Contacts of the strand formed by residues 635 - 639 (chain 6) in PDB entry 5U8T
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 ILE 635 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5506 GLN* 3.6 27.4 - - + +
5516 MET* 3.5 43.3 - - + +
5886 VAL* 3.7 22.8 - - + +
5926 ALA* 3.8 21.5 - - + -
5936 PRO* 4.9 5.8 + - + +
5946 ARG 4.9 2.8 + - - -
5956 SER* 4.1 6.7 - - - -
5966 VAL 3.8 17.2 + - - +
6316 ALA* 6.3 0.4 - - - -
6346 GLY* 1.3 74.6 - - - -
6366 CYS* 1.3 62.8 + - - +
6376 CYS* 4.0 12.1 + - - -
6776 SER* 3.2 20.4 - - - +
6796 LEU* 4.5 1.3 - - + -
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Residues in contact with CYS 636 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5966 VAL* 3.5 24.7 - - - +
5986 THR* 6.1 2.2 - - - -
6086 LEU* 4.4 11.0 - - - -
6286 LEU* 4.2 18.8 - - + -
6316 ALA* 5.0 6.1 - - + -
6346 GLY 3.7 1.0 + - - -
6356 ILE* 1.3 73.4 - - - +
6376 CYS* 1.3 67.8 + - - +
6386 ILE* 4.4 9.4 - - - -
6766 THR* 4.9 2.5 - - - +
6776 SER 2.9 10.3 + - - +
6786 ILE* 3.5 32.7 - - + -
6796 LEU* 2.8 27.7 + - - +
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Residues in contact with CYS 637 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5856 LEU* 3.5 30.1 - - + +
5886 VAL* 3.7 31.0 - - - -
5966 VAL 3.2 8.9 + - - +
5976 TYR* 3.1 31.0 - - + -
5986 THR* 3.1 18.5 + - - +
6356 ILE* 4.1 5.6 - - - -
6366 CYS* 1.3 84.9 - - - +
6386 ILE* 1.3 65.7 + - - +
6796 LEU* 3.0 13.7 - - - +
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Residues in contact with ILE 638 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5856 LEU* 3.8 2.1 - - - +
5976 TYR* 4.3 0.7 - - - -
5986 THR* 3.3 20.0 - - + +
5996 SER 3.8 7.6 - - - +
6086 LEU* 5.7 5.2 - - + -
6366 CYS* 4.4 10.3 - - - -
6376 CYS* 1.3 81.7 - - - +
6396 ASP* 1.3 86.6 + - - +
6406 GLU 5.4 0.4 - - - -
6416 PHE* 5.2 9.9 - - + -
6446 MET* 3.7 37.0 - - + -
6526 ILE* 5.6 4.3 - - + -
6786 ILE* 3.6 33.0 - - + -
6796 LEU 3.5 3.6 + - - -
6806 ALA* 3.1 26.3 - - + +
6816 ALA 3.2 5.7 + - - -
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Residues in contact with ASP 639 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5826 SER* 4.1 16.5 + - - -
5856 LEU* 3.0 23.4 - - - +
5866 LYS* 5.0 1.0 + - - -
5976 TYR* 2.9 23.0 + - - -
5996 SER* 3.2 37.2 - - - +
6386 ILE* 1.3 91.9 - - - +
6406 GLU* 1.3 84.4 + - + +
6416 PHE* 3.7 1.8 - - - -
6816 ALA* 3.3 8.5 - - - +
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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