Contacts of the helix formed by residues 162 - 176 (chain A) in PDB entry 2E9S
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 ASN 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A ILE* 3.8 18.4 - - + +
154A GLU* 3.2 27.8 + - - +
155A THR* 3.8 3.4 - - + +
160A GLY 3.2 2.0 + - - -
161A TYR* 1.3 100.5 + - + +
163A VAL* 1.3 63.7 + - - +
164A LYS 3.4 2.7 - - - -
165A GLN* 3.3 16.1 + - - +
166A LEU* 3.0 22.0 + - - +
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Residues in contact with VAL 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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29A LEU* 3.9 40.4 - - + +
32A ARG* 3.9 27.6 - - + -
33A PHE* 4.2 8.7 - - + +
155A THR* 4.5 2.0 - - - -
156A SER 3.7 18.2 - - - +
157A ALA* 4.1 0.7 - - - -
160A GLY 3.1 19.2 + - - +
161A TYR 3.8 3.6 - - - +
162A ASN* 1.3 76.8 - - - +
164A LYS* 1.3 67.1 + - + +
166A LEU* 3.2 11.2 + - - +
167A PHE* 3.2 27.5 - - + -
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Residues in contact with LYS 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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32A ARG* 6.2 1.4 - - - +
33A PHE* 4.7 19.5 - - + -
36A ASP* 4.5 18.2 + - - -
55A MET* 4.9 2.3 - - - +
160A GLY* 4.7 12.5 + - - -
162A ASN 3.4 0.2 - - - -
163A VAL* 1.3 80.5 - - + +
165A GLN* 1.3 57.9 + - - +
167A PHE* 3.3 4.0 + - - +
168A ARG* 2.9 49.3 + - - +
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Residues in contact with GLN 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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153A ILE* 3.7 16.6 - - + -
162A ASN* 3.3 25.0 + - - +
163A VAL 3.2 0.6 - - - -
164A LYS* 1.3 76.4 - - - +
166A LEU* 1.3 65.6 + - - +
168A ARG* 2.8 47.4 - - - +
169A ARG* 2.9 51.0 + - - +
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Residues in contact with LEU 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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18A PHE* 4.8 1.6 - - + -
29A LEU* 4.5 22.4 - - + -
90A VAL* 4.4 13.2 - - + -
122A MET* 3.4 33.9 - - + -
124A VAL* 3.8 20.2 - - + -
153A ILE* 3.7 17.9 - - + +
155A THR* 4.5 9.4 - - + -
162A ASN 3.0 12.9 + - - +
163A VAL* 3.3 11.0 - - - +
165A GLN* 1.3 77.9 - - - +
167A PHE* 1.3 83.4 + - + +
169A ARG* 3.8 3.8 - - - +
170A VAL* 3.2 26.1 + - + +
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Residues in contact with PHE 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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16A LEU* 4.1 17.0 - - + -
18A PHE* 3.5 33.4 - + - -
29A LEU 4.1 11.2 - - - -
30A ILE* 4.7 4.0 - - - -
33A PHE* 3.5 70.4 - + + -
55A MET* 4.0 6.3 - - - +
64A LEU* 4.1 6.0 - - + +
66A LEU* 4.0 15.3 - - + -
163A VAL* 3.2 25.8 - - + -
164A LYS 3.3 3.7 + - - +
166A LEU* 1.3 93.1 - - + +
168A ARG* 1.3 66.4 + - - +
170A VAL* 3.0 6.9 - - + +
171A ALA* 3.0 26.7 + - - +
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Residues in contact with ARG 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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55A MET* 3.9 17.6 - - + +
56A TYR 5.3 3.8 - - - -
57A LEU* 3.9 13.9 - - + +
164A LYS* 2.9 31.3 + - - +
165A GLN* 2.8 50.6 - - - +
167A PHE* 1.3 76.3 - - - +
169A ARG* 1.3 59.4 + - + +
171A ALA* 3.8 2.2 - - - +
172A SER* 2.8 31.0 + - - -
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Residues in contact with ARG 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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122A MET* 3.9 13.2 - - + +
151A MET* 3.3 34.5 - - + +
152A PHE 2.8 37.5 + - - +
153A ILE* 3.6 19.7 - - - +
165A GLN* 2.9 47.3 + - - +
166A LEU 3.8 3.6 - - - +
168A ARG* 1.3 79.1 - - + +
170A VAL* 1.3 57.8 + - - +
172A SER* 3.4 7.0 + - - -
173A ALA* 3.0 26.5 + - - +
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Residues in contact with VAL 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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16A LEU* 4.0 22.7 - - + -
64A LEU* 5.7 1.6 - - + -
88A VAL* 4.1 24.0 - - + -
90A VAL* 4.9 3.1 - - + -
120A ILE* 4.1 7.3 - - + +
122A MET* 3.9 34.8 - - + -
151A MET* 5.3 0.4 - - - -
166A LEU* 3.2 19.6 + - + +
167A PHE* 3.0 27.1 - - + +
169A ARG* 1.3 72.9 - - - +
171A ALA* 1.3 60.9 + - + +
173A ALA* 3.3 7.5 + - - +
174A LEU* 3.0 32.5 + - + +
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Residues in contact with ALA 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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14A PHE* 5.4 0.3 - - - -
55A MET* 4.1 11.9 - - - -
57A LEU* 3.6 29.2 - - + -
62A VAL* 4.9 4.7 - - + -
64A LEU* 4.7 11.0 - - + -
167A PHE 3.0 18.5 + - - +
168A ARG 3.8 0.4 - - - +
170A VAL* 1.3 75.9 - - - +
172A SER* 1.3 67.0 + - - +
174A LEU* 3.3 11.9 + - - +
175A LEU* 3.0 27.7 + - - +
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Residues in contact with SER 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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57A LEU* 3.6 3.1 - - - +
58A GLU* 2.8 28.9 + - - +
168A ARG* 2.8 19.4 + - - -
169A ARG* 3.6 8.7 - - - -
171A ALA* 1.3 76.3 - - - +
173A ALA* 1.3 61.8 + - - +
175A LEU* 3.2 4.2 + - - +
176A GLU* 3.1 27.3 + - - +
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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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120A ILE* 3.5 32.5 - - + +
151A MET* 4.2 13.2 - - + -
169A ARG 3.0 14.5 + - - +
170A VAL 3.5 6.3 - - - +
171A ALA 3.3 0.2 - - - -
172A SER* 1.3 77.6 - - - +
174A LEU* 1.3 61.4 + - - +
176A GLU* 3.1 25.0 + - - +
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Residues in contact with LEU 174 (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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13A LYS 4.1 6.3 - - - +
14A PHE* 3.4 46.5 - - + -
16A LEU* 4.4 6.5 - - + -
64A LEU* 4.9 1.3 - - + -
87A THR* 3.7 24.5 - - - +
88A VAL* 3.5 21.5 - - + -
120A ILE* 3.5 19.5 - - + -
170A VAL 3.0 16.3 + - - +
171A ALA* 3.5 13.7 - - - +
172A SER 3.2 0.2 - - - -
173A ALA* 1.3 76.9 - - - +
175A LEU* 1.3 61.5 + - - +
176A GLU 3.0 9.1 + - - +
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Residues in contact with LEU 175 (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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14A PHE* 4.1 24.7 - - + -
57A LEU* 3.8 33.9 - - + -
58A GLU* 4.1 16.6 - - - +
60A ARG* 3.9 41.5 + - - +
62A VAL* 4.1 15.0 - - + -
171A ALA 3.0 15.2 + - - +
172A SER 3.2 5.4 + - - +
174A LEU* 1.3 75.2 - - - +
176A GLU* 1.3 60.9 + - - +
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Residues in contact with GLU 176 (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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58A GLU* 4.5 10.7 - - - +
172A SER* 3.1 17.3 + - - +
173A ALA* 3.1 19.4 - - - +
174A LEU 3.0 10.2 - - - +
175A LEU* 1.3 82.0 - - - +
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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