Contacts of the helix formed by residues 137 - 148 (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 GLY 137 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B ALA* 1.3 75.8 - - - +
138B GLY* 1.3 63.3 + - - -
139B ALA 3.3 2.7 - - - -
140B ALA* 3.6 5.0 - - - +
141B ARG* 2.9 31.2 + - - +
162B LYS* 5.6 2.5 - - - -
200B ALA 5.0 1.8 + - - -
289B NAP 3.1 35.5 + - - -
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Residues in contact with GLY 138 (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* 4.9 14.6 - - - -
76B ILE* 6.1 2.9 - - - -
92B ILE* 4.8 2.1 - - - +
94B ALA* 4.7 14.4 - - - +
109B ASN* 5.3 0.3 + - - -
111B ASP* 4.9 4.5 - - - +
137B GLY* 1.3 71.6 - - - -
139B ALA* 1.3 57.4 + - - +
141B ARG* 3.3 12.9 - - - +
142B ALA* 3.0 28.6 + - - +
289B NAP 3.4 11.6 + - - -
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Residues in contact with ALA 139 (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* 5.2 1.2 - - - +
111B ASP* 4.9 3.3 + - - -
138B GLY* 1.3 69.4 - - - +
140B ALA* 1.3 67.2 + - - +
142B ALA* 3.0 7.7 + - - +
143B VAL* 2.9 30.3 + - - +
200B ALA* 4.5 1.1 - - + -
229B LEU* 3.9 19.3 - - + -
255B MET* 4.8 2.5 - - + -
289B NAP 2.6 57.8 + - + +
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Residues in contact with ALA 140 (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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133B ILE* 4.2 10.4 - - + +
135B GLY 3.4 36.1 - - - +
136B ALA* 3.5 11.4 - - - +
137B GLY 3.5 4.3 + - - +
138B GLY 3.5 0.2 - - - -
139B ALA* 1.3 77.8 - - - +
141B ARG* 1.3 54.3 + - - +
143B VAL* 4.1 1.3 - - - +
144B ALA* 2.7 39.9 + - - +
155B ILE* 5.8 0.2 - - + -
166B LEU* 4.7 3.8 - - + -
200B ALA* 3.9 19.6 + - + +
289B NAP 4.4 0.2 + - - -
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Residues in contact with ARG 141 (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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76B ILE* 5.1 11.0 - - - +
92B ILE* 2.8 39.3 + - + +
93B GLY* 4.4 9.9 + - - -
94B ALA* 5.0 6.1 - - - -
136B ALA 4.1 8.3 + - - +
137B GLY 2.9 27.1 + - - +
138B GLY* 3.3 14.8 - - - +
139B ALA 3.1 0.2 - - - -
140B ALA* 1.3 75.2 - - - +
142B ALA* 1.3 57.8 + - - +
144B ALA* 3.8 0.6 - - - +
145B PHE* 2.8 43.4 + - + -
166B LEU* 3.4 32.5 - - + +
169B GLU* 2.8 39.0 + - - -
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ILE* 3.7 18.4 - - + +
109B ASN* 3.7 10.1 - - - +
111B ASP* 3.4 33.7 - - + -
112B GLY* 3.4 11.3 - - - +
138B GLY 3.0 8.3 + - - +
139B ALA 3.0 7.0 + - - +
141B ARG* 1.3 79.3 - - - +
143B VAL* 1.3 57.7 + - - +
145B PHE* 3.9 1.7 - - - +
146B GLU* 3.0 30.1 + - - +
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Residues in contact with VAL 143 (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 4.7 0.9 - - - +
112B GLY* 4.3 4.9 - - - -
115B ALA* 3.6 29.4 - - + -
133B ILE* 4.3 7.9 - - + -
139B ALA 2.9 21.8 + - - +
140B ALA* 4.1 2.9 - - - +
142B ALA* 1.3 70.5 - - + +
144B ALA* 1.3 65.8 + - - +
146B GLU* 3.4 1.3 + - - -
147B LEU* 2.9 47.4 + - + +
198B ILE* 3.9 20.4 - - + -
229B LEU* 4.2 13.9 - - + -
255B MET* 4.0 17.3 - - + -
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Residues in contact with ALA 144 (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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133B ILE* 3.4 24.4 - - + +
140B ALA 2.7 26.3 + - - +
141B ARG* 3.8 2.7 - - - +
143B VAL* 1.3 74.0 - - - +
145B PHE* 1.3 57.3 + - - +
148B ALA* 2.9 36.1 + - - +
153B ILE* 3.6 6.5 - - + +
155B ILE* 4.4 10.5 - - + -
166B LEU* 5.0 0.7 - - + -
170B ILE* 3.5 22.0 - - + -
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Residues in contact with PHE 145 (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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91B LEU* 3.3 38.4 - - + -
92B ILE* 3.9 33.0 - - + -
141B ARG* 2.8 34.8 + - - +
142B ALA 3.9 0.4 - - - +
144B ALA* 1.3 73.7 - - - +
146B GLU* 1.3 61.9 + - - +
148B ALA* 3.7 4.1 + - - -
149B LYS* 3.4 19.8 - - - +
166B LEU* 4.1 13.0 - - + -
169B GLU* 4.1 8.1 - - + -
170B ILE* 3.6 41.5 - - + -
173B LYS* 3.9 26.9 - - + -
174B LEU* 3.4 23.6 - - + +
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Residues in contact with GLU 146 (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* 4.7 2.3 - - - +
92B ILE* 5.6 2.0 - - + +
112B GLY* 3.6 28.9 - - - +
113B ILE* 4.4 18.3 + - - +
116B ARG* 2.6 62.9 + - + +
142B ALA 3.0 19.3 + - - +
143B VAL* 3.8 2.9 - - - +
145B PHE* 1.3 76.5 - - - +
147B LEU* 1.3 58.8 + - + +
149B LYS* 3.1 43.0 + - - +
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ALA* 5.9 1.3 - - + -
116B ARG* 3.5 43.1 - - + +
119B LEU* 4.3 10.8 - - + -
126B VAL* 4.4 9.0 - - + -
131B ILE* 4.0 24.2 - - + -
133B ILE* 4.8 1.8 - - + -
143B VAL* 2.9 28.4 + - + +
144B ALA* 5.2 0.2 - - - -
146B GLU* 1.3 74.7 - - + +
148B ALA* 1.3 58.1 + - - +
149B LYS 3.0 5.9 + - - -
150B ASP 3.3 2.0 + - - -
151B ASN* 3.0 38.0 + - - +
153B ILE* 4.2 9.4 - - + -
198B ILE* 3.6 31.2 - - + -
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ALA 2.9 19.8 + - - +
146B GLU 3.3 0.2 - - - -
147B LEU* 1.3 75.4 - - - +
149B LYS* 1.3 62.9 + - - +
150B ASP 3.2 1.1 + - - -
151B ASN 3.8 13.4 - - - +
153B ILE* 3.4 24.4 - - + +
170B ILE* 3.6 22.0 - - + -
174B LEU* 3.7 7.7 - - + +
176B LYS* 3.3 23.7 - - - +
182B VAL* 4.7 4.3 - - + -
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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