Contacts of the helix formed by residues 639 - 656 (chain B) in PDB entry 1P93
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 MET 639 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556B THR* 3.6 39.5 - - + +
559B ILE* 4.4 13.0 - - + -
560B MET* 4.6 15.0 - - - +
563B LEU* 6.2 0.2 - - - -
629B ILE* 4.4 11.7 - - + -
633B ARG 3.1 19.7 - - - +
634B MET* 2.8 27.8 - - - +
636B LEU* 3.6 28.2 + - + +
637B PRO 3.2 0.4 - - - -
638B ASP* 1.3 74.9 - - - +
640B TYR* 1.3 59.3 + - - +
641B ASP 3.0 1.1 - - - +
642B GLN* 3.0 9.3 + - - +
643B CYS* 2.8 49.0 + - - -
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Residues in contact with TYR 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B MET* 3.4 34.1 + - + +
639B MET* 1.3 74.1 - - - +
641B ASP* 1.3 56.3 + - - +
642B GLN 2.6 17.2 + - - -
643B CYS* 3.9 3.6 - - - +
644B LYS* 2.8 63.1 + - + +
647B LEU* 5.4 8.3 - - + -
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Residues in contact with ASP 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B ASP* 3.6 41.2 - - - +
639B MET 3.0 0.6 - - - +
640B TYR* 1.3 79.8 - - - +
642B GLN* 1.3 57.2 + - - +
644B LYS* 3.3 24.1 + - - +
645B HIS* 4.3 2.8 + - - -
735B TYR* 3.5 20.1 + - - +
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Residues in contact with GLN 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B THR* 5.4 3.4 - - - +
560B MET* 2.9 40.1 - - - +
637B PRO 5.3 0.2 + - - -
638B ASP* 2.7 22.4 + - - +
639B MET* 3.2 14.9 + - - +
640B TYR 2.6 5.7 + - - -
641B ASP* 1.3 76.4 - - - +
643B CYS* 1.3 65.3 + - - +
644B LYS* 3.1 3.6 - - - -
645B HIS* 4.0 18.5 + - + +
646B MET* 3.8 14.7 - - - +
732B LEU* 4.3 0.7 - - - +
735B TYR* 3.2 39.2 + - + -
2999B DEX 3.2 26.5 + - + +
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Residues in contact with CYS 643 (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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621B LEU* 4.0 13.9 - - + -
623B PHE* 5.3 0.9 - - - -
629B ILE* 4.3 8.7 - - - -
634B MET* 3.3 33.4 - - - -
639B MET* 2.8 40.0 + - - +
640B TYR* 3.1 1.5 + - - -
642B GLN* 1.3 83.5 - - - +
644B LYS* 1.3 63.3 + - - +
645B HIS 3.2 0.7 - - - -
646B MET* 3.1 12.9 + - - -
647B LEU* 2.7 38.7 + - + +
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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
----------------------------------------------------------
640B TYR* 2.8 51.1 + - + +
641B ASP* 3.3 30.9 + - - +
643B CYS* 1.3 80.2 - - - +
645B HIS* 1.3 101.7 + - + +
647B LEU* 3.4 5.2 + - - +
648B TYR* 3.3 15.8 + - - +
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Residues in contact with HIS 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B ASP 4.3 3.6 + - - -
642B GLN* 4.0 15.5 - - + +
643B CYS 3.2 0.2 - - - -
644B LYS* 1.3 112.7 - - + +
646B MET* 1.3 55.9 + - - +
648B TYR* 2.6 32.1 - - - +
649B VAL* 3.7 5.0 + - - +
728B VAL* 4.7 14.9 - - + +
731B ASN* 3.2 42.5 + - + +
732B LEU* 4.0 22.4 - - + -
735B TYR* 5.4 6.3 - + - -
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Residues in contact with MET 646 (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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605B ALA* 5.5 4.4 - - + +
608B LEU* 3.0 37.2 - - + +
609B GLY* 4.8 2.1 - - - -
621B LEU* 3.9 26.1 - - + +
623B PHE* 3.5 16.2 - - + -
642B GLN* 3.8 18.4 - - - +
643B CYS* 3.1 10.2 + - - +
645B HIS* 1.3 70.6 - - - +
647B LEU* 1.3 63.0 + - - +
648B TYR 2.9 5.4 - - - -
649B VAL* 3.0 29.0 + - + +
650B SER* 3.6 4.3 + - - -
728B VAL* 6.0 0.2 - - - -
732B LEU* 4.3 20.9 - - + -
2999B DEX 3.5 36.8 - - + -
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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
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619B ASN* 3.2 46.2 - - + +
620B LEU* 4.3 2.5 - - - +
621B LEU* 3.4 32.5 - - + -
634B MET* 4.2 13.5 - - + -
640B TYR* 5.4 7.9 - - + -
643B CYS* 2.7 33.1 + - + +
644B LYS* 3.7 9.2 - - - +
646B MET* 1.3 74.2 - - - +
648B TYR* 1.3 65.9 + - - +
650B SER* 3.1 8.3 + - - +
651B SER* 2.9 29.4 + - - -
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Residues in contact with TYR 648 (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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644B LYS 3.3 6.2 + - - +
645B HIS* 2.6 21.9 + - - +
647B LEU* 1.3 78.0 - - - +
649B VAL* 1.3 71.3 + - + +
651B SER* 3.0 10.1 + - - -
652B GLU* 2.9 54.7 + - + +
721B LEU* 4.2 12.3 - - + +
724B SER* 3.1 32.1 + - - -
725B MET* 6.0 1.8 - - - -
728B VAL* 3.7 21.8 - - + -
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Residues in contact with VAL 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B ALA* 3.9 21.3 - - + +
606B PHE* 4.4 15.5 - - + +
609B GLY* 3.7 18.4 - - - -
645B HIS 4.1 7.6 - - - +
646B MET* 3.0 16.4 + - - +
648B TYR* 1.3 83.0 - - + +
650B SER* 1.3 51.7 + - - +
652B GLU* 2.7 12.8 + - - +
653B LEU* 2.7 46.7 + - + +
721B LEU* 6.2 3.6 - - + -
725B MET* 4.7 18.6 - - + -
728B VAL* 4.8 8.3 - - + -
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Residues in contact with SER 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B GLY* 3.1 28.9 - - - -
612B SER* 3.5 23.4 - - - -
613B TYR* 4.0 8.0 - - - +
619B ASN 4.1 9.6 + - - -
621B LEU* 4.8 0.2 - - - +
646B MET 3.6 1.6 + - - -
647B LEU* 3.1 20.3 + - - +
649B VAL* 1.3 78.7 - - - +
651B SER* 1.3 55.0 + - - +
653B LEU* 3.6 3.2 - - - +
654B HIS* 2.6 34.8 + - - +
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Residues in contact with SER 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 ASN* 6.1 1.3 - - - -
647B LEU* 2.9 21.7 + - - -
648B TYR* 3.0 7.0 + - - -
650B SER* 1.3 73.6 + - - +
652B GLU* 1.3 76.7 + - - +
654B HIS* 3.4 8.2 - - - +
655B ARG* 2.9 27.9 + - - +
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Residues in contact with GLU 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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648B TYR* 2.9 34.6 + - + +
649B VAL* 2.7 14.9 + - - +
651B SER* 1.3 98.1 + - - +
653B LEU* 1.3 69.4 + - - +
654B HIS 2.8 0.7 - - - -
655B ARG* 2.6 47.8 + - - +
656B LEU* 2.8 27.4 + - + +
721B LEU* 3.8 33.2 - - + -
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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
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606B PHE* 4.0 28.3 - - + +
609B GLY* 3.2 9.4 - - - -
610B TRP* 3.2 59.2 - - + +
613B TYR* 3.6 17.6 - - + -
649B VAL* 2.7 24.9 + - + +
650B SER* 3.6 6.1 - - - +
652B GLU* 1.3 71.9 - - - +
654B HIS* 1.3 67.9 + - - +
656B LEU* 3.6 1.7 + - - +
657B GLN 3.4 9.7 + - - -
658B VAL* 3.6 27.9 + - + +
663B TYR* 5.3 0.2 - - + -
666B MET* 5.6 1.3 - - - -
721B LEU* 4.8 11.4 - - + +
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Residues in contact with HIS 654 (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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613B TYR* 3.1 30.5 + + + -
617B SER* 6.1 0.4 - - - -
650B SER 2.6 25.0 + - - +
651B SER* 3.4 9.2 - - - +
652B GLU 2.7 2.2 + - - -
653B LEU* 1.3 77.9 - - - +
655B ARG* 1.3 63.1 + - + +
657B GLN* 2.6 47.4 + - - -
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Residues in contact with ARG 655 (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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651B SER 2.9 10.8 + - - +
652B GLU* 2.6 38.9 + - - +
654B HIS* 1.3 83.7 - - + +
656B LEU* 1.3 94.6 + - - +
657B GLN* 3.2 16.4 + - - +
717B GLN* 4.7 8.7 - - - +
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Residues in contact with LEU 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652B GLU* 2.8 40.5 + - + +
653B LEU* 3.9 0.7 - - - +
655B ARG* 1.3 117.9 - - - +
657B GLN* 1.3 53.7 + - - +
658B VAL* 2.7 18.5 + - + -
714B ARG* 2.4 47.0 + - - +
717B GLN* 4.2 36.6 - - + +
718B LEU* 5.5 4.9 - - + +
721B LEU* 4.9 10.1 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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