Contacts of the helix formed by residues 674 - 684 (chain B) in PDB entry 5FFW
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 ASP 674 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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653B PHE* 3.5 10.8 - - - +
655B GLU* 3.4 22.2 - - - +
656B PRO* 3.2 35.7 - - + +
657B VAL 5.4 0.2 - - - +
672B PRO 5.5 0.3 - - - -
673B MET* 1.3 80.7 - - - +
675B PHE* 1.3 62.6 + - - +
676B PHE* 2.9 24.3 + - - +
677B THR* 2.6 28.3 + - - -
678B MET* 3.1 24.1 + - - +
700B ILE* 3.5 13.9 - - - -
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Residues in contact with PHE 675 (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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641B LEU* 3.7 25.2 - - + +
644B LEU* 3.9 35.7 - - + -
645B GLN* 3.1 47.0 + - + +
648B ASP* 4.2 9.9 - - + -
653B PHE* 2.9 45.1 + - + +
654B SER* 4.3 2.2 - - - +
674B ASP* 1.3 71.0 - - - +
676B PHE* 1.3 60.5 + - - +
678B MET* 3.4 5.8 + - - +
679B LYS* 3.0 26.5 + - - +
697B PHE* 4.1 21.3 - + - -
700B ILE* 3.8 17.9 - - + -
721B LEU* 4.2 10.5 - - + -
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Residues in contact with PHE 676 (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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654B SER 3.1 20.0 + - - +
655B GLU* 4.4 9.6 - - + -
656B PRO* 4.5 14.8 - - + -
674B ASP* 2.9 5.3 + - - +
675B PHE* 1.3 72.5 - - - +
677B THR* 1.3 70.0 + - - +
679B LYS* 3.1 12.1 + - + +
680B GLN* 2.9 60.1 + - + +
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Residues in contact with THR 677 (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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656B PRO* 4.0 9.9 - - - +
672B PRO 5.6 0.4 - - - +
673B MET* 3.9 23.3 - - + -
674B ASP* 2.6 33.6 + - - -
675B PHE 3.4 0.2 - - - -
676B PHE* 1.3 79.4 - - - +
678B MET* 1.3 57.6 + - - +
680B GLN* 3.3 12.7 + - + +
681B ASN* 2.9 39.9 + - - +
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Residues in contact with MET 678 (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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641B LEU* 4.0 20.4 - - + -
644B LEU* 5.5 0.4 - - + -
673B MET* 3.8 11.9 - - - -
674B ASP 3.1 17.8 + - - +
675B PHE* 3.6 9.9 - - - +
676B PHE 3.2 0.2 - - - -
677B THR* 1.3 75.6 - - - +
679B LYS* 1.3 58.4 + - - +
681B ASN* 3.3 1.1 + - - +
682B LEU* 2.8 26.2 + - - +
687B TYR* 3.3 29.6 - - - +
693B PHE* 3.5 54.5 - - + +
696B ASP* 3.9 1.1 - - + -
697B PHE* 3.7 25.1 - - + +
700B ILE* 3.7 19.3 - - - -
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Residues in contact with LYS 679 (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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638B ARG* 3.9 22.4 + - - +
641B LEU* 3.6 21.2 - - + +
642B GLU* 5.6 9.8 - - + +
645B GLN* 6.0 1.8 - - - +
675B PHE 3.0 14.8 + - - +
676B PHE* 3.1 17.2 + - + +
678B MET* 1.3 74.7 - - - +
680B GLN* 1.3 59.9 + - - +
682B LEU* 3.2 4.3 + - + +
683B GLU* 2.8 68.6 + - + +
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Residues in contact with GLN 680 (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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676B PHE* 2.9 58.9 + - + +
677B THR* 3.5 12.4 + - + +
679B LYS* 1.3 74.3 - - - +
681B ASN* 1.3 64.4 + - - +
683B GLU* 3.3 4.0 + - - +
684B ALA* 2.9 25.3 + - - +
686B ARG* 4.0 9.0 - - - +
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Residues in contact with ASN 681 (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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673B MET* 4.5 5.1 - - - +
677B THR* 2.9 31.8 + - - +
678B MET* 3.5 7.4 - - - +
680B GLN* 1.3 75.6 - - - +
682B LEU* 1.3 59.6 + - - +
684B ALA 3.2 7.3 + - - -
685B TYR 3.3 0.2 + - - -
686B ARG* 2.6 73.6 + - + +
687B TYR* 3.1 31.0 + - + -
696B ASP* 3.7 8.7 + - - -
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Residues in contact with LEU 682 (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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634B LEU* 3.6 30.3 - - + +
637B LEU* 3.4 41.1 - - + +
638B ARG* 3.6 37.7 - - + +
641B LEU* 4.1 16.8 - - + -
678B MET 2.8 19.6 + - - +
679B LYS* 3.2 7.8 + - + +
681B ASN* 1.3 71.7 - - - +
683B GLU* 1.3 68.8 + - - +
685B TYR* 3.2 15.6 + - - -
687B TYR* 3.7 19.5 + - + +
693B PHE* 5.0 2.0 - - + -
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Residues in contact with GLU 683 (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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634B LEU* 4.5 7.6 - - - +
638B ARG* 2.8 42.3 + - - +
679B LYS* 2.8 60.4 + - + +
680B GLN* 4.0 4.0 - - - +
682B LEU* 1.3 79.4 - - - +
684B ALA* 1.3 56.4 + - - +
685B TYR* 3.2 22.4 + - - -
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Residues in contact with ALA 684 (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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680B GLN 2.9 18.2 + - - +
681B ASN 3.2 1.5 + - - +
683B GLU* 1.3 73.9 - - - +
685B TYR* 1.3 76.5 + - - +
686B ARG* 3.3 37.7 + - - +
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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