Contacts of the strand formed by residues 648 - 652 (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 THR 648 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459B MET* 3.2 31.1 + - - +
461B HIS 3.6 14.2 + - - -
462B LEU* 3.3 18.4 - - + +
463B LEU 3.1 22.5 + - - -
646B ILE* 3.5 1.9 - - - +
647B PRO* 1.3 74.9 - - - +
649B ARG* 1.3 62.1 + - - +
680B TYR* 3.5 36.8 - - + +
681B LEU 3.8 11.4 - - - +
682B PRO* 4.7 0.7 - - + -
683B PRO* 3.7 15.4 - - - +
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Residues in contact with ARG 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B LEU* 3.9 22.5 - - + +
643B LYS* 3.0 46.5 + - - +
646B ILE* 3.2 16.5 + - - +
647B PRO 3.4 14.3 + - - -
648B THR* 1.3 73.4 - - - +
650B ILE* 1.3 63.7 + - - +
651B ALA 4.1 0.4 - - - -
662B THR 4.8 2.4 + - - -
663B ILE* 2.9 52.9 + - + +
664B LEU* 4.1 12.4 - - + -
665B ASP* 5.0 3.4 - - - +
679B LEU 3.8 1.0 - - - +
681B LEU* 2.9 44.5 + - + +
655C SER* 4.7 9.5 + - - -
656C SER* 4.4 26.7 - - - +
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Residues in contact with ILE 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B LEU* 3.7 17.7 - - + -
459B MET* 5.2 1.3 - - + -
462B LEU* 3.6 26.7 - - + -
463B LEU 3.1 13.0 + - - +
464B VAL* 3.4 7.1 - - + +
465B ALA* 3.1 24.6 + - - +
479B MET* 3.7 23.8 - - + -
648B THR 4.1 0.4 + - - -
649B ARG* 1.3 72.6 - - - +
651B ALA* 1.3 58.9 + - - +
652B PHE* 4.4 13.5 - - + -
663B ILE* 4.7 0.9 - - - -
678B MET* 3.6 32.8 - - + -
679B LEU 4.2 2.7 - - - -
680B TYR* 3.5 29.2 - - + -
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Residues in contact with ALA 651 (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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465B ALA 3.7 4.5 - - - -
649B ARG 4.1 0.6 - - - -
650B ILE* 1.3 72.9 - - - +
652B PHE* 1.3 67.5 + - - +
663B ILE* 3.6 32.3 - - + -
664B LEU* 3.7 25.1 - - + -
669B ALA* 4.0 6.1 - - + -
672B LEU* 3.7 3.1 - - - +
678B MET* 3.2 2.8 - - - -
679B LEU* 2.9 34.3 + - - +
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Residues in contact with PHE 652 (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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464B VAL* 3.5 26.0 - - + -
465B ALA 2.9 28.5 + - - +
470B SER* 3.5 26.5 - - - +
471B GLY 3.7 16.6 - - - -
472B LYS* 3.6 18.2 - - + -
475B GLY* 4.4 11.9 - - - -
479B MET* 5.9 2.0 - - + -
650B ILE* 4.4 8.5 - - + -
651B ALA* 1.3 78.9 - - - +
653B GLN* 1.3 68.6 + - - +
654B VAL* 3.5 7.6 + - - +
669B ALA* 3.8 11.1 - - - +
672B LEU* 3.8 3.6 - - - -
676B GLY* 4.2 15.9 - - - -
677B ASP 3.0 27.1 - - - +
678B MET* 3.5 33.7 - - + -
693B GLY* 5.5 0.7 - - - -
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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