Contacts of the helix formed by residues 694 - 712 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A GLU* 4.4 2.9 + - - +
468A ASP* 5.3 4.0 - - + +
469A GLU* 3.1 25.6 - - + +
470A ILE* 3.4 10.7 - - - +
692A PHE* 4.5 0.3 - - - +
693A PHE* 1.3 78.3 + - - +
695A TYR* 1.3 61.8 + - - +
696A GLY* 3.7 4.9 - - - -
697A GLN* 2.6 64.5 + - - +
698A LEU* 3.3 15.1 + - - +
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Residues in contact with TYR 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 4.4 1.9 - - + +
340A LEU* 3.8 28.5 - - + -
341A GLU* 4.1 2.7 - - + +
469A GLU* 2.7 46.7 + - + +
470A ILE* 3.7 19.7 - - + +
471A ILE* 2.8 31.2 + - + +
483A LEU* 5.0 0.2 - - + -
484A TYR 2.7 28.7 + - - -
485A LYS* 3.9 4.9 - - + -
486A LEU* 3.6 49.6 - - + -
694A ASN* 1.3 69.7 - - - +
696A GLY* 1.3 58.7 + - - +
698A LEU* 3.2 13.8 + - + +
699A ILE* 2.8 37.7 + - + +
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Residues in contact with GLY 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A GLU* 3.8 17.4 + - - -
694A ASN* 3.3 5.5 + - - -
695A TYR* 1.3 79.7 - - - +
697A GLN* 1.3 55.8 + - - +
699A ILE* 3.8 6.5 - - - +
700A ALA* 2.8 32.7 + - - +
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Residues in contact with GLN 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A ASP 4.6 16.2 - - - +
601A PHE* 4.5 6.1 - - - -
602A ILE* 4.3 8.2 - - - +
691A LYS 4.0 2.8 - - - +
692A PHE* 3.6 16.0 - - + +
693A PHE* 2.8 38.6 + - - +
694A ASN* 2.6 55.0 + - - +
696A GLY* 1.3 73.5 - - - +
698A LEU* 1.3 56.5 + - - +
700A ALA* 3.4 6.4 - - - +
701A TYR* 2.9 31.2 + - - +
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Residues in contact with LEU 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A ILE* 5.2 1.6 - - + -
483A LEU* 4.4 15.7 - - + -
485A LYS* 3.7 33.7 - - + -
614A ILE* 4.4 10.3 - - + -
615A SER* 5.0 1.1 - - - +
618A SER* 5.1 0.9 - - - +
692A PHE* 3.5 50.4 - - + +
694A ASN 3.3 10.3 + - - +
695A TYR* 3.2 18.8 + - + +
696A GLY 3.2 0.4 - - - -
697A GLN* 1.3 77.0 - - - +
699A ILE* 1.3 68.0 + - + +
701A TYR* 3.2 5.2 + - + +
702A ILE* 3.0 42.2 + - + +
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Residues in contact with ILE 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A GLU* 5.7 1.1 - - - +
485A LYS* 4.6 9.6 - - + +
486A LEU* 4.0 40.6 - - + +
487A ASN 4.9 1.8 - - - +
488A THR* 3.9 28.0 - - + +
695A TYR* 2.8 25.8 + - + +
696A GLY* 3.8 5.4 - - - +
698A LEU* 1.3 73.6 - - + +
700A ALA* 1.3 58.6 + - - +
702A ILE* 3.1 9.0 + - - +
703A ASP* 2.8 44.4 + - - +
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Residues in contact with ALA 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A PHE* 4.9 2.8 - - - -
599A LYS* 5.2 8.3 - - + +
601A PHE* 3.6 17.3 - - + -
696A GLY 2.8 18.4 + - - +
697A GLN* 3.4 8.7 - - - +
699A ILE* 1.3 78.9 - - - +
701A TYR* 1.3 57.5 + - - +
703A ASP* 3.3 6.7 + - - +
704A SER* 2.8 29.6 + - - -
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Residues in contact with TYR 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A PHE* 3.6 23.7 - + + -
611A THR* 6.0 0.7 - - - -
615A SER* 2.9 35.8 - - - -
680A LEU* 4.0 22.5 - - - +
683A SER* 5.5 4.1 + - - -
686A PHE* 5.4 8.8 + + + +
689A GLY* 4.7 1.6 - - - -
690A VAL* 3.3 50.8 + - + +
692A PHE* 5.0 8.3 - + + -
697A GLN 2.9 16.5 + - - +
698A LEU* 3.2 5.6 + - - +
700A ALA* 1.3 75.7 - - - +
702A ILE* 1.3 61.3 + - + +
704A SER* 3.0 9.6 - - - -
705A LEU* 2.9 56.2 + - + +
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Residues in contact with ILE 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A LYS* 5.4 5.2 - - + +
615A SER* 3.6 41.7 - - - +
618A SER* 3.6 21.8 - - - +
619A LEU* 3.9 25.5 - - + +
622A LEU* 4.3 17.5 - - + -
698A LEU* 3.0 27.3 + - + +
699A ILE* 3.5 8.5 - - + +
701A TYR* 1.3 76.2 - - + +
703A ASP* 1.3 67.9 + - - +
705A LEU* 2.9 20.9 + - + +
706A ASN* 2.9 11.3 + - - +
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Residues in contact with ASP 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A THR* 4.7 7.3 - - - +
590A GLN 5.4 4.2 - - - +
591A MET 5.6 0.3 - - - +
593A PRO* 3.8 21.7 - - + +
596A PHE* 4.1 6.3 - - + -
622A LEU* 4.4 14.6 - - - +
626A HIS* 6.0 0.5 - - - -
699A ILE* 2.8 36.5 + - - +
700A ALA* 3.7 6.7 - - - +
702A ILE* 1.3 73.6 - - - +
704A SER* 1.3 62.9 + - - +
706A ASN* 3.2 11.1 + - - +
707A SER* 3.2 23.6 + - - -
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Residues in contact with SER 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A PHE* 3.2 30.3 - - - -
601A PHE* 4.0 15.1 - - - -
700A ALA 2.8 13.8 + - - -
701A TYR* 3.0 24.5 - - - -
703A ASP* 1.3 78.7 - - - +
705A LEU* 1.3 61.9 + - - +
707A SER* 3.0 14.7 + - - -
708A ASN* 3.3 18.9 + - - +
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Residues in contact with LEU 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A SER* 4.2 18.8 - - - +
616A LEU* 5.8 0.4 - - - -
619A LEU* 4.2 22.0 - - + -
679A LEU* 4.4 25.0 - - + +
680A LEU* 5.1 7.2 - - + -
683A SER* 5.8 3.6 - - - +
701A TYR* 2.9 59.1 + - + +
702A ILE* 2.9 13.4 + - + +
704A SER* 1.3 75.7 - - - +
706A ASN* 1.3 62.7 + - - +
708A ASN* 3.2 22.3 + - - +
709A VAL* 3.1 24.9 + - - +
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Residues in contact with ASN 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A MET 4.0 4.0 - - - +
593A PRO* 4.3 7.4 - - + +
619A LEU* 3.9 9.8 - - + +
622A LEU* 3.6 14.8 - - + +
623A LEU* 3.8 12.2 - - - +
626A HIS* 3.2 27.4 - - - -
702A ILE 2.9 11.7 + - - +
703A ASP* 3.2 18.5 - - - +
704A SER 3.1 0.2 - - - -
705A LEU* 1.3 78.4 - - - +
707A SER* 1.3 57.3 + - - +
709A VAL* 2.9 7.1 + - - +
710A TYR* 2.8 52.6 + - - +
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Residues in contact with SER 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A PRO* 2.9 30.6 - - - +
594A GLY 4.0 3.9 + - - -
596A PHE* 3.3 21.4 - - - -
703A ASP 3.2 8.3 + - - -
704A SER 3.0 7.7 + - - -
706A ASN* 1.3 76.0 - - - +
708A ASN* 1.3 61.1 + - - +
710A TYR* 2.9 3.4 + - - +
711A ASN* 2.7 52.7 + - - +
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Residues in contact with ASN 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A PHE* 5.3 2.6 - - - -
679A LEU* 4.8 10.3 + - + +
682A ASP* 4.0 23.3 + - - +
683A SER* 4.7 17.2 - - - +
704A SER* 3.3 16.2 + - - +
705A LEU* 3.2 26.8 + - - +
707A SER* 1.3 77.7 - - - +
709A VAL* 1.3 63.2 + - + +
711A ASN* 4.1 3.8 + - - +
712A ALA* 3.2 24.3 + - - +
719B PHE* 3.7 5.6 - - - -
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Residues in contact with VAL 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A LEU* 4.4 10.3 - - + -
623A LEU* 3.9 21.1 - - + -
660A LYS* 3.6 18.5 - - + +
664A LEU* 4.0 24.5 - - + -
679A LEU* 4.5 5.6 - - + -
705A LEU 3.3 14.1 - - - +
706A ASN* 2.9 9.0 + - - +
708A ASN* 1.3 78.9 - - - +
710A TYR* 1.3 70.2 + - + +
711A ASN 3.5 0.3 + - - -
712A ALA* 3.6 11.3 + - - +
719B PHE* 3.9 18.6 - - + -
720B PHE* 4.0 19.8 - - + -
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Residues in contact with TYR 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591A MET* 3.7 17.1 - - - +
592A LYS* 4.4 12.8 - - + -
593A PRO* 3.9 17.0 - - + -
623A LEU* 3.4 14.7 - - + +
626A HIS* 2.6 26.0 + - - -
656A ASP* 4.7 0.2 - - - +
657A LEU* 3.4 43.9 - - + +
660A LYS* 2.9 32.6 + - + +
661A GLN* 3.0 29.6 + - + -
706A ASN* 2.8 34.7 + - - +
707A SER* 4.1 4.5 - - - +
709A VAL* 1.3 83.1 - - + +
711A ASN* 1.3 63.2 + - - +
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Residues in contact with ASN 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660A LYS* 4.9 0.9 - - - +
707A SER* 2.7 37.7 + - - +
708A ASN* 4.1 3.1 - - - +
710A TYR* 1.3 73.9 - - - +
712A ALA* 1.3 67.8 + - - +
713A SER* 3.5 1.4 + - - -
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Residues in contact with ALA 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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660A LYS* 3.5 22.5 + - - -
708A ASN 3.2 18.9 + - - +
709A VAL 3.8 2.0 - - - +
710A TYR 3.4 1.6 - - - -
711A ASN* 1.3 82.2 - - - +
713A SER* 1.3 63.6 + - - +
714A ILE* 4.2 0.4 - - - +
718B SER* 4.0 9.6 - - - -
719B PHE* 3.6 11.0 - - + -
720B PHE* 3.6 31.9 - - + -
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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