Contacts of the helix formed by residues 115 - 125 (chain B) in PDB entry 5NV6
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 115 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU* 2.7 24.6 + - - +
113B VAL* 3.7 4.6 - - - +
114B GLY* 1.3 68.4 - - - +
116B THR* 1.4 57.2 + - - +
117B THR 3.4 2.7 - - - -
118B THR* 2.7 26.3 + - - -
119B GLN* 3.0 26.5 + - - +
142B ALA* 3.4 18.9 - - - +
143B PRO 2.7 16.2 + - - -
145B ASN* 3.9 4.7 - - - +
231B LEU* 3.7 15.3 - - - +
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Residues in contact with THR 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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111B GLY* 4.8 10.8 - - - +
114B GLY* 3.2 11.9 + - - +
115B SER* 1.4 72.7 - - - +
117B THR* 1.4 55.3 + - - +
119B GLN* 3.3 18.0 + - - +
120B LEU* 2.8 44.3 + - - +
145B ASN* 2.8 28.3 + - - +
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Residues in contact with THR 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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116B THR* 1.4 73.5 + - - +
118B THR* 1.4 60.1 + - - +
120B LEU* 3.4 13.4 + - + +
121B TYR* 3.1 61.4 + - + +
145B ASN* 2.8 30.4 + - - +
148B TRP* 3.5 26.9 - - + -
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Residues in contact with THR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B LEU* 4.4 6.7 - - + -
115B SER* 2.7 29.1 + - - -
116B THR 3.4 0.4 - - - -
117B THR* 1.4 75.4 - - - +
119B GLN* 1.3 51.7 + - - +
121B TYR* 3.5 3.6 + - - +
122B THR* 2.7 36.4 + - - +
140B ILE* 4.4 13.5 - - + -
142B ALA* 4.1 12.1 - - + -
143B PRO* 2.8 29.1 + - + +
145B ASN* 5.0 0.2 + - - -
148B TRP* 3.1 15.8 + - - +
171B LEU* 3.9 19.7 - - + +
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Residues in contact with GLN 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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107B TYR* 2.8 69.3 + - + +
108B GLU* 3.9 10.7 + - - +
110B LEU* 3.8 11.4 - - + +
111B GLY* 3.2 32.5 - - - +
115B SER 3.0 13.3 + - - +
116B THR* 3.3 17.2 - - - +
118B THR* 1.3 73.4 - - - +
120B LEU* 1.4 61.2 + - - +
122B THR* 3.3 8.8 + - - -
123B ASP* 3.1 13.1 - - - +
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Residues in contact with LEU 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 THR* 2.8 33.8 + - - +
117B THR* 3.4 14.3 + - + +
119B GLN* 1.4 73.4 - - - +
121B TYR* 1.3 63.8 + - + +
123B ASP* 3.0 21.4 - - - +
124B ARG* 3.4 30.1 + - - +
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Residues in contact with TYR 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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117B THR* 3.1 37.6 + - + +
118B THR 3.9 3.8 - - - +
119B GLN 3.4 0.2 - - - -
120B LEU* 1.3 75.5 - - + +
122B THR* 1.3 64.4 + - - +
123B ASP 3.5 0.2 - - - -
124B ARG* 3.5 23.8 + - - -
125B THR* 3.4 26.2 + - - +
148B TRP* 3.5 47.8 - + - +
156B LEU* 3.9 18.7 - - + +
160B VAL* 3.7 31.3 - - + +
167B LEU* 3.4 28.6 - - + +
171B LEU* 3.7 14.8 - - + +
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Residues in contact with THR 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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107B TYR* 3.8 14.4 - - + -
110B LEU* 4.3 2.6 - - - +
118B THR* 2.7 21.8 + - - +
119B GLN* 3.3 10.3 + - - -
121B TYR* 1.3 75.9 - - - +
123B ASP* 1.4 58.8 + - - +
125B THR* 2.7 25.8 + - - -
126B GLU 3.9 1.6 + - - -
128B LEU* 3.8 10.0 - - + +
129B ARG 3.6 24.0 + - - +
132B MET* 3.5 32.8 - - - -
140B ILE* 5.5 1.4 - - - +
171B LEU* 4.3 13.7 - - - +
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Residues in contact with ASP 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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107B TYR* 3.4 17.6 + - - +
119B GLN 3.1 13.6 + - - +
120B LEU* 3.0 27.8 - - - +
122B THR* 1.4 75.7 - - - +
124B ARG* 1.4 67.8 + - - +
126B GLU* 3.0 33.1 + - - +
129B ARG* 3.8 31.6 - - - +
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Residues in contact with ARG 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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120B LEU* 3.4 24.5 + - - +
121B TYR* 3.6 41.2 - - - +
122B THR 3.2 0.8 - - - -
123B ASP* 1.4 80.8 - - - +
125B THR* 1.4 62.3 + - - +
126B GLU* 3.2 12.3 + - - +
160B VAL* 4.2 17.8 + - - +
163B VAL* 3.7 37.1 - - + +
167B LEU* 4.4 0.4 - - + -
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Residues in contact with THR 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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121B TYR 3.4 15.0 + - - +
122B THR 2.7 19.8 + - - -
124B ARG* 1.4 75.7 - - - +
126B GLU* 1.4 59.7 + - - +
127B LYS* 3.1 10.6 + - - +
128B LEU* 3.4 18.8 + - + +
163B VAL* 3.4 28.5 - - - +
164B ASN* 3.3 22.0 + - - -
167B LEU* 3.9 8.3 - - + -
168B LEU* 3.8 31.9 - - + +
171B LEU* 4.1 8.3 - - + -
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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