Contacts of the helix formed by residues 642 - 654 (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 642 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B GLY 4.7 1.4 + - - -
608B GLY* 5.8 0.2 - - - -
641B ASP* 1.3 73.1 - - - +
643B GLY* 1.3 66.7 - - - +
644B LYS 3.3 1.8 - - - -
645B GLN* 2.6 21.1 + - - +
646B ALA* 3.1 10.8 + - - -
676B GLY 5.7 0.4 - - - -
677B GLY 6.2 0.7 - - - -
13G T 3.9 28.1 + - - +
14G C 3.5 20.4 - - - -
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Residues in contact with GLY 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B ALA* 4.8 6.7 - - - +
637B ILE* 5.4 0.9 - - - -
638B ALA* 4.4 22.0 - - - -
640B HIS 2.9 16.4 + - - -
641B ASP 3.8 0.2 + - - -
642B GLY* 1.3 72.5 - - - +
644B LYS* 1.3 65.5 + - - +
646B ALA* 2.8 21.5 + - - +
647B LEU* 2.9 19.8 + - - +
13G T 5.1 0.2 + - - -
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Residues in contact with LYS 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B GLN* 3.3 50.0 + - + +
612B ALA* 4.4 6.5 - - - +
615B THR* 3.5 25.9 + - + -
642B GLY 3.0 2.6 + - - -
643B GLY* 1.3 69.3 - - - +
645B GLN* 1.3 74.6 + - - +
647B LEU* 3.5 1.8 + - - +
648B GLU* 2.8 62.5 + - - +
13G T 3.9 17.1 + - - +
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Residues in contact with GLN 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B GLY 2.6 13.8 + - - +
644B LYS* 1.3 89.6 - - - +
646B ALA* 1.3 61.9 + - - +
648B GLU* 3.4 10.0 + - - +
649B THR* 2.6 33.7 + - - -
652B ARG* 4.5 1.7 + - - -
678B ARG* 2.6 39.8 + - + +
13G T 3.4 42.7 + - - +
14G C 3.8 20.9 - - - +
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Residues in contact with ALA 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B ILE* 4.5 15.3 - - + -
642B GLY 3.1 9.6 + - - +
643B GLY* 2.8 19.2 + - - +
645B GLN* 1.3 69.0 - - - +
647B LEU* 1.3 65.7 + - - +
649B THR* 2.7 15.9 + - - -
650B VAL* 2.9 16.8 + - - +
672B ALA* 4.9 11.0 - - + +
677B GLY* 4.7 8.7 - - - +
678B ARG* 4.1 23.2 - - - +
681B LEU* 5.4 1.3 - - + -
14G C 5.2 0.2 + - - -
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Residues in contact with LEU 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B ALA 4.4 0.4 - - - +
615B THR* 2.9 33.0 - - - +
616B VAL* 3.5 27.1 - - + +
619B LEU* 4.3 16.7 - - + +
623B LEU* 4.5 21.8 - - + +
634B VAL* 4.6 8.1 - - + +
637B ILE* 3.7 35.2 - - + -
638B ALA* 4.5 8.3 - - + -
643B GLY 2.9 19.0 + - - +
644B LYS 3.8 3.8 - - - +
646B ALA* 1.3 73.1 - - - +
648B GLU* 1.3 65.0 + - - +
649B THR 2.9 1.6 + - - -
650B VAL* 3.0 7.6 + - + +
651B GLN* 2.9 21.5 + - - +
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Residues in contact with GLU 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B THR* 3.9 9.1 - - + +
618B ARG* 4.1 18.9 + - - +
619B LEU* 4.6 5.2 - - + -
644B LYS* 2.8 59.8 + - + +
645B GLN* 4.1 8.6 + - - +
647B LEU* 1.3 72.1 - - - +
649B THR* 1.3 57.4 + - - +
651B GLN* 3.4 13.3 - - - +
652B ARG* 2.9 41.1 + - - +
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Residues in contact with THR 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B GLN 2.6 18.1 + - - -
646B ALA 2.7 15.5 + - - -
648B GLU* 1.3 70.1 - - - +
650B VAL* 1.3 58.1 + - - -
652B ARG* 2.8 46.9 + - - +
653B LEU* 2.9 38.1 + - + +
678B ARG* 3.3 18.3 + - + +
681B LEU* 3.8 13.2 - - + -
682B GLU* 4.2 16.6 - - + -
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Residues in contact with VAL 650 (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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623B LEU* 4.4 17.3 - - + -
627B HIS* 5.2 1.0 - - - +
629B LEU* 6.3 2.2 - - + -
637B ILE* 4.9 12.8 - - + -
646B ALA 2.9 12.7 + - - +
647B LEU* 3.6 9.2 - - + +
649B THR* 1.3 71.9 - - - +
651B GLN* 1.3 67.0 + - - +
653B LEU* 4.8 0.7 - - - -
654B LEU* 2.9 52.2 + - + +
668B VAL* 4.4 18.4 - - + -
672B ALA* 4.6 13.7 - - + -
681B LEU* 3.6 23.6 - - + -
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Residues in contact with GLN 651 (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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619B LEU* 4.8 15.4 - - + +
622B VAL* 4.7 18.6 - - + -
623B LEU* 4.9 6.0 - - + +
627B HIS* 5.1 14.2 - - + -
647B LEU 2.9 11.6 + - - +
648B GLU* 3.4 16.5 - - - +
650B VAL* 1.3 78.8 - - - +
652B ARG* 1.3 68.7 + - - +
653B LEU* 3.0 6.2 + - - -
654B LEU 4.3 1.4 + - - -
655B PRO* 4.5 7.8 - - - +
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Residues in contact with ARG 652 (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* 4.5 2.6 + - - -
648B GLU* 2.9 36.8 + - - +
649B THR* 2.8 59.3 + - - +
651B GLN* 1.3 82.6 + - - +
653B LEU* 1.3 68.8 + - + +
655B PRO* 5.3 2.7 - - - +
656B VAL* 5.8 0.2 - - - +
678B ARG* 4.1 17.4 - - - +
682B GLU* 4.0 11.9 + - - -
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Residues in contact with LEU 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649B THR* 2.9 38.5 + - + +
650B VAL* 4.8 1.6 - - - -
651B GLN 3.0 1.0 + - - -
652B ARG* 1.3 94.3 - - + +
654B LEU* 1.3 56.5 + - - +
655B PRO* 2.6 26.3 - - - +
656B VAL* 3.1 35.9 + - + +
657B LEU* 6.3 2.5 - - + -
681B LEU* 4.0 15.9 - - + -
682B GLU* 4.4 5.8 - - + +
685B VAL* 3.5 35.0 - - + -
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Residues in contact with LEU 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627B HIS* 3.5 39.5 - - + +
629B LEU* 5.3 7.6 - - + -
650B VAL* 2.9 40.7 + - + +
653B LEU* 1.3 69.6 - - - +
655B PRO* 1.3 72.3 - - + +
656B VAL* 5.2 0.9 - - - -
657B LEU* 3.6 11.8 + - + +
658B CYS* 4.3 13.4 + - - +
659B GLN* 4.8 1.9 + - - +
665B PRO* 5.0 10.1 - - + +
668B VAL* 3.7 41.7 - - + -
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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