Contacts of the strand formed by residues 1511 - 1517 (chain A) in PDB entry 3CLY
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 ALA1511 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1499A GLU* 4.1 19.3 - - + +
1500A ALA 3.6 6.5 - - - +
1501A VAL* 3.7 22.9 - - + +
1509A LYS 3.3 4.1 + - - +
1510A GLU* 1.3 74.6 - - - +
1512A VAL* 1.3 63.2 + - - +
1513A THR 4.3 0.2 + - - -
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Residues in contact with VAL1512 (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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1499A GLU* 3.4 4.4 - - - -
1500A ALA* 2.7 38.1 + - - +
1503A ILE* 3.4 31.0 - - + -
1504A ASP* 4.6 13.0 - - + -
1510A GLU* 4.1 11.2 - - + +
1511A ALA* 1.3 79.8 - - - +
1513A THR* 1.3 76.7 + - - +
1514A VAL* 3.4 11.6 + - + +
1551A LEU* 5.4 2.9 - - + -
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Residues in contact with THR1513 (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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1497A MET* 3.8 32.1 - - + -
1498A ALA 3.3 4.7 - - - +
1499A GLU* 3.0 25.0 + - - +
1512A VAL* 1.3 79.5 - - - +
1514A VAL* 1.3 65.2 + - - +
1566A TYR* 3.5 32.1 + - + +
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Residues in contact with VAL1514 (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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1481A LEU* 4.5 1.6 - - + -
1497A MET* 3.4 8.8 - - - +
1498A ALA* 2.6 52.1 + - + +
1500A ALA* 4.1 17.9 - - + -
1503A ILE* 4.8 1.3 - - + -
1512A VAL* 3.8 16.6 - - + +
1513A THR* 1.3 80.3 - - - +
1515A ALA* 1.3 62.9 + - - +
1516A VAL* 4.3 3.4 - - + -
1551A LEU* 3.4 27.4 - - + -
1563A ILE* 3.6 21.5 - - + -
1564A VAL 3.6 7.2 - - - +
1565A GLU* 5.1 0.4 - - - -
1566A TYR* 3.8 12.4 - - - +
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Residues in contact with ALA1515 (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 LEU* 4.2 8.7 - - + -
1495A VAL* 4.9 2.7 - - + -
1496A VAL 3.3 7.2 - - - +
1497A MET* 4.6 0.4 - - - +
1514A VAL* 1.3 77.2 - - - +
1516A VAL* 1.3 62.4 + - - +
1563A ILE* 3.5 4.0 - - - +
1564A VAL* 2.8 40.8 + - + +
1565A GLU 4.2 0.9 - - - +
1566A TYR* 4.3 1.5 - - - +
1803A ACP 3.2 43.1 - - + +
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Residues in contact with VAL1516 (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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1481A LEU* 4.2 17.0 - - + -
1483A LEU* 5.1 2.9 - - + -
1494A GLN 3.6 1.6 - - - +
1495A VAL* 3.3 5.4 - - - -
1496A VAL* 2.7 50.0 + - + +
1498A ALA* 3.8 24.7 - - + -
1514A VAL* 4.3 3.1 - - + -
1515A ALA* 1.3 80.2 - - - +
1517A LYS* 1.3 66.8 + - - +
1518A MET* 4.5 6.9 - - + +
1561A TYR* 3.6 39.3 - - + -
1562A VAL 3.4 5.2 - - - +
1563A ILE* 4.2 11.9 - - + -
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Residues in contact with LYS1517 (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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1494A GLN 3.5 6.5 - - - +
1495A VAL* 4.1 10.1 - - + +
1516A VAL* 1.3 74.7 - - - +
1518A MET* 1.3 70.2 + - - +
1531A LEU* 3.7 20.8 - - + +
1534A GLU* 2.6 33.2 + - - +
1560A LEU 3.8 0.3 - - - +
1561A TYR* 3.6 2.8 - - - -
1562A VAL* 2.9 45.5 + - + +
1564A VAL* 6.0 4.0 - - + +
1644A ASP* 3.6 5.3 + - - +
1803A ACP 2.6 62.5 + - - +
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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