Contacts of the strand formed by residues 630 - 636 (chain B) in PDB entry 2C11
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 TYR 630 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576B ALA* 3.9 16.8 - - + -
577B PHE 3.4 18.6 - - - +
578B LEU* 3.8 24.2 - - + -
579B VAL* 3.4 13.2 - - - +
626B SER 3.6 22.4 - - - -
627B TRP* 3.2 10.9 + - - +
628B GLU 3.1 1.0 - - - +
629B ARG* 1.3 94.0 + - + +
631B GLN* 1.3 61.5 + - - +
632B LEU* 3.8 11.9 - - - +
633B ALA* 4.6 4.5 - - + -
660B PHE* 4.3 11.2 - + + -
661B SER* 4.0 18.8 + - - -
664B ILE* 3.3 33.0 - - + +
677B TRP 5.8 0.2 - - - +
679B THR* 3.0 27.1 + - - +
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Residues in contact with GLN 631 (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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577B PHE* 2.7 9.2 + - + +
578B LEU 3.3 7.4 - - - +
579B VAL* 3.5 22.4 - - + +
580B GLY* 3.2 16.8 + - - -
581B SER 3.2 20.0 + - - +
583B THR* 3.5 27.5 + - - +
607B MET* 3.8 23.8 - - + +
609B SER* 6.0 5.1 - - - +
611B ALA* 6.2 1.8 - - + -
630B TYR* 1.3 75.8 - - - +
632B LEU* 1.3 66.0 + - + +
678B VAL* 3.7 2.3 - - - -
679B THR* 3.1 33.6 + - - +
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Residues in contact with LEU 632 (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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575B ALA 3.8 2.8 - - - +
576B ALA* 3.5 0.3 - - - -
577B PHE* 2.6 41.5 + - + +
583B THR* 6.3 0.9 - - + -
587B LEU* 3.6 31.4 - - + -
605B ILE* 4.6 17.5 - - + -
607B MET* 4.0 21.5 - - + -
630B TYR* 3.3 4.9 - - - +
631B GLN* 1.3 87.6 - - + +
633B ALA* 1.3 89.3 + - - +
634B VAL* 4.1 7.4 - - + -
676B ALA* 4.0 13.2 - - + -
677B TRP 3.2 25.1 - - - +
678B VAL* 4.3 5.8 - - + -
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Residues in contact with ALA 633 (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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575B ALA 3.4 7.2 - - - -
576B ALA* 4.0 16.6 - - + -
630B TYR* 4.6 5.6 - - + -
632B LEU* 1.3 81.8 - - - +
634B VAL* 1.3 65.2 + - - +
635B THR* 5.0 0.2 - - + -
660B PHE* 4.5 18.4 - - + -
664B ILE* 4.3 17.7 - - + -
677B TRP* 2.7 36.3 + - + -
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Residues in contact with VAL 634 (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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539B VAL* 3.9 28.7 - - + -
572B GLU* 3.8 21.7 + - - +
575B ALA* 3.4 20.3 + - + +
587B LEU* 5.8 2.5 - - + -
589B LEU* 4.2 15.3 - - + -
605B ILE* 5.7 0.9 - - + -
632B LEU* 4.1 17.3 - - + -
633B ALA* 1.3 79.5 - - - +
635B THR* 1.3 69.3 + - - +
664B ILE* 5.9 0.2 - - - +
669B ILE* 3.8 6.8 - - + +
674B LEU* 3.9 22.4 - - + -
675B VAL 3.4 13.2 - - - +
676B ALA* 4.3 7.0 - - + -
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Residues in contact with THR 635 (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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572B GLU* 3.5 17.0 - - + +
633B ALA* 4.9 1.8 - - + -
634B VAL* 1.3 82.6 - - - +
636B GLN* 1.3 68.4 + - - +
637B ARG* 3.1 1.2 + - - -
641B GLU* 4.3 5.8 + - - -
660B PHE* 5.4 0.2 - - + -
663B PHE* 3.6 29.4 - - + +
664B ILE* 4.4 11.2 - - + -
669B ILE* 4.2 5.2 - - - -
674B LEU* 3.3 6.7 - - - +
675B VAL* 3.0 37.6 + - - +
677B TRP* 3.1 31.1 + - + +
1743B CA 4.5 0.4 - - - -
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Residues in contact with GLN 636 (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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572B GLU* 3.2 13.1 + - - +
635B THR* 1.3 73.1 + - - +
637B ARG* 1.3 61.3 + - - +
638B LYS* 2.9 34.8 + - + +
641B GLU* 3.6 9.2 - - - +
667B GLU* 3.0 35.6 - - + +
668B THR* 2.8 38.7 + - - +
669B ILE* 4.5 2.9 - - + -
672B LYS* 4.2 21.9 + - + +
673B ASP 3.5 8.7 - - - +
674B LEU* 4.6 1.1 - - - -
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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