Contacts of the strand formed by residues 1514 - 1519 (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 LYS1514 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1509A ASP* 3.5 4.0 - - - +
1510A VAL* 3.0 34.6 + - + -
1511A GLY 3.1 16.7 + - - +
1512A ALA 3.5 1.5 - - - +
1513A GLY* 1.3 77.7 - - - +
1515A TYR* 1.3 69.0 + - - +
1526A ASP* 4.1 27.4 - - + -
1527A VAL 3.6 11.0 - - - +
1528A LEU* 4.5 25.1 - - + +
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Residues in contact with TYR1515 (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 37.7 - + + -
1487A VAL* 6.0 0.7 - - + -
1506A ILE* 3.8 24.0 - - + -
1508A ARG 3.4 15.0 - - - +
1509A ASP* 4.0 25.1 + - + -
1510A VAL* 3.9 6.5 - - - +
1513A GLY* 4.0 26.2 - - - -
1514A LYS* 1.3 76.0 - - - +
1516A LYS* 1.3 61.5 + - - +
1517A LEU* 3.7 1.4 + - + +
1526A ASP* 3.2 2.3 - - - -
1527A VAL* 2.8 31.4 + - - -
1529A GLY* 4.0 12.1 - - - -
1532A ILE* 3.7 31.0 - - + -
1602A LEU* 4.8 9.9 + - + -
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Residues in contact with LYS1516 (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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1506A ILE* 3.4 7.6 - - - +
1507A THR* 2.9 44.5 + - - +
1508A ARG* 2.9 52.8 + - + +
1510A VAL* 3.6 9.3 - - + +
1515A TYR* 1.3 72.2 - - - +
1517A LEU* 1.3 65.4 + - - +
1524A GLU* 4.9 14.8 - - + +
1525A CYS* 3.7 6.8 - - - +
1526A ASP* 2.7 35.2 + - - +
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Residues in contact with LEU1517 (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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1491A VAL* 3.5 29.2 - - + -
1493A ALA* 3.7 18.6 - - + -
1504A GLY* 4.3 6.5 - - - -
1505A LYS 3.7 18.4 - - - +
1506A ILE* 4.1 6.1 - - + -
1507A THR* 4.4 2.7 - - - -
1515A TYR* 4.1 2.2 - - + +
1516A LYS* 1.3 82.0 - - - +
1518A LEU* 1.3 60.0 + - - +
1519A PHE* 3.8 20.4 - - + -
1524A GLU* 3.1 29.2 - - - +
1525A CYS 2.8 17.0 + - - +
1527A VAL* 3.9 16.2 - - + -
1532A ILE* 3.6 31.0 - - + -
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Residues in contact with LEU1518 (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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1504A GLY* 3.2 1.1 - - - -
1505A LYS* 2.9 43.7 + - + +
1507A THR* 3.6 24.8 - - + +
1517A LEU* 1.3 73.6 - - - +
1519A PHE* 1.3 72.4 + - - +
1520A ASP* 4.5 1.4 - - - +
1522A GLY* 3.8 20.2 - - - +
1523A TYR 3.7 0.4 - - - -
1524A GLU* 3.4 30.5 - - + +
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Residues in contact with PHE1519 (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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1493A ALA* 3.4 41.1 - - + -
1494A LYS 4.2 8.5 - - - -
1495A TRP* 3.5 36.6 - + - -
1502A TYR* 3.6 31.2 - + + -
1503A SER 3.7 11.2 - - - +
1504A GLY* 3.8 2.2 - - - -
1517A LEU* 3.9 15.7 - - + -
1518A LEU* 1.3 80.4 - - - +
1520A ASP* 1.3 58.8 + - - +
1521A ASP* 3.1 19.1 - - - +
1522A GLY* 2.7 26.0 + - - -
1523A TYR* 2.8 22.8 + - + +
1524A GLU* 4.7 0.4 - - - -
1525A CYS* 3.7 16.8 - - - -
1527A VAL* 4.5 0.2 - - + -
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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