Contacts of the strand formed by residues 1449 - 1453 (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 TRP1449 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1446B SER 4.2 8.3 - - - -
1447B CYS* 3.3 42.4 - - + -
1448B VAL* 1.3 77.7 + - - +
1450B VAL* 1.3 61.3 + - - +
1464B PHE* 3.4 43.7 - - + -
1465B ASP* 5.3 1.1 - - - -
1466B LEU* 3.4 30.0 - - + +
1494B MET* 3.9 13.9 - - + -
1495B VAL 3.3 23.3 - - - -
1496B TRP* 3.6 25.1 - + - +
1552B VAL* 3.5 1.0 - - - -
1553B PHE* 2.7 67.5 + - + -
1554B VAL 5.7 0.4 - - - -
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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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1435B TYR* 4.8 14.1 - - + -
1437B VAL* 3.7 31.9 - - + -
1448B VAL* 4.1 13.5 - - + -
1449B TRP* 1.3 77.7 - - - +
1451B GLY* 1.3 61.9 + - - +
1494B MET* 3.4 4.4 - - - -
1495B VAL* 3.2 26.5 + - - +
1516B ILE* 3.8 22.7 - - + +
1529B PHE* 3.8 8.9 - - + -
1551B ALA 3.7 3.8 - - - +
1552B VAL* 3.8 31.0 - - + -
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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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1435B TYR* 5.7 1.2 - - - -
1449B TRP 4.3 0.2 - - - -
1450B VAL* 1.3 80.7 - - - +
1452B TRP* 1.3 66.8 + - - -
1493B TYR 3.2 14.0 + - - -
1529B PHE* 3.7 17.5 - - - -
1550B PRO* 3.6 5.0 - - - +
1551B ALA* 2.8 32.4 + - - +
1553B PHE* 5.6 0.8 - - - -
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Residues in contact with TRP1452 (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* 3.7 30.1 - - + -
1435B TYR* 4.7 27.6 - + + -
1451B GLY* 1.3 77.0 - - - -
1453B VAL* 1.3 58.4 + - - +
1493B TYR* 2.6 54.3 + - + +
1518B CYS* 5.0 3.0 - - + +
1520B VAL* 3.6 34.6 - - + +
1527B MET* 3.5 25.1 - - + -
1529B PHE* 3.9 22.2 - + - -
1548B LEU* 3.8 16.6 - - + -
1549B PHE 3.2 6.5 - - - -
1550B PRO* 3.5 45.1 - - + -
1551B ALA* 4.9 0.7 - - - -
1575B LEU* 5.7 6.7 - - + -
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Residues in contact with VAL1453 (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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1245B PHE* 5.3 5.6 - - + -
1290B ARG* 3.8 15.7 - - + -
1452B TRP* 1.3 75.2 - - - +
1454B THR* 1.4 72.4 + - - +
1457B TYR* 3.6 32.1 - - + -
1491B ASN 4.0 4.9 - - - +
1492B CYS* 4.2 8.5 - - + +
1493B TYR* 5.9 0.9 - - - +
1548B LEU* 3.3 5.0 - - - -
1549B PHE* 2.5 64.4 + - + +
1551B ALA* 3.6 22.2 - - + -
1553B PHE* 5.2 5.6 - - + -
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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