Contacts of the helix formed by residues 633 - 647 (chain B) in PDB entry 6FF7
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 GLY 633 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210B ASN* 3.9 18.8 - - - -
588B ILE* 5.4 6.5 - - - +
631B GLY 5.1 0.7 - - - -
632B THR* 1.3 83.0 + - - +
634B GLU* 1.3 61.5 + - - -
635B LEU 3.6 1.6 - - - -
636B TYR* 4.0 9.1 - - - +
637B LEU* 3.3 24.6 + - - +
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Residues in contact with GLU 634 (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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210B ASN* 5.3 0.4 - - - +
633B GLY* 1.3 72.1 - - - -
635B LEU* 1.3 62.2 + - - +
636B TYR 3.3 0.2 - - - -
637B LEU* 3.5 3.3 + - - +
638B ASP* 2.9 27.3 + - - +
882B GLY 6.2 1.6 - - - +
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Residues in contact with LEU 635 (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 GLU* 1.3 75.0 - - - +
636B TYR* 1.3 61.2 + - - +
638B ASP* 3.2 9.4 - - + +
639B CYS* 3.0 28.4 + - - +
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Residues in contact with TYR 636 (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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210B ASN* 4.4 19.7 - - + +
211B PHE* 6.1 0.4 - - - -
632B THR* 4.9 5.8 - - - +
633B GLY* 4.0 22.1 + - - +
634B GLU 3.3 0.2 - - - -
635B LEU* 1.3 77.7 - - - +
637B LEU* 1.3 57.2 + - - +
639B CYS* 3.3 6.2 + - - +
640B VAL* 2.9 27.9 + - - +
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Residues in contact with LEU 637 (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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319A LEU* 5.3 11.6 - - + +
631B GLY* 5.8 7.9 - - - -
632B THR 5.9 0.4 - - - +
633B GLY 3.3 17.8 + - - +
634B GLU* 4.1 3.1 - - - +
636B TYR* 1.3 76.4 - - - +
638B ASP* 1.3 60.1 + - - +
640B VAL* 3.5 9.4 - - + +
641B MET* 2.9 32.1 + - - +
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Residues in contact with ASP 638 (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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316A PHE* 4.8 17.5 - - + -
318A TYR* 4.2 16.2 - - + +
319A LEU* 5.6 4.4 - - - +
634B GLU 2.9 19.7 + - - +
635B LEU* 3.2 13.5 - - + +
636B TYR 3.2 0.2 - - - -
637B LEU* 1.3 76.9 - - - +
639B CYS* 1.3 57.3 + - - +
641B MET* 3.3 3.3 + - - +
642B HIS* 2.9 29.0 + - - +
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Residues in contact with CYS 639 (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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173B THR* 5.2 12.1 - - - +
181B ILE* 4.6 20.6 - - + -
635B LEU 3.0 16.0 + - - +
636B TYR* 3.9 4.7 - - - +
638B ASP* 1.3 74.0 - - - +
640B VAL* 1.3 60.0 + - - +
642B HIS* 3.4 8.1 + - - +
643B ASP* 3.0 30.5 + - - +
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Residues in contact with VAL 640 (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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610B VAL* 5.1 10.3 - - + +
614B TYR* 5.5 11.0 - - + -
636B TYR 2.9 17.5 + - - +
637B LEU* 3.5 12.1 - - - +
638B ASP 3.2 0.2 - - - -
639B CYS* 1.3 77.3 - - - +
641B MET* 1.3 56.2 + - - +
643B ASP* 3.4 3.5 + - - +
644B LEU* 2.9 29.8 + - - +
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Residues in contact with MET 641 (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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318A TYR* 4.0 27.4 - - + +
319A LEU* 5.5 2.9 - - + -
637B LEU 2.9 17.1 + - - +
638B ASP 4.0 3.1 - - - +
640B VAL* 1.3 73.9 - - - +
642B HIS* 1.3 60.3 + - - +
644B LEU* 3.7 7.7 - - - +
645B ARG* 2.9 32.7 + - - +
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Residues in contact with HIS 642 (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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318A TYR* 5.0 5.1 - - + +
173B THR* 5.0 13.9 - - - -
638B ASP 2.9 17.7 + - - +
639B CYS* 3.5 10.1 - - - +
640B VAL 3.3 0.2 - - - -
641B MET* 1.3 76.9 - - - +
643B ASP* 1.3 57.4 + - - +
645B ARG* 4.0 2.5 - - - +
646B LYS* 3.0 33.1 + - - +
647B MET 4.2 0.2 + - - -
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Residues in contact with ASP 643 (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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610B VAL* 5.9 3.6 - - + -
639B CYS 3.0 17.2 + - - +
640B VAL* 4.1 3.1 - - - +
642B HIS* 1.3 75.5 - - - +
644B LEU* 1.3 57.3 + - - +
647B MET* 3.4 16.3 + - + +
648B TYR* 3.2 28.4 + - - +
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Residues in contact with LEU 644 (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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606B GLY 5.4 4.7 - - - +
607B LEU* 6.0 2.0 - - - -
610B VAL* 4.9 14.1 - - + +
640B VAL 2.9 19.3 + - - +
641B MET* 3.7 9.2 - - - +
643B ASP* 1.3 78.8 - - - +
645B ARG* 1.3 61.6 + - - +
648B TYR* 4.7 5.8 - - - -
649B SER* 3.2 30.3 + - - +
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Residues in contact with ARG 645 (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 MET 2.9 18.1 + - - +
642B HIS* 4.1 2.7 - - - +
644B LEU* 1.3 78.4 - - - +
646B LYS* 1.3 60.0 + - + +
649B SER 2.9 20.3 - - - +
650B GLU* 3.4 12.5 - - - -
651B ILE 4.3 9.7 + - - +
653B ILE* 5.7 8.5 - - + +
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Residues in contact with LYS 646 (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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642B HIS 3.0 13.4 + - - +
645B ARG* 1.3 79.3 - - + +
647B MET* 1.3 61.1 + - - +
650B GLU* 5.3 5.8 - - - +
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Residues in contact with MET 647 (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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487B GLY* 5.5 7.7 - - - -
643B ASP* 3.4 22.2 + - + +
645B ARG 3.6 0.4 - - - -
646B LYS* 1.3 81.7 - - - +
648B TYR* 1.3 63.3 + - + +
649B SER 3.7 0.9 - - - -
650B GLU* 5.5 2.0 - - - -
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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