Contacts of the helix formed by residues 659 - 664 (chain B) in PDB entry 6T8B
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 659 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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640A GLY* 4.6 2.6 - - - +
643A LYS* 5.0 0.9 - - - +
644A ALA* 3.5 23.0 + - + +
632B ARG* 2.8 40.6 + - + +
654B VAL* 4.3 13.5 - - + -
655B SER* 4.2 1.0 - - - -
656B SER* 3.3 36.0 + - - +
657B LYS* 3.0 1.2 - - - +
658B ILE* 1.3 79.6 - - - +
660B SER* 1.3 62.0 + - - +
661B ARG 3.1 1.6 - - - -
662B THR* 2.5 29.2 + - - -
663B ILE* 3.9 6.5 + - - +
14G T 4.7 1.6 + - - -
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Residues in contact with SER 660 (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 VAL* 3.5 25.1 - - - +
656B SER 4.3 3.8 - - - -
657B LYS* 3.2 10.0 + - - -
659B ASP* 1.3 78.7 - - - +
661B ARG* 1.3 58.4 + - - +
662B THR 3.2 0.2 - - - -
663B ILE* 3.5 6.6 + - - +
664B LEU* 3.2 23.6 + - - +
666B GLN 3.4 13.9 + - - +
667B GLY* 4.0 9.2 - - - -
669B ALA* 3.1 34.7 + - - +
670B GLU 4.5 0.9 - - - -
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Residues in contact with ARG 661 (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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657B LYS* 3.2 14.8 + - - +
658B ILE* 3.3 51.1 - - - +
659B ASP 3.1 1.4 - - - -
660B SER* 1.3 75.8 - - - +
662B THR* 1.3 60.0 + - - +
663B ILE 3.4 0.4 - - - -
665B ASP* 3.4 39.8 - - - +
666B GLN* 4.1 9.2 - - - +
667B GLY* 4.7 5.4 - - - +
13G A 4.9 8.5 + - - -
14G T 4.9 8.9 + - - -
8H T 5.8 0.2 + - - -
9H A 4.1 40.8 + - - -
10H T 3.5 26.6 - - - -
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Residues in contact with THR 662 (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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463B LEU* 5.5 0.2 - - - +
632B ARG* 4.0 26.4 - - - +
633B PRO* 3.5 26.2 + - - +
643B LYS* 4.0 19.3 + - - +
649B ARG* 4.8 3.3 + - - -
658B ILE 3.6 16.4 - - - +
659B ASP 2.5 19.2 + - - +
661B ARG* 1.3 80.4 - - - +
663B ILE* 1.3 65.8 + - - +
665B ASP 4.7 0.2 - - - -
14G T 4.2 9.2 - - - +
15G A 3.4 22.4 - - - +
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Residues in contact with ILE 663 (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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463B LEU* 4.6 4.5 - - + +
465B ALA* 3.5 28.7 - - + -
466B GLY 4.5 0.4 - - - +
632B ARG* 5.0 2.7 - - - -
633B PRO* 3.5 27.8 - - + -
649B ARG* 2.9 56.6 + - + +
651B ALA* 3.6 29.8 - - + -
654B VAL* 3.8 29.2 - - + -
659B ASP 4.1 6.5 - - - +
660B SER* 3.5 5.7 + - - +
661B ARG 3.4 0.2 - - - -
662B THR* 1.3 82.1 - - - +
664B LEU* 1.3 61.8 + - - +
665B ASP 3.4 0.4 - - - -
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Residues in contact with LEU 664 (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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649B ARG* 4.1 11.7 - - + +
651B ALA* 3.7 17.5 - - + -
660B SER 3.2 5.0 + - - +
663B ILE* 1.3 77.7 - - + +
665B ASP* 1.3 63.4 + - - +
666B GLN* 3.0 35.0 + - + +
668B GLY 5.0 0.4 - - - +
669B ALA* 3.7 17.9 - - + -
679B LEU* 3.5 55.2 - - + +
681B LEU* 3.3 43.0 - - + +
688B PRO* 4.7 5.8 - - + -
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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