Contacts of the helix formed by residues 694 - 712 (chain B) in PDB entry 3F7F
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 ASN 694 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B GLU* 4.5 2.7 - - - +
468B ASP* 5.4 4.3 - - + -
469B GLU* 3.1 25.4 - - + +
470B ILE* 3.4 10.9 - - - +
692B PHE* 4.5 0.3 - - - +
693B PHE* 1.3 78.5 + - - +
695B TYR* 1.3 62.4 + - - +
696B GLY* 3.7 4.7 - - - -
697B GLN* 2.6 64.8 + - - +
698B LEU* 3.3 15.2 + - - +
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Residues in contact with TYR 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.4 1.9 - - + +
340B LEU* 3.8 28.9 - - + -
341B GLU* 4.1 2.2 - - + +
469B GLU* 2.7 46.9 + - + +
470B ILE* 3.7 19.2 - - + +
471B ILE* 2.8 30.8 + - + +
483B LEU* 5.0 0.2 - - + -
484B TYR 2.7 29.3 + - - -
485B LYS* 3.9 4.9 - - + -
486B LEU* 3.6 49.4 - - + -
694B ASN* 1.3 69.9 - - - +
696B GLY* 1.3 60.1 + - - +
698B LEU* 3.2 13.4 + - + +
699B ILE* 2.8 37.5 + - + +
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Residues in contact with GLY 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B GLU* 3.8 16.7 + - - -
694B ASN* 3.3 5.7 + - - -
695B TYR* 1.3 79.8 - - - +
697B GLN* 1.3 56.1 + - - +
699B ILE* 3.8 6.8 - - - +
700B ALA* 2.8 32.2 + - - +
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Residues in contact with GLN 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B ASP 4.6 16.4 - - - +
601B PHE* 4.5 6.1 - - - -
602B ILE* 4.3 8.4 - - - +
691B LYS 4.0 2.8 - - - +
692B PHE* 3.6 16.2 - - + +
693B PHE* 2.8 39.2 + - - +
694B ASN* 2.6 55.0 + - - +
696B GLY* 1.3 73.2 - - - +
698B LEU* 1.3 57.4 + - - +
700B ALA* 3.4 6.4 - - - +
701B TYR* 2.9 31.0 + - - +
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Residues in contact with LEU 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B ILE* 5.1 1.8 - - + -
483B LEU* 4.4 15.5 - - + -
485B LYS* 3.6 33.9 - - + -
614B ILE* 4.4 10.3 - - + -
615B SER* 5.0 1.1 - - - +
618B SER* 5.1 0.9 - - - +
692B PHE* 3.5 50.4 - - + +
694B ASN 3.3 10.5 + - - +
695B TYR* 3.2 18.8 + - + +
696B GLY 3.2 0.4 - - - -
697B GLN* 1.3 76.8 - - - +
699B ILE* 1.3 68.3 + - + +
701B TYR* 3.2 5.2 + - + +
702B ILE* 3.0 42.0 + - + +
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Residues in contact with ILE 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B GLU* 5.7 1.1 - - - +
485B LYS* 4.6 9.9 - - + +
486B LEU* 4.0 38.6 - - + +
487B ASN 5.0 0.7 - - - +
488B THR* 3.9 28.7 - - + +
695B TYR* 2.8 27.6 + - + +
696B GLY* 3.9 5.4 - - - +
698B LEU* 1.3 74.0 - - + +
700B ALA* 1.3 58.4 + - - +
702B ILE* 3.1 9.2 + - + +
703B ASP* 2.8 44.4 + - - +
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Residues in contact with ALA 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B PHE* 4.9 2.8 - - - -
599B LYS* 5.2 8.5 - - + +
601B PHE* 3.6 17.1 - - + -
696B GLY 2.8 19.2 + - - +
697B GLN* 3.4 8.5 - - - +
699B ILE* 1.3 79.0 - - - +
701B TYR* 1.3 57.5 + - - +
703B ASP* 3.3 6.6 + - - +
704B SER* 2.8 28.9 + - - -
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Residues in contact with TYR 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B PHE* 3.6 23.8 - + + -
611B THR* 6.1 0.7 - - - -
615B SER* 2.9 35.8 - - - -
680B LEU* 4.0 22.7 - - - +
683B SER* 5.5 4.1 + - - -
686B PHE* 5.4 8.8 + + + +
689B GLY* 4.7 1.4 - - - -
690B VAL* 3.3 49.8 + - + +
692B PHE* 5.0 8.1 - + + -
697B GLN 2.9 17.1 + - - +
698B LEU* 3.2 5.6 + - - +
700B ALA* 1.3 75.1 - - - +
702B ILE* 1.3 60.5 + - + +
704B SER* 3.0 9.5 - - - -
705B LEU* 2.9 56.2 + - + +
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Residues in contact with ILE 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B LYS* 5.4 5.2 - - + +
615B SER* 3.6 41.7 - - - +
618B SER* 3.6 22.4 - - - +
619B LEU* 3.9 25.2 - - + +
622B LEU* 4.3 17.0 - - + -
698B LEU* 3.0 27.6 + - + +
699B ILE* 3.6 8.5 - - + +
701B TYR* 1.3 74.7 - - + +
703B ASP* 1.3 68.2 + - - +
704B SER 2.9 1.3 - - - -
705B LEU* 2.9 11.7 + - + +
706B ASN* 2.9 19.9 + - - +
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Residues in contact with ASP 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B THR* 4.7 7.4 - - - +
590B GLN 5.4 4.2 - - - +
591B MET 5.6 0.3 - - - +
593B PRO* 3.7 22.1 - - + +
596B PHE* 4.1 6.3 - - + -
622B LEU* 4.4 14.2 - - - +
626B HIS* 6.0 0.5 - - - -
699B ILE* 2.8 36.9 + - - +
700B ALA* 3.7 6.7 - - - +
702B ILE* 1.3 73.4 - - - +
704B SER* 1.3 63.3 + - - +
706B ASN* 3.2 11.1 + - - +
707B SER* 3.1 23.4 + - - -
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Residues in contact with SER 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B PHE* 3.2 30.0 - - - -
601B PHE* 4.1 15.0 - - - -
700B ALA 2.8 13.6 + - - -
701B TYR* 3.0 24.5 - - - -
703B ASP* 1.3 76.0 - - - +
705B LEU* 1.3 63.7 + - - +
707B SER* 3.1 14.9 + - - -
708B ASN* 3.3 18.7 + - - +
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Residues in contact with LEU 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B SER* 4.2 19.1 - - - +
616B LEU* 5.8 0.4 - - - -
619B LEU* 4.2 21.8 - - + -
679B LEU* 4.4 24.8 - - + +
680B LEU* 5.1 6.7 - - + -
683B SER* 5.8 3.6 - - - +
701B TYR* 2.9 59.8 + - + +
702B ILE* 2.9 13.7 + - + +
704B SER* 1.3 76.6 - - - +
706B ASN* 1.3 62.7 + - - +
708B ASN* 3.2 22.5 + - - +
709B VAL* 3.1 24.8 + - - +
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Residues in contact with ASN 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B MET 4.0 4.0 - - - +
593B PRO* 4.3 7.1 - - + +
619B LEU* 4.0 10.3 - - + +
622B LEU* 3.6 15.4 - - + +
623B LEU* 3.8 12.8 - - - +
626B HIS* 3.2 27.4 - - - -
702B ILE 2.9 11.7 + - - +
703B ASP* 3.2 18.8 - - - +
704B SER 3.1 0.2 - - - -
705B LEU* 1.3 77.3 - - - +
707B SER* 1.3 57.4 + - - +
709B VAL* 2.9 7.0 + - - +
710B TYR* 2.8 52.4 + - - -
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Residues in contact with SER 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B PRO* 3.0 30.3 - - - +
594B GLY 4.0 3.8 + - - -
596B PHE* 3.3 21.0 - - - -
703B ASP 3.1 8.7 + - - -
704B SER 3.1 8.0 + - - -
706B ASN* 1.3 75.8 - - - +
708B ASN* 1.3 60.4 + - - +
710B TYR* 3.0 3.4 + - - +
711B ASN* 2.7 52.3 + - - +
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Residues in contact with ASN 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A PHE* 3.7 5.7 - - - -
596B PHE* 5.4 2.6 - - - -
679B LEU* 4.8 10.1 + - + +
682B ASP* 4.0 22.9 + - - +
683B SER* 4.7 17.2 - - - +
704B SER* 3.3 16.8 + - - +
705B LEU* 3.2 27.4 + - - +
707B SER* 1.3 77.8 - - - +
709B VAL* 1.3 62.4 + - + +
711B ASN* 4.1 3.8 + - - +
712B ALA* 3.2 24.4 + - - +
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Residues in contact with VAL 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A PHE* 3.9 18.2 - - + -
720A PHE* 4.0 19.5 - - + -
619B LEU* 4.3 10.3 - - + -
623B LEU* 3.9 21.8 - - + -
660B LYS* 3.6 19.3 - - + +
664B LEU* 4.1 24.7 - - + -
679B LEU* 4.5 5.6 - - + -
705B LEU 3.3 14.6 - - - +
706B ASN* 2.9 8.5 + - - +
708B ASN* 1.3 78.5 - - - +
710B TYR* 1.3 70.3 + - + +
711B ASN 3.5 0.5 + - - -
712B ALA* 3.6 9.9 + - - +
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Residues in contact with TYR 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591B MET* 3.7 11.2 - - - +
592B LYS* 4.4 12.6 - - + -
593B PRO* 3.9 16.6 - - + -
623B LEU* 3.3 14.6 - - + +
626B HIS* 2.6 32.2 + - - -
656B ASP* 4.7 0.2 - - - +
657B LEU* 3.4 43.0 - - + +
660B LYS* 3.0 31.9 + - + +
661B GLN* 3.0 29.7 + - + -
706B ASN* 2.8 35.8 + - - +
707B SER* 4.1 4.7 - - - +
709B VAL* 1.3 83.2 - - + +
711B ASN* 1.3 64.5 + - - +
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Residues in contact with ASN 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660B LYS* 4.8 0.9 - - - +
707B SER* 2.7 38.7 + - - +
708B ASN* 4.6 3.1 - - - +
710B TYR* 1.3 74.3 - - - +
712B ALA* 1.3 67.2 + - - +
713B SER* 3.5 1.7 + - - -
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Residues in contact with ALA 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A SER* 4.1 9.4 - - - -
719A PHE* 3.6 11.2 - - + -
720A PHE* 3.6 32.1 - - + -
660B LYS* 3.5 22.7 + - - -
708B ASN 3.2 18.9 + - - +
709B VAL 3.8 2.0 - - - +
710B TYR 3.4 1.6 - - - -
711B ASN* 1.3 82.3 - - - +
713B SER* 1.3 63.5 + - - +
714B ILE* 4.7 0.2 - - - -
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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