Contacts of the strand formed by residues 677 - 681 (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 SER 677 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5506 GLN* 4.1 17.9 + - - -
5686 ASP* 3.1 23.5 + - - -
5696 ILE* 3.5 11.9 - - - -
5706 ASN* 3.6 5.2 - - - +
6346 GLY 3.2 5.4 + - - +
6356 ILE* 3.2 35.3 - - - +
6366 CYS* 2.9 27.9 + - - +
6766 THR* 1.3 74.1 - - - +
6786 ILE* 1.3 59.6 + - - +
6796 LEU 4.0 0.2 - - - -
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Residues in contact with ILE 678 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5706 ASN* 2.6 32.5 + - - +
5716 ILE 4.0 3.1 + - - +
5726 CYS* 5.2 2.1 - - - -
6086 LEU* 4.5 0.9 - - + -
6286 LEU* 4.1 16.2 - - + -
6366 CYS* 3.5 30.1 - - + +
6386 ILE* 3.6 27.1 - - + -
6416 PHE* 5.9 2.5 - - + -
6526 ILE* 4.5 17.0 - - + -
6556 ALA* 6.1 1.3 - - + -
6566 MET* 3.5 34.7 - - + +
6766 THR* 3.7 7.4 + - - +
6776 SER* 1.3 75.5 - - - +
6796 LEU* 1.3 60.4 + - - +
6806 ALA* 4.3 2.0 + - + -
7096 PHE* 5.1 13.0 - - + -
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Residues in contact with LEU 679 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5476 ILE* 4.6 24.0 - - + -
5506 GLN* 3.1 36.6 - - + +
5716 ILE* 3.1 30.1 - - + +
5736 VAL* 5.8 3.6 - - + -
5846 PHE* 5.8 3.4 - - + -
5856 LEU* 3.3 31.9 - - + -
5886 VAL* 4.6 5.8 - - + -
6356 ILE* 4.5 0.9 - - + -
6366 CYS 2.8 20.9 + - - +
6376 CYS* 3.0 21.9 - - - -
6386 ILE 3.5 0.2 + - - -
6776 SER 4.0 1.2 - - - -
6786 ILE* 1.3 75.1 - - - +
6806 ALA* 1.3 71.1 + - - +
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Residues in contact with ALA 680 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5716 ILE 2.9 7.6 + - - +
5726 CYS* 3.1 6.2 - - - +
5736 VAL* 2.8 25.5 + - - +
5856 LEU* 4.9 1.3 - - - -
6386 ILE* 3.1 30.1 - - + +
6416 PHE* 3.4 31.0 - - + -
6786 ILE* 5.2 1.3 - - + -
6796 LEU* 1.3 87.3 - - - +
6816 ALA* 1.3 62.7 + - - +
6826 ALA 4.3 0.2 - - - -
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Residues in contact with ALA 681 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5736 VAL* 3.0 25.4 - - + +
5816 LYS* 3.4 28.8 + - + +
5826 SER* 6.1 0.2 - - - +
5856 LEU* 4.4 13.6 - - + +
6386 ILE 3.2 5.9 + - - -
6396 ASP* 3.3 9.1 - - - +
6406 GLU* 2.7 25.8 + - - +
6416 PHE* 4.4 0.9 - - - -
6806 ALA* 1.3 78.2 - - - +
6826 ALA* 1.3 55.6 + - - +
6836 ASN* 4.1 0.9 + - - -
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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
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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