Contacts of the helix formed by residues 718 - 729 (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 SER 718 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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682A ASP* 5.5 2.5 - - - -
712A ALA* 4.0 11.0 - - - -
713A SER 3.1 34.0 + - - -
716B GLU* 3.3 4.0 + - - +
717B ASN* 1.3 79.7 + - - +
719B PHE* 1.3 66.1 + - - +
720B PHE* 3.3 14.8 + - - +
721B MET* 3.1 22.9 + - - +
722B THR* 3.2 14.6 + - - -
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Residues in contact with PHE 719 (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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664A LEU* 3.8 15.3 - - + -
667A LEU* 4.5 1.8 - - + -
675A LEU* 4.4 6.5 - - + -
678A VAL* 3.7 36.3 - - + +
679A LEU* 3.7 18.2 - - + -
682A ASP* 3.7 26.7 + - - +
708A ASN 3.7 11.0 - - - -
709A VAL* 3.9 18.8 - - + -
712A ALA* 3.6 26.9 - - + -
718B SER* 1.3 73.9 - - - +
720B PHE* 1.3 102.9 + + - +
722B THR* 3.3 8.8 + - - -
723B PHE* 2.9 25.6 + - - +
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Residues in contact with PHE 720 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A LYS* 4.0 19.7 - - + -
663A LEU* 3.7 30.7 - - + -
664A LEU* 3.9 12.1 - - - -
667A LEU* 3.8 14.6 - - + -
709A VAL* 4.0 15.0 - - + -
712A ALA* 3.6 28.0 - - + -
713A SER 4.1 6.5 - - - +
714A ILE* 4.2 17.0 - - + -
718B SER* 3.0 8.9 + - - +
719B PHE* 1.3 113.7 - + - +
721B MET* 1.3 64.8 + - - +
723B PHE* 3.3 2.8 + - - +
724B PHE* 3.0 42.1 + + + -
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Residues in contact with MET 721 (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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713A SER 4.5 5.6 - - - +
714A ILE* 5.1 5.6 - - - -
715A THR 4.4 10.1 - - - +
716A GLU* 4.5 5.6 - - + -
721A MET* 3.2 54.7 - - + +
716B GLU* 3.7 14.5 - - + +
717B ASN* 2.7 32.1 - - - +
718B SER* 3.1 17.4 + - - +
720B PHE* 1.3 81.7 - - - +
722B THR* 1.3 62.9 + - - +
724B PHE* 3.4 27.3 + - + +
725B ARG* 3.0 24.6 + - - +
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Residues in contact with THR 722 (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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678A VAL* 3.7 21.1 - - + -
716B GLU* 3.0 34.8 + - - +
718B SER 3.2 10.2 + - - -
719B PHE* 3.6 11.6 - - - -
720B PHE 3.2 0.2 - - - -
721B MET* 1.3 73.9 - - - +
723B PHE* 1.3 66.1 - - - +
725B ARG* 3.5 5.8 + - - +
726B SER* 3.0 35.7 + - - +
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Residues in contact with PHE 723 (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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667A LEU* 3.5 63.0 - - + -
670A GLN* 4.3 6.1 - - + -
671A ASP* 3.8 19.5 - - + -
674A LEU* 3.4 33.6 - - + +
675A LEU* 3.7 22.2 - - - -
678A VAL* 4.1 11.7 - - + -
728A ILE* 4.5 5.2 - - + -
719B PHE 2.9 17.9 + - - +
720B PHE 3.5 4.5 - - - +
722B THR* 1.3 73.9 - - - +
724B PHE* 1.3 74.1 + + - +
726B SER* 3.1 2.6 + - - -
727B TYR* 2.9 45.9 + + + +
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Residues in contact with PHE 724 (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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663A LEU* 4.2 23.1 - - + -
667A LEU* 3.9 14.6 - - + -
716A GLU* 5.9 0.2 - - - -
724A PHE* 3.4 30.5 - - + -
725A ARG* 3.8 30.1 - - + -
728A ILE* 3.5 42.0 - - + -
729A ILE* 5.3 0.9 - - + -
720B PHE* 3.0 24.8 + - + -
721B MET* 3.5 37.2 - - + +
723B PHE* 1.3 85.1 - + - +
725B ARG* 1.3 62.2 + - - +
727B TYR* 3.2 3.1 + - - +
728B ILE* 3.0 24.1 + - - +
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Residues in contact with ARG 725 (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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724A PHE* 3.8 32.7 - - + -
537B THR* 3.5 36.2 + - - +
539B GLU* 4.7 8.9 + - - -
659B TYR* 3.1 21.1 - - + +
663B LEU* 5.3 0.7 - - + -
716B GLU* 3.0 40.2 + - - +
721B MET 3.0 13.1 + - - +
722B THR* 3.9 7.6 - - - +
724B PHE* 1.3 79.6 - - - +
726B SER* 1.3 85.6 + - - +
729B ILE* 2.6 58.4 + - + +
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Residues in contact with SER 726 (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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674A LEU* 3.8 25.7 - - - +
677A GLU* 5.2 1.7 + - - -
678A VAL* 5.1 0.2 - - - +
722B THR* 3.0 24.9 + - - +
723B PHE 3.6 2.5 - - - -
725B ARG* 1.3 100.4 + - - +
727B TYR* 1.3 64.0 + - - +
729B ILE* 3.4 16.8 - - - +
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Residues in contact with TYR 727 (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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670A GLN* 3.0 59.5 + - + +
671A ASP* 3.9 18.8 - - + -
674A LEU* 4.0 6.7 - - + -
727A TYR* 6.0 4.7 - + - -
728A ILE* 3.9 20.4 - - + -
400B LYS* 5.3 1.9 + - - -
723B PHE* 2.9 36.3 + + + +
724B PHE 3.5 3.8 - - - +
726B SER* 1.3 80.1 - - - +
728B ILE* 1.3 64.7 + - + +
729B ILE* 4.8 0.2 - - - +
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Residues in contact with ILE 728 (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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723A PHE* 4.5 5.2 - - + -
724A PHE* 3.5 50.9 - - + +
727A TYR* 3.9 33.7 - - + -
728A ILE* 4.4 10.1 - - + -
400B LYS* 2.8 27.8 + - - +
666B ASN* 3.4 17.5 + - - +
667B LEU* 4.2 9.4 - - + -
670B GLN* 3.9 10.8 - - - +
724B PHE 3.0 16.6 + - - +
725B ARG 4.1 0.7 - - - +
727B TYR* 1.3 82.7 - - + +
729B ILE* 1.3 63.0 + - - +
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Residues in contact with ILE 729 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A PHE* 5.3 1.5 - - + -
400B LYS* 3.3 13.9 + - - -
533B LEU* 3.8 24.7 - - + -
537B THR* 5.1 3.4 - - + -
659B TYR* 4.1 18.6 - - + +
662B PHE* 3.8 24.9 - - + -
663B LEU* 3.3 34.3 - - + -
666B ASN* 4.2 6.8 - - - +
725B ARG* 2.6 50.8 + - + +
726B SER* 3.4 15.4 - - - +
727B TYR 4.8 0.5 - - - +
728B ILE* 1.3 82.0 - - - +
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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