Contacts of the strand formed by residues 1501 - 1511 (chain A) in PDB entry 2G3R
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 PHE1501 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1492A VAL* 3.6 20.1 - - + +
1493A ALA 3.2 6.7 - - - +
1494A LYS* 3.5 36.8 - - + -
1499A GLY 3.7 14.8 - - - -
1500A TYR* 1.3 76.8 - - - +
1502A TYR* 1.3 60.6 + - - +
1531A ASP* 3.6 22.0 - - - -
1533A LEU* 3.7 28.5 - - + -
1587A ILE* 3.5 9.9 - - - +
1588A LEU* 2.7 39.3 + - + -
1589A SER 3.8 13.9 - - - -
1590A LEU* 4.1 4.3 - - - -
1593A GLY* 3.6 29.2 - - - -
1594A ASN* 4.0 9.6 - - - -
1597A ARG* 4.8 5.4 - - + -
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Residues in contact with TYR1502 (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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1492A VAL* 3.3 5.8 - - - -
1493A ALA 2.8 27.4 + - - +
1495A TRP* 3.8 24.0 - + + -
1498A ASN* 2.9 21.8 + - - -
1500A TYR* 3.5 37.9 - - + +
1501A PHE* 1.3 73.7 - - - +
1503A SER* 1.3 67.2 + - - +
1504A GLY 3.6 0.5 + - - -
1519A PHE* 3.6 24.7 - + + -
1521A ASP* 5.4 9.4 - - - +
1547A LEU* 5.8 2.2 - - + -
1587A ILE* 3.6 38.5 - - + +
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Residues in contact with SER1503 (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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1490A ARG* 4.1 6.1 - - - -
1491A VAL 3.4 10.8 - - - -
1492A VAL* 4.2 10.8 - - - +
1502A TYR* 1.3 75.5 - - - +
1504A GLY* 1.3 58.7 + - - +
1519A PHE* 3.7 5.9 - - - +
1520A ASP* 2.9 45.0 + - - +
1538A ILE* 6.4 1.1 - - - -
1583A ARG* 4.0 29.0 + - - +
1584A MET* 4.5 6.4 - - - +
1586A VAL 5.0 7.3 + - - -
1587A ILE* 5.6 0.6 - - - +
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Residues in contact with GLY1504 (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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1490A ARG* 3.4 8.8 + - - +
1491A VAL* 2.9 34.0 + - - +
1502A TYR 3.6 1.2 + - - -
1503A SER* 1.3 76.2 - - - +
1505A LYS* 1.3 64.7 + - - +
1517A LEU* 4.3 5.4 - - - -
1518A LEU 3.2 14.4 - - - -
1519A PHE* 3.8 4.0 - - - -
1520A ASP* 3.5 10.9 + - - -
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Residues in contact with LYS1505 (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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1488A GLY* 4.6 11.6 + - - +
1489A LEU 3.1 12.3 - - - +
1490A ARG* 3.8 45.5 - - + +
1491A VAL* 4.5 0.2 - - - -
1504A GLY* 1.3 79.5 - - - +
1506A ILE* 1.3 67.9 + - - +
1507A THR* 3.3 8.2 + - + +
1517A LEU* 4.0 5.7 - - - +
1518A LEU* 2.9 45.4 + - + +
1520A ASP* 5.0 2.2 - - - +
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Residues in contact with ILE1506 (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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1486A PHE* 3.7 31.0 - - + +
1487A VAL* 4.1 6.5 - - + -
1488A GLY* 2.8 31.4 + - - -
1489A LEU 3.1 8.4 + - - +
1491A VAL* 4.1 20.8 - - + +
1505A LYS* 1.3 73.6 - - - +
1507A THR* 1.3 59.0 + - - +
1508A ARG 3.6 23.3 - - - +
1515A TYR* 3.8 19.1 - - + -
1516A LYS 3.4 7.0 - - - +
1517A LEU* 4.1 19.3 - - + +
1532A ILE* 4.2 6.1 - - + -
1602A LEU* 3.8 28.7 - - + -
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Residues in contact with THR1507 (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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1487A VAL* 3.8 16.6 - - - +
1505A LYS* 3.5 18.2 - - + +
1506A ILE* 1.3 74.9 - - - +
1508A ARG* 1.3 64.7 + - - +
1516A LYS* 2.9 33.6 + - - +
1517A LEU 4.4 1.2 - - - -
1518A LEU* 3.6 26.9 - - + +
1524A GLU* 5.0 4.1 + - - +
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Residues in contact with ARG1508 (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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1487A VAL* 4.0 10.3 - - - -
1506A ILE* 3.6 7.5 - - - +
1507A THR* 1.3 82.3 + - - +
1509A ASP* 1.3 73.3 + - - +
1510A VAL* 4.8 6.3 - - - +
1515A TYR* 3.4 4.5 - - - -
1516A LYS* 2.9 65.2 + - + +
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Residues in contact with ASP1509 (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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1485A SER* 6.3 2.2 - - - -
1487A VAL* 3.9 14.2 - - + +
1508A ARG* 1.3 82.0 - - - +
1510A VAL* 1.3 60.9 + - - +
1511A GLY* 3.0 21.7 + - - -
1513A GLY 5.3 0.7 + - - -
1514A LYS 3.5 6.1 + - - +
1515A TYR* 4.0 24.8 - - + -
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Residues in contact with VAL1510 (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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1508A ARG* 3.6 8.7 + - - +
1509A ASP* 1.3 71.2 - - - +
1511A GLY* 1.3 56.1 + - - +
1514A LYS* 3.0 32.8 + - + +
1515A TYR 3.9 0.4 - - - -
1516A LYS* 3.6 36.6 - - + +
1526A ASP* 3.7 30.1 - - - +
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Residues in contact with GLY1511 (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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1509A ASP* 3.0 19.0 + - - -
1510A VAL* 1.3 82.2 - - - +
1512A ALA* 1.3 72.2 + - - +
1513A GLY 3.2 3.1 - - - -
1514A LYS* 3.1 18.8 + - - +
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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