Contacts of the helix formed by residues 114 - 127 (chain B) in PDB entry 3N3B
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 GLN 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B MET* 5.3 0.2 - - - -
112B LEU 5.8 0.4 - - - +
113B CYS* 1.3 74.8 - - - +
115B THR* 1.3 66.8 + - - +
116B LYS* 4.2 17.5 - - + +
117B ASP* 3.2 27.3 + - - +
118B VAL* 3.1 23.1 + - - +
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Residues in contact with THR 115 (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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12A ASN* 6.4 1.3 - - + -
13A LYS* 4.7 7.4 - - - +
113B CYS 4.1 1.0 + - - -
114B GLN* 1.3 76.3 - - - +
116B LYS* 1.3 58.4 + - - +
118B VAL* 3.4 7.1 + - + +
119B ASP* 3.1 49.0 + - - +
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Residues in contact with LYS 116 (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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114B GLN* 3.4 17.4 - - + +
115B THR* 1.3 78.3 - - - +
117B ASP* 1.3 84.8 + - - +
119B ASP* 3.7 8.5 + - - +
120B ALA* 3.1 26.7 + - - +
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Residues in contact with ASP 117 (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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57B MET* 3.7 29.5 - - + +
114B GLN* 3.2 30.8 + - + +
116B LYS* 1.3 96.7 + - - +
118B VAL* 1.3 59.2 + - - +
120B ALA* 3.5 7.5 + - - +
121B ALA* 3.1 27.0 + - - +
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Residues in contact with VAL 118 (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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10A ASN* 5.2 2.5 - - - +
12A ASN* 5.7 2.5 - - - +
57B MET* 4.3 5.4 - - - -
109B PHE* 3.8 37.9 - - + +
113B CYS* 3.6 24.0 - - + -
114B GLN 3.1 17.3 + - - +
115B THR* 3.7 9.2 - - + +
117B ASP* 1.3 75.7 - - - +
119B ASP* 1.3 60.9 + - - +
121B ALA* 3.2 7.2 + - - +
122B TYR* 3.0 57.0 + - + -
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Residues in contact with ASP 119 (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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10A ASN* 4.8 4.9 + - - -
13A LYS* 3.2 30.4 + - - -
115B THR* 3.1 25.7 + - - +
116B LYS* 3.9 8.6 - - - +
118B VAL* 1.3 81.5 - - - +
120B ALA* 1.3 57.4 + - - +
122B TYR* 3.4 9.5 + - - +
123B ALA* 3.1 27.0 + - - +
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Residues in contact with ALA 120 (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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116B LYS 3.1 19.0 + - - +
117B ASP* 3.7 9.2 - - - +
118B VAL 3.3 0.2 - - - -
119B ASP* 1.3 76.1 - - - +
121B ALA* 1.3 57.8 + - - +
123B ALA* 3.4 8.2 + - - +
124B TRP* 3.0 26.3 + - - +
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Residues in contact with ALA 121 (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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54B GLN* 6.6 0.2 - - + -
57B MET* 3.8 31.0 - - + +
58B ARG* 4.0 11.9 - - + +
61B THR* 3.3 13.9 + - + -
117B ASP 3.1 14.1 + - - +
118B VAL 3.2 8.7 + - - +
120B ALA* 1.3 75.2 - - - +
122B TYR* 1.3 58.9 + - - +
124B TRP* 3.4 8.3 + - - +
125B SER* 3.0 31.7 + - - -
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Residues in contact with TYR 122 (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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8A ALA* 3.8 33.0 - - + -
9A ILE 3.6 15.0 + - - -
10A ASN* 3.4 33.4 - - + -
61B THR* 3.8 27.8 - - + +
64B THR* 4.0 6.2 - - + +
106B SER* 4.1 3.6 + - - -
109B PHE* 3.6 17.7 - + - -
118B VAL* 3.0 44.4 + - + -
119B ASP* 3.6 12.1 - - - +
120B ALA 3.4 0.2 - - - -
121B ALA* 1.3 76.1 - - - +
123B ALA* 1.3 60.5 + - - +
125B SER* 3.4 4.6 + - - -
126B GLU* 3.1 28.4 + - + +
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Residues in contact with ALA 123 (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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119B ASP 3.1 13.2 + - - +
120B ALA* 3.6 10.8 - - - +
122B TYR* 1.3 72.7 - - - +
124B TRP* 1.3 66.0 + - - +
126B GLU* 3.3 7.6 + - - +
127B GLU* 3.2 30.8 + - + +
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Residues in contact with TRP 124 (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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58B ARG* 3.5 70.0 - - + +
120B ALA 3.0 14.6 + - - +
121B ALA* 3.5 9.0 - - - +
122B TYR 3.3 0.2 - - - -
123B ALA* 1.3 77.7 - - - +
125B SER* 1.3 66.2 + - - +
127B GLU* 3.4 5.1 + - - +
128B ASN* 3.1 60.1 + - + +
131B LEU* 5.7 0.4 - - + -
236B TYR* 4.6 7.2 - + - -
239B GLU* 3.9 19.1 - - + -
240B LEU* 4.2 30.5 - - + -
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Residues in contact with SER 125 (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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58B ARG 3.9 4.2 + - - -
61B THR* 2.8 35.5 + - - -
62B GLY 3.7 6.6 + - - -
65B LEU* 5.9 1.8 - - - -
121B ALA 3.0 8.5 + - - -
122B TYR* 3.6 8.1 - - - -
123B ALA 3.3 0.2 - - - -
124B TRP* 1.3 86.0 - - - +
126B GLU* 1.3 59.7 - - - +
128B ASN* 3.4 9.6 + - - +
131B LEU* 3.6 26.9 - - - +
132B GLN* 3.1 17.6 - - - +
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Residues in contact with GLU 126 (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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6A ILE 4.8 1.9 - - - +
7A SER* 4.4 20.6 + - - -
8A ALA* 4.9 2.9 + - - +
65B LEU* 4.7 9.0 - - - +
122B TYR* 3.1 18.8 + - + +
123B ALA* 3.6 11.4 - - - +
124B TRP 3.3 0.4 - - - -
125B SER* 1.3 76.7 - - - +
127B GLU* 1.3 71.9 + - - +
128B ASN 3.4 0.2 - - - -
132B GLN* 3.6 31.7 + - - +
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Residues in contact with GLU 127 (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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123B ALA* 3.2 19.5 + - + +
124B TRP* 3.4 5.4 + - - +
125B SER 3.3 0.2 - - - -
126B GLU* 1.3 87.3 - - + +
128B ASN* 1.3 61.0 + - - +
129B ALA* 3.5 4.0 + - - +
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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