Contacts of the strand formed by residues 636 - 639 (chain F) 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 ASN 636 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35E LYS* 3.5 34.5 + - - +
635F THR* 1.3 77.9 - - - +
637F LEU* 1.3 88.3 + - - +
638F ILE* 3.5 4.9 + - - +
677F ALA* 5.6 2.3 - - - +
678F GLN* 4.2 8.9 - - - +
702F TRP* 3.1 41.8 - - + +
1637F MET* 4.6 2.6 - - - +
1638F ALA* 3.5 27.9 + - - +
1693F GLN* 6.1 1.6 - - - -
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Residues in contact with LEU 637 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636F ASN* 1.3 89.0 + - - +
638F ILE* 1.3 59.3 + - - +
639F ASN* 5.8 0.4 - - - -
677F ALA* 4.8 19.3 - - + +
678F GLN* 3.5 21.1 + - - +
1635F THR* 4.1 19.3 - - - -
1636F MET 3.4 9.9 - - - +
1637F MET* 4.6 3.8 - - + +
1692F ALA* 4.8 7.9 - - + +
1693F GLN* 3.9 36.6 - - + +
1696F HIS* 4.0 36.6 - - + +
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Residues in contact with ILE 638 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636F ASN 4.3 2.7 - - - +
637F LEU* 1.3 75.8 - - - +
639F ASN* 1.3 78.7 + - - +
640F TYR* 4.1 2.3 + - - -
678F GLN* 3.3 30.1 - - - +
697F GLY 5.3 7.2 - - - +
702F TRP 5.4 2.5 - - - +
703F GLY* 3.7 9.6 - - - -
704F GLY* 3.4 30.7 - - - +
1635F THR* 3.6 1.0 - - - -
1636F MET* 2.8 46.6 + - + +
1638F ALA* 3.9 26.0 - - + -
1647F CYS* 6.5 0.2 - - + -
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Residues in contact with ASN 639 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637F LEU 5.5 0.6 - - - +
638F ILE* 1.3 94.3 - - - +
640F TYR* 1.3 69.7 + - - +
641F VAL* 5.0 1.6 - - - +
676F THR* 3.1 37.9 + - - +
677F ALA* 4.7 1.0 + - - +
678F GLN* 3.8 24.1 + - - +
681F HIS* 5.3 8.1 - - + -
697F GLY 5.7 0.5 - - - +
704F GLY* 5.0 4.9 - - - -
784F SER* 5.9 4.5 - - - +
1634F LEU 2.7 26.9 + - - +
1635F THR* 3.4 16.8 - - - -
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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