Contacts of the strand formed by residues 1514 - 1521 (chain B) in PDB entry 6X34
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 LEU1514 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1439B VAL* 3.5 33.6 + - + +
1440B PHE 5.5 0.2 + - - -
1445B PRO* 5.2 13.7 - - + -
1497B GLY 5.9 1.6 - - - +
1500B PHE* 6.6 0.2 - - + -
1501B VAL* 4.4 23.8 - - + +
1512B THR 3.6 5.5 + - - +
1513B ASP* 1.3 76.6 - - - +
1515B VAL* 1.3 64.0 + - - +
1516B ILE* 5.6 2.8 - - + +
1532B ASN* 5.6 4.9 - - + -
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Residues in contact with VAL1515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1436B SER* 5.8 3.4 - - - -
1437B VAL 3.5 20.4 - - - +
1438B ARG* 3.8 26.9 - - + +
1439B VAL 4.4 1.8 - - - +
1513B ASP* 5.5 2.9 - - + -
1514B LEU* 1.3 79.3 - - - +
1516B ILE* 1.3 68.2 + - - +
1532B ASN* 3.3 35.7 + - + +
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Residues in contact with ILE1516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1434B TYR* 5.6 0.4 - - - -
1436B SER* 3.5 24.5 - - - -
1437B VAL* 3.7 17.8 + - + -
1448B VAL* 5.8 2.0 - - + -
1450B VAL* 3.8 36.3 - - + +
1495B VAL* 5.1 13.7 - - + +
1497B GLY* 5.8 7.4 - - - -
1500B PHE* 4.3 21.8 - - + -
1514B LEU* 5.6 3.6 - - + -
1515B VAL* 1.3 80.7 - - - +
1517B GLY* 1.3 62.0 + - - +
1529B PHE* 6.5 0.7 - - + -
1530B THR 3.3 12.3 - - - +
1531B ALA* 4.2 10.5 - - - -
1532B ASN 4.8 0.7 - - - +
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Residues in contact with GLY1517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1434B TYR* 4.4 15.9 - - - -
1435B TYR 3.7 5.4 - - - -
1436B SER* 4.6 1.1 - - - -
1516B ILE* 1.3 76.6 - - - +
1518B CYS* 1.3 62.4 + - - +
1529B PHE* 3.6 5.7 - - - +
1530B THR* 2.5 49.8 + - - +
1531B ALA 4.1 3.6 + - - -
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Residues in contact with CYS1518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1433B TYR 3.3 11.3 - - - +
1434B TYR* 3.6 9.9 - - - -
1435B TYR* 3.1 41.7 + - + +
1452B TRP* 5.0 2.5 - - - +
1517B GLY* 1.3 75.3 - - - +
1519B LEU* 1.3 61.0 + - - +
1520B VAL* 4.1 8.7 - - + -
1528B THR 3.7 7.0 - - - -
1529B PHE* 3.8 22.7 - - + +
1530B THR* 4.2 3.2 - - - +
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Residues in contact with LEU1519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1432B THR* 6.1 4.0 - - - -
1433B TYR 3.5 7.6 - - - +
1518B CYS* 1.3 74.2 - - - +
1520B VAL* 1.3 61.2 + - - +
1526B LEU 3.7 3.5 - - - +
1527B MET* 3.7 1.7 - - - -
1528B THR* 2.8 50.7 + - - +
1530B THR* 6.2 1.6 - - - -
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Residues in contact with VAL1520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1295B VAL* 5.8 8.1 - - + -
1432B THR* 4.9 0.9 - - - -
1433B TYR* 3.1 46.7 + - + +
1435B TYR* 6.2 0.7 - - + -
1452B TRP* 3.6 40.4 - - + +
1518B CYS* 5.0 4.7 - - + -
1519B LEU* 1.3 80.4 - - - +
1521B ASP* 1.3 70.1 + - - +
1525B GLY 6.0 0.2 - - - +
1527B MET* 3.8 37.9 - - + +
1529B PHE* 5.7 0.9 - - + -
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Residues in contact with ASP1521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1297B PHE* 4.8 4.3 - - - +
1431B THR* 3.3 20.2 - - - +
1432B THR* 5.1 2.7 - - - -
1433B TYR* 4.9 0.7 - - - -
1519B LEU 4.3 0.6 + - - -
1520B VAL* 1.3 84.5 - - - +
1522B LEU* 1.3 61.8 + - - +
1523B ALA* 3.5 2.5 - - + +
1525B GLY* 3.8 36.5 + - - +
1526B LEU 4.7 6.6 + - - +
1542B VAL* 5.9 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