Contacts of the strand formed by residues 676 - 680 (chain B) in PDB entry 3QJM
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 PHE 676 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666B LEU* 4.2 7.9 - - + -
674B PHE* 3.6 23.1 - - + -
675B GLY* 1.3 77.6 - - - +
677B VAL* 1.3 62.5 + - - +
678B LEU* 4.1 15.9 - - + -
702B LEU* 3.4 31.2 - - + -
704B SER 3.3 13.7 - - - +
705B VAL* 4.2 12.8 - - + +
706B ASP* 4.6 2.6 + - - +
711B ALA* 3.7 19.3 - - + -
716B LEU* 5.0 4.3 - - + -
722B LEU* 5.2 3.1 - - + -
742B ILE* 4.4 7.9 - - + -
749B LEU* 3.8 26.2 - - + -
751B VAL* 5.9 0.9 - - + -
644D THR 3.8 0.2 - - - +
645D ASN* 3.7 1.6 - - - +
646D LEU* 2.8 59.3 + - + +
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Residues in contact with VAL 677 (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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676B PHE* 1.3 74.8 - - - +
678B LEU* 1.3 65.8 + - - +
702B LEU* 3.5 4.7 - - - +
703B GLU* 2.7 45.0 + - + -
704B SER* 2.9 33.5 + - - +
643D GLU* 3.9 23.1 - - + -
644D THR 3.4 11.0 - - - +
645D ASN* 3.4 33.2 - - - +
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Residues in contact with LEU 678 (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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676B PHE* 4.0 16.1 + - + -
677B VAL* 1.3 72.8 - - - +
679B ARG* 1.3 59.8 + - - +
700B GLN* 3.8 23.8 - - + +
701B TYR 3.3 22.2 - - - +
702B LEU* 4.3 3.1 - - + +
722B LEU* 3.8 20.2 - - + -
735B HIS* 3.4 18.3 - - + +
738B VAL* 3.5 32.1 - - + -
739B VAL* 4.4 9.2 - - + -
742B ILE* 4.2 6.7 - - + -
643D GLU* 3.3 5.5 - - - -
644D THR 2.9 35.3 + - - +
646D LEU* 4.1 9.6 - - + -
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Residues in contact with ARG 679 (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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677B VAL 3.8 0.4 + - - -
678B LEU* 1.3 75.4 - - - +
680B GLY* 1.3 62.4 + - - +
700B GLN* 3.3 7.4 - - - -
701B TYR* 2.9 61.4 + - + +
703B GLU* 3.3 44.3 + - + -
642D ASP 3.3 14.7 - - - +
643D GLU* 3.6 26.5 + - + +
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Residues in contact with GLY 680 (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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679B ARG* 1.3 80.5 - - - +
681B ALA* 1.3 67.0 + - - -
699B LEU 3.4 11.9 - - - -
700B GLN* 3.1 12.9 - - - +
701B TYR* 4.5 4.3 - - - -
735B HIS* 3.6 8.0 + - - +
642D ASP 3.1 26.5 + - - +
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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