 4.2 10.3 - - + -
22B LEU* 4.2 9.2 - - + -
23B THR* 3.8 29.2 - - - -
26B PHE* 3.3 49.6 - + + -
47B ILE* 4.9 0.9 - - - -
56B LEU* 4.4 4.4 - - + +
58B LEU* 3.8 34.5 - - + -
82B ILE* 3.4 28.5 - - + -
156B ALA* 3.3 21.8 - - + -
157B VAL 3.3 3.4 + - - +
159B VAL* 1.3 82.8 - - + +
161B ARG* 1.3 65.6 + - - +
163B ILE* 3.2 22.4 - - + +
164B ILE* 3.4 14.8 + - - +
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Residues in contact with ARG 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A GLU* 3.9 18.7 + - - -
136A ALA* 3.9 19.2 - - - +
139A GLU* 4.3 8.5 + - - +
47B ILE* 4.3 13.5 - - + +
48B THR 5.2 2.0 - - - -
49B VAL* 3.4 38.1 - - + +
154B GLN* 4.3 5.3 - - - +
157B VAL* 2.9 21.2 + - - +
158B ASP* 2.7 32.6 + - - +
160B PHE* 1.3 77.1 - - - +
162B ARG* 1.3 64.7 + - - +
164B ILE* 3.2 7.6 + - - +
165B LEU* 3.0 33.0 + - + +
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Residues in contact with ARG 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLU* 2.9 40.9 + - - +
135A LYS* 3.5 23.5 - - - +
136A ALA 4.3 1.6 - - - +
139A GLU* 2.8 42.4 + - - -
115B MET* 3.5 27.6 - - + -
144B ALA* 3.7 25.4 - - + -
145B PHE 6.1 0.2 - - - -
146B LEU* 4.5 1.8 - - + -
158B ASP 2.9 18.8 + - - +
160B PHE 3.2 0.2 - - - -
161B ARG* 1.3 80.8 - - - +
163B ILE* 1.3 57.1 + - - +
165B LEU* 3.1 27.0 + - - +
166B GLU* 2.7 33.8 + - - +
169B LYS* 4.4 3.2 - - - +
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Residues in contact with ILE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 3.9 32.7 - - + +
56B LEU* 5.7 0.9 - - + -
80B GLY* 4.2 5.2 - - - -
81B TYR 3.5 23.1 - - - +
82B ILE* 4.1 17.9 - - + -
113B PRO* 3.8 27.5 - - + +
114B ILE 3.9 2.5 - - - +
115B MET* 3.7 24.1 - - + +
159B VAL 3.2 3.2 + - - +
160B PHE* 3.2 27.8 - - + +
162B ARG* 1.3 78.1 - - - +
164B ILE* 1.3 64.5 + - + +
166B GLU* 3.5 9.7 + - + -
167B ALA* 3.5 12.0 + - - +
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ARG* 5.4 6.5 - - + -
9B ILE* 5.9 1.3 - - + -
47B ILE* 3.5 32.3 - - + -
49B VAL* 4.0 19.5 - - + -
54B TYR* 3.7 43.3 - - + -
56B LEU* 3.9 24.7 - - + -
160B PHE 3.4 14.6 - - - +
161B ARG 3.2 6.7 + - - +
162B ARG 3.2 0.4 - - - -
163B ILE* 1.3 81.5 - - + +
165B LEU* 1.3 62.9 + - - +
167B ALA* 3.2 11.2 + - - +
168B GLU* 3.1 22.8 - - - +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLU* 3.6 22.7 - - + +
49B VAL* 3.7 22.7 - - + -
50B ASN* 5.5 7.6 - - + -
161B ARG* 3.0 36.2 + - + +
162B ARG* 3.4 36.6 - - - +
164B ILE* 1.3 74.0 - - - +
166B GLU* 1.3 65.7 + - - +
167B ALA 3.3 0.7 + - - -
168B GLU* 3.5 25.5 + - + +
169B LYS* 3.3 21.0 + - - +
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Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B PRO* 4.3 13.2 - - + +
114B ILE 3.8 13.9 + - - +
115B MET* 4.9 0.4 - - + -
142B ASN 4.3 7.6 - - - +
143B ALA 4.2 2.3 - - - -
144B ALA* 3.6 42.0 + - + +
162B ARG* 2.7 28.4 + - + +
163B ILE* 3.6 18.2 - - + +
165B LEU* 1.3 73.7 - - - +
167B ALA* 1.3 58.1 + - - +
169B LYS* 3.0 50.7 + - - +
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Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ARG* 5.3 9.9 - - - +
79B ASN 5.0 4.0 - - - +
113B PRO* 3.7 25.6 - - + +
163B ILE 3.5 6.7 + - - +
164B ILE* 3.2 13.2 + - - +
165B LEU 3.2 1.0 - - - -
166B GLU* 1.3 75.9 - - - +
168B GLU* 1.3 66.9 + - + +
169B LYS* 3.0 10.1 + - - +
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Residues in contact with GLU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ARG* 4.5 10.8 + - - +
54B TYR* 3.2 33.7 + - - +
164B ILE* 3.1 27.0 - - - +
165B LEU* 3.5 19.9 + - + +
166B GLU 3.5 0.2 - - - -
167B ALA* 1.3 81.6 - - - +
169B LYS* 1.3 68.0 + - - +
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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
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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