Contacts of the helix formed by residues 676 - 688 (chain B) in PDB entry 4OSI
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 GLY 676 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641B ASP 4.3 8.1 + - - -
674B ASN 3.6 0.2 + - - -
675B GLY* 1.3 75.0 - - - +
677B GLY* 1.3 61.0 + - - +
679B PRO* 2.8 34.3 - - - +
680B ALA* 3.2 14.0 + - - +
711B GLY* 5.2 2.9 - - - -
712B ARG 5.2 0.2 + - - -
14G C 4.0 24.7 + - - -
15G T 4.1 6.2 + - - +
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Residues in contact with GLY 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B GLY* 6.2 1.0 - - - -
646B ALA* 4.7 9.5 - - - +
671B ILE 5.0 1.6 - - - -
672B ALA* 4.3 19.3 - - - -
674B ASN 3.7 10.5 + - - -
675B GLY 3.5 1.8 - - - -
676B GLY* 1.3 73.6 - - - +
678B ARG* 1.3 68.9 + - - +
679B PRO* 3.7 0.2 - - - +
680B ALA* 2.8 18.9 + - - +
681B LEU* 2.9 19.2 + - - +
14G C 4.8 1.6 + - - -
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Residues in contact with ARG 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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645B GLN* 2.6 45.0 + - + -
646B ALA* 4.1 12.2 - - - +
649B THR* 3.3 26.3 + - - +
652B ARG* 4.1 16.6 - - - +
677B GLY* 1.3 71.2 - - - +
679B PRO* 1.4 65.1 - - + +
681B LEU* 3.4 7.2 + - - +
682B GLU* 2.9 62.5 + - - +
14G C 3.2 23.2 + - - +
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Residues in contact with PRO 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
676B GLY* 2.8 31.4 - - - +
677B GLY 3.2 0.2 - - - -
678B ARG* 1.4 95.7 - - + +
680B ALA* 1.3 64.1 + - - +
682B GLU* 3.9 10.6 - - + +
683B SER* 2.9 27.9 + - - -
712B ARG* 3.4 41.7 - - + +
14G C 3.7 19.5 - - - +
15G T 3.8 10.5 - - - +
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Residues in contact with ALA 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B ILE* 4.4 13.5 - - + +
676B GLY 3.2 11.3 + - - +
677B GLY* 2.8 12.8 + - - +
679B PRO* 1.3 73.7 - - - +
681B LEU* 1.3 67.6 + - - +
683B SER* 3.4 3.6 + - - -
684B ILE* 2.9 24.7 + - - +
707B ALA* 4.4 16.5 - - + +
711B GLY* 3.7 22.7 - - - -
712B ARG 3.9 11.1 - - - +
715B LEU* 6.1 0.2 - - - -
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Residues in contact with LEU 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B ALA* 4.6 2.5 - - - +
649B THR* 3.8 22.9 - - + -
650B VAL* 3.6 33.7 - - + +
653B LEU* 4.0 13.7 - - + -
657B LEU* 5.6 10.1 - - + -
668B VAL* 5.0 8.3 - - + +
671B ILE* 3.4 31.6 - - + -
672B ALA* 4.6 9.6 - - + -
677B GLY 2.9 18.4 + - - +
678B ARG* 3.4 6.3 - - - +
680B ALA* 1.3 71.1 - - - +
682B GLU* 1.3 57.2 + - - +
683B SER 2.3 20.8 + - - -
684B ILE* 2.6 20.9 + - + -
685B VAL* 2.9 12.2 + - + -
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Residues in contact with GLU 682 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B THR* 4.2 9.6 - - + -
652B ARG* 4.0 10.9 + - - -
653B LEU* 4.4 3.3 - - + +
678B ARG* 2.9 55.8 + - + +
679B PRO* 4.0 7.9 - - + +
681B LEU* 1.3 75.8 - - - +
683B SER* 1.3 55.3 + - - +
685B VAL* 3.2 12.9 - - - +
686B ALA* 3.0 28.1 + - - +
712B ARG* 5.7 2.3 + - - -
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Residues in contact with SER 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B PRO 2.9 18.2 + - - -
680B ALA 3.4 5.0 + - - -
681B LEU 2.3 11.9 + - - -
682B GLU* 1.3 66.3 - - - +
684B ILE* 1.3 66.1 + - - -
685B VAL 3.0 0.9 - - - -
686B ALA* 2.6 31.1 + - - +
687B GLN* 2.9 13.7 + - - +
712B ARG* 4.0 22.9 - - - -
715B LEU* 3.5 27.4 - - - +
716B ASP* 5.0 2.4 + - - -
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Residues in contact with ILE 684 (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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657B LEU* 4.7 27.6 - - + -
663B LEU* 6.2 2.7 - - + -
671B ILE* 4.6 15.0 - - + -
680B ALA 2.9 11.6 + - - +
681B LEU* 2.6 10.5 + - + +
683B SER* 1.3 76.2 + - - +
685B VAL* 1.3 64.7 + - - +
687B GLN* 3.8 4.0 - - + +
688B LEU* 3.0 30.1 + - + +
703B LEU* 3.5 46.2 - - + +
704B VAL* 4.3 3.6 - - + +
707B ALA* 4.3 8.7 - - + -
715B LEU* 3.7 22.9 - - + -
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Residues in contact with VAL 685 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B LEU* 3.5 42.0 - - + -
656B VAL* 5.0 14.1 - - + -
657B LEU* 5.4 8.3 - - + -
681B LEU* 2.9 14.8 + - + +
682B GLU* 3.2 11.4 - - - +
684B ILE* 1.3 83.1 - - + +
686B ALA* 1.3 65.2 + - + +
688B LEU* 3.3 2.1 - - - +
689B SER* 2.5 35.7 + - - +
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Residues in contact with ALA 686 (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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682B GLU 3.0 9.7 + - - +
683B SER* 2.6 15.6 + - - +
685B VAL* 1.3 80.4 - - - +
687B GLN* 1.3 56.6 + - + +
689B SER* 3.1 7.9 + - - -
690B ARG* 2.8 34.1 + - + +
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Residues in contact with GLN 687 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683B SER* 2.9 16.8 + - - +
684B ILE* 3.8 3.6 - - + +
686B ALA* 1.3 71.8 - - + +
688B LEU* 1.3 57.6 + - - +
689B SER 3.4 2.5 - - - -
690B ARG 3.8 7.4 - - - +
691B PRO* 3.0 40.1 - - + +
692B ASP* 3.9 17.5 + - - +
697B ALA* 4.3 11.8 - - - +
703B LEU* 4.5 16.9 - - - +
715B LEU* 5.5 11.5 - - + +
718B VAL* 6.0 1.4 - - - +
719B LYS* 4.4 25.4 - - + +
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Residues in contact with LEU 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657B LEU* 5.7 6.5 - - + -
661B HIS* 2.9 53.4 + - + +
663B LEU* 6.1 2.2 - - + -
684B ILE* 3.0 27.5 + - + +
685B VAL* 3.3 4.3 - - - +
687B GLN* 1.3 77.4 - - - +
689B SER* 1.3 57.0 + - - +
690B ARG 3.6 0.4 - - - -
691B PRO* 4.4 15.3 - - + -
700B ASN* 3.1 41.3 - - + +
703B LEU* 4.1 17.5 - - + -
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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