Contacts of the strand formed by residues 1472 - 1477 (chain D) in PDB entry 6PUO
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 SER1472 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1377D VAL* 3.8 1.5 - - - +
1378D LYS* 2.9 32.2 + - - +
1385D TRP* 4.1 13.3 - - - -
1470D GLY 3.8 0.6 - - - -
1471D ALA* 1.3 85.2 - - - +
1473D ILE* 1.3 77.9 + - - +
1474D ARG* 5.0 2.8 - - - +
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Residues in contact with ILE1473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1375D LEU* 4.8 21.8 - - + -
1376D VAL 3.5 8.3 - - - +
1377D VAL* 3.7 27.8 - - + +
1385D TRP* 4.7 0.2 - - - -
1406D LEU* 5.1 18.2 - - + +
1464D LEU* 5.8 5.4 - - + -
1466D ALA* 3.7 31.9 - - + +
1472D SER* 1.3 85.6 + - - +
1474D ARG* 1.3 66.6 + - - +
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Residues in contact with ARG1474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447D PHE* 4.1 11.9 - - - +
1375D LEU* 3.5 10.1 - - - +
1376D VAL* 3.0 30.1 + - - +
1385D TRP* 3.7 39.9 - - + +
1472D SER* 5.0 3.1 - - - +
1473D ILE* 1.3 77.1 - - - +
1475D TRP* 1.3 67.5 + - - +
1476D GLN* 2.7 39.9 + - - +
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Residues in contact with TRP1475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1352D VAL* 3.9 17.5 - - + -
1353D THR 5.3 0.2 - - - -
1354D ARG* 3.2 57.1 - - + +
1373D GLU* 3.6 28.5 - - + +
1374D VAL 3.3 22.9 - - - -
1375D LEU* 3.4 40.4 - - + +
1449D PHE* 5.0 14.8 - + - -
1457D LEU* 6.5 0.9 - - + -
1460D LEU* 6.3 2.2 - - + -
1461D ASN* 6.2 2.6 - - - +
1474D ARG* 1.3 85.5 - - - +
1476D GLN* 1.3 69.7 - - - +
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Residues in contact with GLN1476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447D PHE* 3.4 22.6 - - - +
1373D GLU* 3.3 5.0 - - - +
1374D VAL* 2.5 51.2 + - + +
1376D VAL* 3.7 20.0 - - + +
1385D TRP* 5.3 2.1 - - - -
1474D ARG* 2.7 47.9 + - - +
1475D TRP* 1.3 79.9 - - - +
1477D VAL* 1.3 77.1 + - - +
1482D ILE* 6.1 2.9 - - + -
1483D PRO* 5.1 8.9 - - + +
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Residues in contact with VAL1477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1356D ARG* 4.2 36.1 - - - +
1371D MET* 4.4 11.9 - - + -
1372D LEU 3.4 11.2 - - - +
1373D GLU* 4.3 8.4 - - + +
1374D VAL* 5.3 0.8 - - - +
1476D GLN* 1.3 88.3 - - + +
1478D VAL* 1.3 74.9 + - - +
1479D ASP* 3.7 4.8 + - + +
1482D ILE* 4.9 5.7 - - - +
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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