Contacts of the helix formed by residues 1423 - 1430 (chain A) in PDB entry 2NVX
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 GLY1423 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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847A ASP* 4.5 5.6 - - - -
859A SER* 3.9 19.6 - - - -
1398A MET* 4.1 7.0 - - - -
1422A ARG* 1.3 84.0 - - - +
1424A VAL* 1.3 68.9 + - - +
1425A SER 3.8 0.4 - - - -
1426A GLU* 2.9 17.1 + - - +
1427A ASN* 3.3 17.0 + - - +
1435A PRO* 4.4 2.6 - - - +
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Residues in contact with VAL1424 (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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846A GLU* 3.2 17.0 - - + +
847A ASP* 3.9 26.4 - - + +
1063A MET* 4.1 10.3 - - + -
1398A MET* 4.2 4.9 - - - -
1423A GLY* 1.3 67.8 - - - +
1425A SER* 1.3 55.5 + - - +
1426A GLU 2.7 3.9 + - - -
1427A ASN* 2.7 33.6 + - - +
1428A VAL* 3.4 12.8 + - + +
1434A ALA* 5.0 1.7 - - + +
1435A PRO* 5.8 0.2 - - - -
1436A ILE* 3.5 36.8 - - + -
1135B ARG* 3.9 9.2 - - - +
1139B ILE* 3.6 25.1 - - + -
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Residues in contact with SER1425 (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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341A MET* 3.7 6.0 - - - +
843A LYS* 2.6 27.1 + - - -
846A GLU* 2.7 15.9 + - - -
1397A LEU 4.8 0.7 - - - -
1398A MET* 4.0 14.6 - - - -
1401A SER* 3.5 20.0 - - - -
1423A GLY 3.8 0.2 - - - -
1424A VAL* 1.3 77.9 - - - +
1426A GLU* 1.3 62.4 + - - +
1428A VAL* 3.3 4.8 + - - +
1429A ILE* 3.1 29.8 + - - +
1135B ARG* 3.4 15.0 + - - +
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Residues in contact with GLU1426 (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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859A SER* 5.2 0.7 - - - -
1395A GLY* 3.7 9.9 - - - -
1397A LEU* 3.7 11.5 - - + +
1398A MET* 3.2 44.7 - - - +
1419A ASP* 3.3 36.7 - - - +
1420A ASP* 5.6 0.9 - - - +
1421A CYS* 3.7 17.9 + - + -
1422A ARG 3.3 7.4 + - - -
1423A GLY* 2.9 31.1 + - - +
1424A VAL 2.7 5.3 + - - -
1425A SER* 1.3 74.8 - - - +
1427A ASN* 1.3 56.8 + - - +
1429A ILE* 3.6 3.3 + - - +
1430A LEU* 3.3 33.2 + - - +
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Residues in contact with ASN1427 (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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14A VAL 5.0 2.9 - - - +
1421A CYS* 3.8 21.5 + - - +
1423A GLY 3.3 12.7 + - - -
1424A VAL 2.7 14.8 + - - +
1426A GLU* 1.3 71.7 - - - +
1428A VAL* 1.3 58.0 + - - -
1429A ILE 3.3 0.2 - - - -
1430A LEU* 3.9 6.5 - - - +
1431A GLY* 3.0 5.0 + - - -
1432A GLN* 2.9 55.7 + - - +
1433A MET 4.5 3.5 - - - +
1434A ALA* 3.9 21.5 - - + -
1435A PRO* 3.1 33.2 - - - +
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Residues in contact with VAL1428 (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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340A LEU* 3.5 23.8 - - - +
341A MET* 4.0 11.7 - - - -
343A LYS* 5.0 0.5 - - - -
1424A VAL* 3.4 16.1 + - + +
1425A SER 3.3 8.4 + - - +
1427A ASN* 1.3 75.7 - - - +
1429A ILE* 1.3 66.1 - - - +
1431A GLY* 3.2 11.6 + - - -
1434A ALA* 5.5 4.3 - - + -
1135B ARG* 3.7 42.8 - - - +
1147B LEU* 4.0 17.9 - - + -
1151B LEU* 3.6 22.1 - - + +
1197B PRO* 4.7 2.9 - - - +
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Residues in contact with ILE1429 (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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336A ILE* 4.7 14.6 - - + -
340A LEU* 3.4 48.8 - - + +
341A MET* 4.8 8.3 - - + -
1397A LEU* 3.7 43.1 - - + +
1400A CYS* 5.5 0.9 - - + -
1401A SER* 4.8 5.6 - - - -
1425A SER 3.1 19.8 + - - +
1426A GLU* 3.8 5.2 - - - +
1428A VAL* 1.3 80.9 - - + +
1430A LEU* 1.3 67.2 + - + +
1431A GLY 3.2 0.9 + - - -
1197B PRO* 3.6 9.7 - - - +
1200B ALA* 3.7 8.6 - - + +
1203B LEU* 4.3 14.8 - - + -
1204B PHE* 5.0 4.0 - - + -
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Residues in contact with LEU1430 (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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14A VAL* 3.5 26.7 - - + +
17A VAL* 4.4 3.4 - - + -
1397A LEU* 5.1 2.5 - - + -
1421A CYS* 4.0 20.2 - - + -
1426A GLU 3.3 18.9 + - - +
1427A ASN* 4.6 3.6 - - - +
1428A VAL 3.3 0.4 - - - -
1429A ILE* 1.3 79.9 - - + +
1431A GLY* 1.3 64.5 + - - +
1432A GLN* 3.6 21.9 - - + +
1196B ILE* 3.2 35.4 - - + +
1197B PRO* 3.2 8.6 - - - +
1200B ALA* 5.0 0.9 - - + -
1204B PHE* 4.0 21.1 - - + -
1216B LEU* 3.8 26.2 - - + -
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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