Contacts of the strand formed by residues 1451 - 1457 (chain A) in PDB entry 4NM6
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 ARG1451 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1449A SER* 5.6 1.3 - - - +
1450A PHE* 1.3 79.3 - - - +
1452A ARG* 1.3 68.2 + - - +
1453A LYS* 5.7 0.3 - - - +
1847A TRP* 3.7 44.2 - - + -
1848A SER 3.3 8.5 - - - +
1849A ASP* 2.7 27.6 + - - +
1851A GLU* 3.3 27.6 - - + +
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Residues in contact with ARG1452 (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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1450A PHE* 3.8 36.8 - - + +
1451A ARG* 1.3 83.4 + - - +
1453A LYS* 1.3 66.5 + - + +
1454A VAL* 6.2 0.4 - - + -
1847A TRP* 3.1 7.1 - - - +
1848A SER* 2.5 42.8 + - - +
1887A LYS* 5.1 11.2 - - - +
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Residues in contact with LYS1453 (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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1451A ARG 5.7 0.4 - - - +
1452A ARG* 1.3 84.4 - - + +
1454A VAL* 1.3 64.4 + - - +
1845A GLU* 4.7 26.4 + - + +
1846A VAL 3.6 7.6 - - - +
1847A TRP* 3.9 8.3 - - + +
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Residues in contact with VAL1454 (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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1191A GLN* 4.8 11.9 - - + +
1271A CYS* 6.6 0.7 - - + -
1272A ALA* 5.6 10.3 - - + +
1273A CYS* 5.8 8.1 - - - -
1452A ARG* 4.2 0.6 + - + -
1453A LYS* 1.3 76.2 - - - +
1455A ARG* 1.3 79.2 + - - +
1845A GLU* 3.4 6.0 - - - +
1846A VAL* 2.7 42.5 + - + +
1848A SER* 3.1 27.8 - - - +
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Residues in contact with ARG1455 (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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1270A THR 4.3 0.7 - - - +
1271A CYS* 4.3 2.6 - - - +
1272A ALA* 3.7 38.0 + - + +
1276A LEU* 4.1 16.2 - - + +
1454A VAL* 1.3 88.9 - - - +
1456A MET* 1.3 60.1 + - - +
1457A LEU 4.2 0.2 - - - -
1843A SER* 3.5 34.6 + - - +
1844A ASP* 3.4 14.6 - - - +
1845A GLU* 3.9 28.7 + - + +
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Residues in contact with MET1456 (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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1191A GLN* 3.9 21.8 - - - +
1270A THR* 3.6 27.4 - - + +
1271A CYS* 5.5 0.9 - - - -
1454A VAL* 3.9 0.6 + - + -
1455A ARG* 1.3 75.6 - - - +
1457A LEU* 1.3 74.5 + - - +
1458A ALA* 3.5 1.8 + - - -
1843A SER* 3.8 2.9 - - - -
1844A ASP* 2.7 42.0 + - + +
1846A VAL* 3.7 28.7 - - + -
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Residues in contact with LEU1457 (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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1265A LEU* 5.5 0.2 - - + -
1270A THR* 2.9 36.8 + - - +
1271A CYS 4.0 17.0 - - - +
1272A ALA* 4.4 3.8 - - + -
1276A LEU* 3.7 40.4 - - + -
1456A MET* 1.3 80.5 - - - +
1458A ALA* 1.3 63.9 + - - +
1459A GLU 3.3 17.3 + - - +
1461A VAL* 4.2 24.5 - - + -
1842A GLY 3.6 10.5 - - - +
1843A SER* 3.9 5.4 - - - -
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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