Contacts of the helix formed by residues 636 - 654 (chain O) in PDB entry 5A31
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 ILE 636 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1754A PHE* 3.6 44.4 - - + +
1761A MET* 4.2 9.0 - - + -
1764A LYS* 5.3 2.9 - - + +
1767A ILE* 4.5 5.6 - - + -
1768A LEU* 4.1 24.7 - - + -
1771A PHE* 4.2 23.3 - - + -
631O GLN* 3.0 23.9 + - + +
634O LEU* 4.2 10.1 - - + +
635O GLY* 1.3 79.9 - - - +
637O PRO* 1.3 66.2 - - - +
638O GLU 3.4 1.3 - - - -
639O GLN* 3.3 27.2 + - + +
640O ALA 3.2 14.7 + - - -
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Residues in contact with PRO 637 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1764A LYS* 5.2 4.3 - - + -
632O LEU* 4.2 17.7 - - + +
635O GLY* 3.0 24.9 - - - +
636O ILE* 1.3 75.2 - - - +
638O GLU* 1.3 79.3 + - - +
640O ALA* 3.0 7.4 + - - +
641O LEU* 2.9 26.5 + - - +
670O CYS* 4.2 6.4 - - - +
673O ALA* 3.6 35.9 - - + +
674O SER 4.2 6.7 - - - +
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Residues in contact with GLU 638 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1759A VAL* 4.3 19.2 - - + +
1761A MET* 3.8 23.2 - - + +
1764A LYS* 3.9 13.0 - - - +
637O PRO* 1.3 90.6 - - - +
639O GLN* 1.3 61.2 + - - +
641O LEU* 3.7 8.8 - - - +
642O SER* 3.0 29.5 + - - -
673O ALA 4.7 0.3 - - - +
674O SER* 3.8 34.6 - - - -
677O SER* 3.9 18.4 - - - -
678O TYR* 6.2 2.5 - - + -
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Residues in contact with GLN 639 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1752A GLU 3.7 9.9 + - - -
1753A TYR* 3.3 28.3 + - - +
1754A PHE* 4.0 6.6 + - - +
1756A LYS 2.7 25.1 + - - -
1757A PRO 3.3 10.3 - - - +
1758A THR* 3.2 27.0 + - - +
1761A MET* 3.6 10.7 - - + +
1768A LEU* 4.7 1.3 - - - -
631O GLN* 3.4 10.2 - - + +
636O ILE* 3.3 32.1 - - + +
638O GLU* 1.3 77.5 - - - +
640O ALA* 1.3 64.2 + - - +
642O SER* 3.5 4.0 + - - -
643O LEU* 3.1 20.1 + - - +
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Residues in contact with ALA 640 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628O ALA* 3.2 30.5 - - + +
631O GLN* 3.0 23.8 + - + +
632O LEU 3.9 3.1 - - - +
636O ILE 3.2 3.6 + - - +
637O PRO 3.0 11.5 + - - +
639O GLN* 1.3 76.6 - - - +
641O LEU* 1.3 59.1 + - - +
643O LEU* 3.2 6.1 + - - +
644O LEU* 2.8 31.3 + - - +
670O CYS* 3.9 13.5 - - - -
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Residues in contact with LEU 641 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637O PRO 2.9 11.9 + - - +
638O GLU* 3.7 9.6 - - - +
639O GLN 3.3 0.2 - - - -
640O ALA* 1.3 78.2 - - - +
642O SER* 1.3 61.9 + - - +
644O LEU* 3.2 16.5 + - + +
645O HIS* 3.2 40.0 + - + +
667O VAL* 4.5 15.7 - - + +
670O CYS* 3.7 18.2 - - + +
671O GLN* 3.7 30.7 - - + +
674O SER* 3.7 21.5 - - - +
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Residues in contact with SER 642 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1758A THR* 3.9 28.8 + - - +
1759A VAL* 5.3 5.5 + - - +
126I THR* 5.4 8.5 + - - +
638O GLU 3.0 17.0 + - - -
639O GLN 3.8 3.8 - - - -
641O LEU* 1.3 78.0 - - - +
643O LEU* 1.3 60.4 + - - +
645O HIS* 3.5 25.4 + - - +
646O MET* 4.2 9.2 + - - +
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Residues in contact with LEU 643 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1753A TYR* 3.2 41.3 - - + +
126I THR* 6.5 0.7 - - - -
624O VAL* 3.6 29.7 - - + +
627O LEU* 4.7 1.8 - - + -
628O ALA* 3.7 24.2 - - + -
631O GLN* 3.4 21.3 - - - +
639O GLN 3.1 14.4 + - - +
640O ALA 3.2 5.1 + - - +
642O SER* 1.3 73.4 - - - +
644O LEU* 1.3 74.4 - - + +
646O MET* 3.2 22.8 + - - +
647O ALA* 3.6 3.1 + - - +
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Residues in contact with LEU 644 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625O LEU* 4.4 13.7 - - + -
628O ALA* 3.8 20.9 - - + -
640O ALA 2.8 16.0 + - - +
641O LEU* 3.3 12.6 - - + +
643O LEU* 1.3 81.6 - - + +
645O HIS* 1.3 52.4 + - - +
647O ALA* 3.2 6.3 + - + +
648O ILE* 2.8 42.0 + - + +
651O ILE* 5.4 1.8 - - + -
663O ALA* 5.5 1.6 - - + +
666O LEU* 3.8 34.5 - - + +
667O VAL* 3.7 39.9 - - + -
670O CYS* 4.4 10.3 - - + -
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Residues in contact with HIS 645 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250I ARG* 5.0 2.9 + - - -
372I TRP* 4.0 24.1 + + - -
375I LYS* 3.6 40.0 + - - +
641O LEU* 3.2 42.2 + - + +
642O SER* 3.7 17.3 - - - +
643O LEU 3.2 0.8 - - - -
644O LEU* 1.3 74.4 - - - +
646O MET* 1.3 76.1 + - + +
648O ILE* 3.5 15.6 - - - +
649O GLU* 4.0 8.0 + - - +
667O VAL* 5.2 1.5 - - + +
671O GLN* 5.8 1.3 - - - -
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Residues in contact with MET 646 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I THR* 4.1 35.0 - - + +
127I SER 3.5 22.9 - - - +
128I PHE* 3.6 28.5 - - + +
250I ARG* 3.7 16.8 + - - +
375I LYS* 6.1 1.1 - - - +
642O SER 4.7 7.4 - - - +
643O LEU* 3.2 12.7 + - - +
645O HIS* 1.3 90.1 - - + +
647O ALA* 1.3 59.0 + - - +
649O GLU* 3.8 2.3 + - - +
650O PRO* 3.0 22.9 - - - +
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Residues in contact with ALA 647 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621O SER* 4.0 5.5 + - - +
624O VAL* 3.4 38.4 - - + -
625O LEU 4.8 2.0 - - - +
643O LEU 3.6 2.8 + - - +
644O LEU* 3.2 10.0 + - + +
646O MET* 1.3 78.9 - - - +
648O ILE* 1.3 66.0 + - - +
650O PRO* 3.0 17.2 - - - +
651O ILE* 3.2 28.4 + - + +
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Residues in contact with ILE 648 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372I TRP* 3.3 34.8 - - + +
644O LEU* 2.8 27.0 + - + +
645O HIS* 3.5 15.0 - - - +
647O ALA* 1.3 72.5 - - - +
649O GLU* 1.3 68.4 + - - +
651O ILE* 3.2 6.7 + - + +
652O LEU* 2.9 57.7 + - + +
663O ALA* 3.2 36.8 - - + -
664O MET* 4.3 3.4 - - - -
667O VAL* 4.0 22.9 - - + -
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Residues in contact with GLU 649 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250I ARG* 3.3 26.1 + - - +
254I LYS* 4.8 2.1 + - - -
365I GLU* 3.9 18.5 - - - +
368I GLY* 3.6 10.5 - - - -
369I MET* 3.1 59.0 - - + +
372I TRP* 5.0 7.4 - - + -
376I TYR* 4.9 3.3 + - + -
645O HIS 4.2 7.6 - - - +
646O MET 3.8 4.9 + - - +
647O ALA 3.2 0.2 - - - -
648O ILE* 1.3 85.9 - - + +
650O PRO* 1.3 74.0 - - + +
652O LEU* 3.5 5.1 + - - +
653O ALA* 3.2 15.4 + - - +
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Residues in contact with PRO 650 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250I ARG* 5.7 1.8 - - - +
434O ARG* 6.0 0.9 - - - +
617O GLN* 3.5 33.6 + - + +
621O SER* 4.1 10.5 - - - +
646O MET 3.0 27.6 - - - +
647O ALA* 3.0 16.8 - - - +
649O GLU* 1.3 87.2 - - + +
651O ILE* 1.3 63.6 + - - +
653O ALA* 3.4 12.3 + - + +
654O ASP* 3.6 19.6 - - - +
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Residues in contact with ILE 651 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621O SER* 3.4 33.0 + - - +
625O LEU* 4.0 28.7 - - + -
644O LEU* 5.4 1.8 - - + -
647O ALA* 3.2 29.6 + - + +
648O ILE* 3.6 9.4 - - + +
650O PRO* 1.3 77.0 - - - +
652O LEU* 1.3 63.9 + - - +
653O ALA 3.3 0.7 + - - -
654O ASP 5.1 1.3 - - - -
655O GLY* 3.5 23.7 + - - -
659O ASP* 4.0 37.5 - - + +
660O LYS* 3.9 5.0 - - - +
663O ALA* 4.1 14.1 - - + -
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Residues in contact with LEU 652 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367I LYS* 5.7 0.7 - - - +
368I GLY* 4.3 2.7 - - - +
371I SER* 3.7 23.9 + - - +
372I TRP* 3.8 35.0 - - + +
648O ILE* 2.9 50.7 + - + +
649O GLU* 4.0 3.4 - - - +
651O ILE* 1.3 76.3 - - - +
653O ALA* 1.3 64.2 + - - +
660O LYS* 2.9 59.1 + - + +
663O ALA* 4.4 1.1 - - + -
664O MET* 4.1 16.2 - - + -
700O TYR* 4.7 2.0 - - - +
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Residues in contact with ALA 653 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364I SER 3.8 16.8 - - - +
365I GLU* 4.8 4.7 - - - +
367I LYS* 3.7 24.1 + - - +
368I GLY* 3.7 25.1 - - - +
649O GLU* 3.2 9.0 + - - +
650O PRO* 3.6 13.9 - - + +
651O ILE 3.2 0.6 - - - -
652O LEU* 1.3 80.6 - - - +
654O ASP* 1.3 69.6 + - - +
660O LYS* 4.1 7.1 + - - -
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Residues in contact with ASP 654 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364I SER* 4.5 12.8 - - - -
433O GLY 3.0 20.2 - - - +
434O ARG* 4.1 15.2 - - - +
435O SER* 3.6 34.7 + - - +
436O THR* 4.4 9.8 + - - +
480O GLN* 5.3 4.0 - - - +
617O GLN* 4.8 4.2 + - - -
618O TYR* 3.5 19.3 - - - -
650O PRO 3.6 12.8 + - - +
651O ILE* 3.7 4.8 - - - +
653O ALA* 1.3 85.8 - - - +
655O GLY* 1.3 57.3 + - - +
660O LYS* 4.9 0.9 - - - +
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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