Contacts of the strand formed by residues 1446 - 1452 (chain B) in PDB entry 6XAF
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 PRO1446 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1413B ALA 3.6 5.6 - - - +
1414B LEU* 3.6 21.5 - - + -
1415B TYR* 3.0 26.2 + - - +
1444B SER 3.1 11.2 - - - +
1445B SER* 1.3 85.7 - - - +
1447B VAL* 1.3 62.0 + - - +
1481B ALA* 3.7 9.4 - - + +
1483B ARG* 4.0 18.4 - - + -
1507B GLU* 4.6 6.5 - - + +
1511B PHE* 3.6 36.6 - - + -
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Residues in contact with VAL1447 (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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1415B TYR* 3.4 12.3 - - + +
1417B ALA* 3.8 28.3 - - + +
1435B LEU* 4.1 13.9 - - + -
1438B ILE* 4.0 15.7 - - + -
1445B SER 4.0 1.3 - - - +
1446B PRO* 1.3 80.0 - - - +
1448B ILE* 1.3 69.9 + - - +
1449B LEU* 4.4 3.8 - - + +
1480B PRO* 3.6 34.1 - - + -
1481B ALA 3.0 9.8 + - - +
1482B ILE* 3.5 11.4 - - + +
1483B ARG* 2.9 27.8 + - - +
1484B ASP 3.9 0.3 + - - -
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Residues in contact with ILE1448 (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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1414B LEU* 4.0 23.8 - - + -
1415B TYR 2.8 8.9 + - - +
1416B LEU* 3.4 16.4 - - + +
1417B ALA 2.9 23.6 + - - -
1447B VAL* 1.3 78.8 - - - +
1449B LEU* 1.3 63.1 + - - +
1450B VAL* 3.8 0.7 + - + -
1483B ARG* 4.7 4.9 - - + -
1484B ASP 3.6 6.3 - - - +
1486B HIS* 3.7 30.3 - - + +
1500B LEU* 3.8 15.0 - - + -
1503B THR* 3.9 24.7 - - + -
1504B ILE* 4.0 25.6 - - + -
1507B GLU* 4.0 12.8 - - + -
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Residues in contact with LEU1449 (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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1417B ALA* 3.4 23.1 - - + +
1419B TYR* 3.8 16.6 - - + -
1428B VAL* 5.9 0.2 - - + -
1431B MET* 3.7 28.3 - - + -
1435B LEU* 5.5 2.7 - - + -
1447B VAL* 4.1 4.1 - - + -
1448B ILE* 1.3 71.6 - - - +
1450B VAL* 1.3 55.7 + - - +
1451B GLY 4.2 0.2 - - - -
1469B ILE* 4.0 26.2 - - + -
1473B LEU* 3.6 27.8 - - + -
1482B ILE* 4.3 20.6 - - + +
1484B ASP 3.0 8.5 + - - +
1485B TYR* 3.0 16.0 - - + -
1486B HIS* 2.8 31.9 + - - +
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Residues in contact with VAL1450 (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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1350B LEU* 4.0 22.7 - - + -
1416B LEU* 3.9 20.0 - - + -
1417B ALA 2.9 11.8 + - - +
1418B VAL* 3.3 7.5 - - + +
1419B TYR* 3.0 28.1 + - - +
1448B ILE* 4.0 2.9 - - + +
1449B LEU* 1.3 79.8 - - - +
1451B GLY* 1.3 64.0 + - - +
1452B THR* 3.8 2.9 + - + -
1486B HIS* 3.6 9.0 - - + +
1488B VAL* 3.8 27.8 - - + -
1500B LEU* 3.9 33.9 - - + -
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Residues in contact with GLY1451 (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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1419B TYR* 3.3 33.7 - - - -
1421B LEU* 4.7 5.3 - - - +
1450B VAL* 1.3 72.0 - - - +
1452B THR* 1.3 63.6 + - - -
1454B LEU 4.9 0.7 + - - -
1486B HIS 2.8 14.4 + - - -
1487B PHE* 3.4 6.2 - - - +
1488B VAL* 2.9 28.2 + - - +
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Residues in contact with THR1452 (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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1345B SER 2.5 23.2 + - - +
1346B GLY 4.5 5.4 - - - +
1350B LEU* 4.8 2.9 - - + -
1418B VAL* 3.6 25.6 - - + -
1419B TYR 2.7 13.4 + - - -
1420B ASP* 3.8 0.5 - - - -
1421B LEU* 2.9 26.9 + - - +
1450B VAL* 4.5 5.6 - - + -
1451B GLY* 1.3 73.7 - - - -
1453B HIS* 1.3 83.1 + - - +
1454B LEU 3.2 3.4 - - - -
1488B VAL* 3.3 12.8 - - + -
1490B ALA* 4.1 17.5 - - + -
1602B GDP 4.0 9.0 - - - -
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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