Contacts of the strand formed by residues 653 - 659 (chain B) in PDB entry 2YA6
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 653 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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651B THR* 2.9 34.8 + - - -
652B GLY* 1.3 77.9 - - - +
654B LEU* 1.3 62.4 + - - +
655B GLN* 3.5 3.8 + - - +
672B ARG* 3.1 41.8 + - - +
673B TYR 3.6 14.8 - - - +
674B PRO* 4.0 25.0 - - + +
676B VAL 3.4 9.0 - - - +
677B LYS* 5.0 3.1 - - - -
678B ASP* 3.7 16.1 - - - +
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Residues in contact with LEU 654 (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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646B PHE* 4.0 11.9 - - + -
653B ASP* 1.3 75.9 - - - +
655B GLN* 1.3 64.8 + - - +
656B VAL* 3.9 11.2 - - + -
671B LYS 3.4 1.9 - - - +
672B ARG* 3.2 6.1 - - - -
673B TYR* 2.9 38.5 + - + +
676B VAL* 3.0 34.5 + - + +
678B ASP* 4.5 5.4 - - + -
683B MET* 3.5 37.7 - - + -
698B LEU* 3.9 17.3 - - + -
700B ASN* 5.6 0.4 - - - +
724B TRP* 3.6 31.6 - - + -
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Residues in contact with GLN 655 (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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611B ARG* 4.8 6.1 + - - -
627B ARG 4.8 3.8 + - - +
628B ALA 5.9 0.2 - - - -
629B GLN 4.3 11.4 + - - +
630B ASN* 5.0 3.6 + - - -
646B PHE* 3.5 1.0 - - - -
647B MET* 2.9 49.3 + - + +
649B GLY* 3.5 28.6 - - - -
650B LEU 3.6 3.4 - - - +
651B THR* 3.4 41.3 + - - +
653B ASP 3.5 2.8 + - - +
654B LEU* 1.3 74.9 - - - +
656B VAL* 1.3 66.8 + - - +
670B ILE* 3.7 26.8 - - + +
671B LYS 3.5 3.8 - - - -
672B ARG* 4.2 11.0 - - + +
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Residues in contact with VAL 656 (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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644B LYS* 3.8 24.9 - - + +
645B LEU 3.3 7.0 - - - +
646B PHE* 3.5 35.0 - - + -
654B LEU* 3.9 6.1 - - + -
655B GLN* 1.3 80.7 - - - +
657B ALA* 1.3 71.2 + - - +
658B THR* 4.8 2.4 + - - +
669B ASP 4.4 1.0 - - - +
670B ILE* 3.5 6.7 - - - +
671B LYS* 2.8 43.8 + - + +
673B TYR* 3.8 30.1 - - + -
722B LEU* 4.6 4.0 - - + -
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Residues in contact with ALA 657 (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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607B VAL* 3.7 37.7 - - + -
643B VAL 3.7 0.2 - - - +
644B LYS* 3.4 5.0 - - - -
645B LEU* 2.8 33.8 + - + +
647B MET* 3.7 14.0 - - + +
656B VAL* 1.3 75.0 - - - +
658B THR* 1.3 65.0 + - - +
666B TRP* 3.8 11.4 - - + -
667B GLU 5.9 1.1 - - - +
669B ASP 4.7 5.6 - - - +
670B ILE* 4.6 2.5 - - + -
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Residues in contact with THR 658 (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 ASP* 4.0 23.3 - - + +
643B VAL 3.3 8.1 - - - +
644B LYS* 2.7 37.7 + - - +
656B VAL* 4.8 2.8 + - - +
657B ALA* 1.3 78.6 - - - +
659B SER* 1.3 61.8 + - - +
660B LYS* 4.9 1.6 - - - -
666B TRP* 3.2 6.4 - - - -
667B GLU* 2.8 58.0 + - - +
669B ASP 5.0 5.2 + - - -
671B LYS* 6.2 0.2 - - - +
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Residues in contact with SER 659 (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 GLY 4.6 0.3 - - - +
642B ASP* 3.6 5.2 - - - +
643B VAL* 2.9 35.5 + - - +
658B THR* 1.3 73.7 - - - +
660B LYS* 1.3 60.6 + - - +
661B ASP* 2.9 8.1 + - - -
662B GLY 4.6 0.2 + - - -
663B GLY* 2.7 34.6 + - - -
665B THR 2.8 24.0 + - - -
666B TRP* 3.3 19.5 - - - +
667B GLU 4.8 0.2 - - - +
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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