Contacts of the helix formed by residues 110 - 124 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ASN* 2.9 7.9 + - - -
97A THR* 3.9 16.5 + - - +
108A TYR* 4.9 0.4 - - + -
109A ASN* 1.3 75.1 - - - +
111A ASP* 1.3 67.2 + - - +
112A GLY 3.1 2.5 - - - -
113A ILE* 3.9 8.9 - - + +
114A GLY* 2.9 23.0 + - - -
259A GLN* 2.8 38.1 + - - +
262A VAL* 3.7 32.8 - - + -
263A ALA 4.1 6.5 - - - +
266A ILE* 4.3 13.5 - - + -
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Residues in contact with ASP 111 (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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75A LYS* 3.2 26.9 + - - -
96A ASN* 3.0 27.4 + - - +
109A ASN* 3.0 14.2 + - - +
110A THR* 1.3 77.9 + - - +
112A GLY* 1.3 64.2 + - - +
114A GLY* 3.9 0.3 - - - -
115A ALA* 3.2 10.4 + - - +
142A ALA* 3.8 15.6 - - + +
255A MET* 3.1 33.3 - - + +
259A GLN* 3.2 15.3 - - - +
288A NAP 5.4 7.4 - - - -
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Residues in contact with GLY 112 (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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88A ASP* 5.2 3.4 - - - -
92A ILE* 4.7 5.4 - - - -
109A ASN* 3.7 7.1 + - - +
110A THR* 3.1 1.0 - - - +
111A ASP* 1.3 79.4 - - - +
113A ILE* 1.3 65.2 + - - +
115A ALA* 3.3 10.4 + - - +
116A ARG 3.3 7.3 + - - -
142A ALA* 3.7 26.8 - - - +
143A VAL 4.7 0.4 - - - -
146A GLU* 3.6 21.2 - - - +
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Residues in contact with ILE 113 (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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88A ASP* 5.0 12.1 - - + +
109A ASN 4.8 9.9 - - - +
110A THR* 3.4 9.5 + - + +
112A GLY* 1.3 73.1 - - - +
114A GLY* 1.3 59.2 + - - +
116A ARG* 2.9 15.0 + - + +
117A MET* 2.8 49.8 + - + +
146A GLU* 4.2 15.3 + - - +
262A VAL* 4.2 27.1 - - + -
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Residues in contact with GLY 114 (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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110A THR 2.9 18.5 + - - -
111A ASP 3.9 1.3 - - - -
113A ILE* 1.3 77.7 - - - +
115A ALA* 1.3 51.1 + - - +
117A MET* 3.2 2.8 + - - +
118A ALA* 2.8 35.7 + - - +
255A MET* 4.2 7.9 - - - -
258A TYR* 3.8 11.2 - - - +
259A GLN* 3.9 22.9 - - - -
262A VAL* 5.0 0.6 - - - +
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Residues in contact with ALA 115 (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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111A ASP 3.2 11.8 + - - +
112A GLY 3.3 6.9 + - - +
114A GLY* 1.3 74.0 - - - +
116A ARG* 1.3 61.3 + - - +
118A ALA* 3.6 8.2 - - - +
119A LEU* 3.6 22.9 + - - +
143A VAL* 3.7 36.8 - - + -
147A LEU* 5.5 2.2 - - + +
198A ILE* 5.7 0.2 - - - +
227A MET* 3.8 11.9 - - + +
255A MET* 3.7 20.4 - - - +
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Residues in contact with ARG 116 (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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112A GLY 3.3 8.9 + - - +
113A ILE* 2.9 17.1 + - - +
115A ALA* 1.3 75.9 - - - +
117A MET* 1.3 58.6 + - - +
118A ALA 3.1 0.9 - - - -
119A LEU* 2.7 26.2 + - + +
120A GLU* 2.9 52.3 + - + +
125A ARG* 3.8 3.8 - - - +
126A VAL* 3.1 24.6 + - + +
146A GLU* 3.0 50.1 + - + +
147A LEU* 4.1 21.2 - - + +
149A LYS* 4.8 2.6 - - - +
150A ASP* 3.1 30.0 + - - -
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Residues in contact with MET 117 (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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113A ILE* 2.8 32.0 + - + +
114A GLY* 3.7 3.8 - - - +
116A ARG* 1.3 74.8 - - + +
118A ALA* 1.3 64.7 + - - +
119A LEU 3.0 1.0 + - - -
120A GLU* 4.5 7.4 - - - +
121A GLU* 3.0 46.3 + - + +
258A TYR* 3.2 46.4 - - + +
261A ALA* 4.5 4.9 - - + -
262A VAL* 3.4 32.3 - - + -
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Residues in contact with ALA 118 (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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114A GLY 2.8 17.6 + - - +
115A ALA* 3.6 10.3 - - - +
117A MET* 1.3 75.8 - - - +
119A LEU* 1.3 60.6 - - - +
121A GLU* 5.0 0.9 - - - +
122A GLU* 3.7 13.9 - - - +
227A MET* 3.9 16.6 - - - -
250A ILE* 4.0 12.2 - - + +
254A GLY* 3.6 6.3 - - - -
255A MET* 3.5 26.9 - - + +
258A TYR* 3.8 14.2 - - - -
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Residues in contact with LEU 119 (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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115A ALA 3.6 13.7 - - - +
116A ARG* 2.7 7.5 + - - +
118A ALA* 1.3 78.7 - - - +
120A GLU* 1.3 56.7 + - + +
122A GLU* 2.6 29.5 + - - +
123A ILE* 2.8 26.7 + - + +
126A VAL* 4.5 12.8 - - + -
147A LEU* 4.1 31.2 - - + -
196A ILE* 4.4 25.1 - - + -
198A ILE* 4.1 10.3 - - + -
225A VAL* 4.5 0.7 - - + -
227A MET* 3.7 20.6 - - + -
250A ILE* 3.7 24.2 - - + -
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A ARG* 2.9 61.0 + - + +
117A MET* 4.5 6.4 - - - +
119A LEU* 1.3 72.1 - - - +
121A GLU* 1.3 57.0 + - + +
122A GLU 2.5 13.3 + - - -
123A ILE 2.7 0.3 + - - -
124A GLY* 2.5 47.8 + - - +
125A ARG* 3.4 21.6 + - - +
126A VAL* 3.1 21.6 + - + +
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Residues in contact with GLU 121 (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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117A MET* 3.0 37.7 + - + +
118A ALA 5.0 0.9 - - - +
120A GLU* 1.3 74.3 - - + +
122A GLU* 1.3 60.2 + - + +
258A TYR* 3.5 36.0 + - + +
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Residues in contact with GLU 122 (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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118A ALA 3.7 14.1 - - - +
119A LEU 2.6 13.7 + - - +
120A GLU 2.5 9.6 + - - -
121A GLU* 1.3 76.5 - - - +
123A ILE* 1.3 55.0 + - - +
124A GLY 3.9 0.4 - - - -
248A LYS* 3.1 58.9 + - - +
249A THR 4.7 4.3 - - - +
250A ILE* 4.0 22.5 - - + +
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Residues in contact with ILE 123 (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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119A LEU* 2.8 28.3 + - + +
120A GLU 2.7 3.8 + - - -
122A GLU* 1.3 82.9 - - + +
124A GLY* 1.3 71.1 + - - +
125A ARG 4.4 2.1 - - - +
126A VAL* 4.0 10.5 - - + -
129A LYS* 5.3 8.7 + - - +
196A ILE* 3.9 28.7 - - + -
225A VAL* 4.4 20.9 - - + -
248A LYS* 4.1 24.0 - - + +
250A ILE* 4.8 1.1 - - + -
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Residues in contact with GLY 124 (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 GLU* 2.5 35.5 + - - -
122A GLU 3.9 0.4 - - - -
123A ILE* 1.3 76.2 - - - +
125A ARG* 1.3 71.6 + - - +
126A VAL* 3.4 7.1 + - - +
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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