Contacts of the helix formed by residues 110 - 124 (chain B) in PDB entry 1NVT
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 THR 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B ASN* 2.9 12.2 + - - -
97B THR* 3.6 16.0 + - - +
108B TYR* 4.8 0.7 - - + -
109B ASN* 1.3 77.2 - - - +
111B ASP* 1.3 58.6 + - - +
112B GLY 3.4 1.6 - - - -
113B ILE* 3.6 10.0 + - + +
114B GLY* 2.8 28.8 + - - -
117B MET* 5.1 0.2 - - - +
259B GLN* 2.9 36.0 + - - +
262B VAL* 3.5 33.7 - - + -
263B ALA 4.1 6.1 - - - +
266B ILE* 4.3 13.7 - - + -
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Residues in contact with ASP 111 (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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75B LYS* 2.9 27.6 + - - +
96B ASN* 3.2 24.0 + - - +
109B ASN* 3.1 14.0 + - - +
110B THR* 1.3 78.1 + - - +
112B GLY* 1.3 65.2 + - - +
114B GLY* 3.2 1.6 + - - -
115B ALA* 2.9 19.1 + - - +
138B GLY 4.9 1.6 - - - +
139B ALA* 4.9 4.4 - - - -
142B ALA* 3.4 14.7 - - + +
255B MET* 3.3 29.5 - - + +
259B GLN* 3.5 12.9 - - - +
289B NAP 3.9 10.8 - - - -
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Residues in contact with GLY 112 (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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92B ILE* 5.0 4.9 - - - +
109B ASN* 3.8 3.2 + - - -
110B THR 3.4 0.2 - - - -
111B ASP* 1.3 78.4 - - - +
113B ILE* 1.3 62.8 + - - +
115B ALA* 3.1 13.2 + - - +
116B ARG 3.1 10.2 + - - -
142B ALA* 3.4 33.6 - - - +
143B VAL* 4.1 3.1 - - - -
146B GLU* 3.6 18.7 - - - +
147B LEU* 6.1 0.2 - - - +
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Residues in contact with ILE 113 (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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88B ASP* 4.6 17.7 - - - +
109B ASN 4.0 18.8 - - - +
110B THR* 4.0 9.4 - - + +
111B ASP 3.4 0.4 - - - -
112B GLY* 1.3 72.4 - - - +
114B GLY* 1.3 63.6 + - - +
116B ARG* 3.1 5.5 + - + +
117B MET* 2.9 51.4 + - + +
146B GLU* 4.3 20.4 - - - +
262B VAL* 4.8 14.4 - - + -
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Residues in contact with GLY 114 (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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110B THR 2.8 19.4 + - - -
111B ASP 3.5 1.8 - - - -
113B ILE* 1.3 77.5 - - - +
115B ALA* 1.3 60.7 + - - +
117B MET* 3.5 13.3 + - - +
118B ALA* 3.0 24.6 + - - +
255B MET* 3.9 8.2 - - - -
258B TYR* 3.8 5.6 - - - +
259B GLN* 4.0 17.5 - - - -
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Residues in contact with ALA 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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111B ASP 2.9 8.7 + - - +
112B GLY 3.1 8.0 + - - +
114B GLY* 1.3 74.6 - - - +
116B ARG* 1.3 57.3 + - - +
118B ALA* 3.4 3.4 + - - +
119B LEU* 2.9 31.2 + - - +
143B VAL* 3.6 38.4 - - + -
147B LEU* 5.8 1.6 - - + -
227B MET* 4.0 12.9 - - + +
255B MET* 3.8 18.9 - - + +
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Residues in contact with ARG 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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112B GLY 3.1 11.5 + - - +
113B ILE* 3.1 8.7 + - + +
115B ALA* 1.3 76.6 - - - +
117B MET* 1.3 54.9 + - + +
119B LEU* 3.1 4.6 + - - -
120B GLU* 2.6 82.2 + - + +
125B ARG* 3.2 9.0 - - - +
126B VAL* 3.1 21.8 + - - +
146B GLU* 2.6 57.4 + - + +
147B LEU* 3.5 24.0 - - + +
149B LYS* 4.6 2.2 - - - +
150B ASP* 3.1 23.6 + - - -
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Residues in contact with MET 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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113B ILE* 2.9 48.5 + - + +
114B GLY* 3.6 12.8 - - - +
116B ARG* 1.3 76.8 - - + +
118B ALA* 1.3 57.8 + - - +
120B GLU* 4.6 4.5 - - - -
121B GLU* 2.8 34.3 + - - +
258B TYR* 3.7 35.0 - - + +
261B ALA* 6.3 0.2 - - - -
262B VAL* 3.3 34.3 - - + -
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Residues in contact with ALA 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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114B GLY 3.0 12.6 + - - +
115B ALA* 3.8 4.5 - - - +
117B MET* 1.3 78.6 - - - +
119B LEU* 1.3 61.2 + - - +
121B GLU* 4.3 5.0 - - - +
122B GLU* 3.5 20.3 + - - +
227B MET* 4.9 9.0 - - - -
250B ILE* 4.6 7.7 - - + +
251B ASN 6.0 0.2 - - - +
254B GLY* 3.4 38.4 - - - +
255B MET* 3.4 7.9 - - + +
258B TYR* 3.7 10.5 - - - -
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Residues in contact with LEU 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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115B ALA 2.9 18.8 + - - +
116B ARG* 3.6 3.6 - - - +
118B ALA* 1.3 79.4 - - - +
120B GLU* 1.3 58.1 + - - +
122B GLU* 3.2 4.5 + - - +
123B ILE* 3.0 45.4 + - + +
126B VAL* 3.8 26.0 - - + -
131B ILE* 5.1 0.2 - - + -
147B LEU* 4.3 26.2 - - + -
196B ILE* 4.3 17.7 - - + -
198B ILE* 4.4 12.6 - - + -
225B VAL* 4.5 7.2 - - + -
227B MET* 4.2 16.5 - - + -
250B ILE* 3.7 23.8 - - + -
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Residues in contact with GLU 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 ARG* 2.6 67.2 + - + +
117B MET* 4.1 4.2 - - - +
119B LEU* 1.3 69.0 - - - +
121B GLU* 1.3 60.8 + - - +
122B GLU 3.1 1.8 - - - -
124B GLY* 2.7 44.7 + - - +
125B ARG* 3.5 22.7 + - - +
126B VAL* 3.4 22.5 + - + +
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Residues in contact with GLU 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 MET 2.8 23.2 + - - +
118B ALA* 4.3 5.6 - - - +
120B GLU* 1.3 73.1 - - - +
122B GLU* 1.3 75.4 + - - +
124B GLY 4.8 0.3 + - - -
254B GLY* 5.8 1.4 - - - -
258B TYR* 3.6 32.8 + - + +
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Residues in contact with GLU 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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118B ALA 3.5 12.3 + - - +
119B LEU 3.2 8.3 + - - +
120B GLU 3.1 0.2 - - - -
121B GLU* 1.3 98.8 - - + +
123B ILE* 1.3 63.3 + - - +
124B GLY 3.8 0.4 - - - -
248B LYS* 3.4 32.6 + - - +
249B THR 4.6 2.4 - - - +
250B ILE* 3.4 41.2 - - + +
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Residues in contact with ILE 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 LEU* 3.0 29.3 + - + +
122B GLU* 1.3 86.9 - - + +
124B GLY* 1.3 67.5 + - - +
125B ARG 4.4 3.4 - - - +
126B VAL* 4.1 7.9 - - + -
129B LYS* 5.6 6.5 - - - -
196B ILE* 3.8 29.2 - - + -
225B VAL* 4.4 24.0 - - + -
248B LYS* 4.1 19.5 - - + -
250B ILE* 4.6 4.3 - - + -
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Residues in contact with GLY 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 GLU* 2.7 41.4 + - - +
121B GLU 4.6 0.8 + - - -
122B GLU 3.8 0.4 - - - -
123B ILE* 1.3 75.1 - - - +
125B ARG* 1.3 68.0 + - - +
126B VAL* 3.4 5.0 + - - +
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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