Contacts of the strand formed by residues 633 - 637 (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 SER 633 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554B GLY* 3.9 12.9 - - - +
555B PRO 4.8 3.1 - - - +
573B PRO* 3.4 25.3 - - - +
574B VAL 4.8 1.2 + - - -
589B SER* 4.1 5.6 - - - -
590B ARG 4.7 1.6 + - - -
631B THR 3.5 4.1 + - - -
632B GLU* 1.3 77.1 - - - +
634B THR* 1.3 61.8 + - - +
645B LEU* 3.2 25.0 - - - +
646B PHE 3.0 15.3 - - - -
647B MET* 3.7 20.4 - - - -
648B ARG 4.6 0.2 - - - +
682B GLN* 6.1 1.0 - - - +
683B MET* 4.9 6.1 - - - +
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Residues in contact with THR 634 (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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555B PRO 6.1 0.2 - - - -
557B THR 5.1 6.1 + - - -
573B PRO* 4.5 2.5 - - - -
633B SER* 1.3 74.7 - - - +
635B VAL* 1.3 63.2 + - - +
636B VAL* 5.2 0.2 - - - -
645B LEU* 3.6 3.5 - - - -
646B PHE* 2.8 56.1 + - + -
683B MET* 3.6 26.2 - - + -
684B SER* 3.6 8.8 - - - -
685B ALA* 3.1 43.5 + - + +
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Residues in contact with VAL 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B THR 5.2 3.5 + - - +
558B GLY* 4.8 1.8 - - - -
559B ILE* 3.3 39.5 - - + +
571B LEU* 3.7 23.3 - - + +
573B PRO* 3.8 25.7 - - + +
591B VAL* 4.6 3.8 - - + -
634B THR* 1.3 75.7 + - - +
636B VAL* 1.3 70.0 + - - +
643B VAL* 3.4 28.5 - - + -
644B LYS 3.4 4.7 - - - +
645B LEU* 3.9 15.9 - - + -
685B ALA 4.2 4.3 - - - +
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Residues in contact with VAL 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B ILE* 3.8 8.3 - - + -
635B VAL* 1.3 79.0 - - - +
637B GLN* 1.3 67.6 + - - +
638B LEU* 4.0 2.1 + - + +
643B VAL* 3.4 3.1 - - - -
644B LYS* 2.7 40.3 + - + +
646B PHE* 3.9 26.7 - - + -
685B ALA* 3.4 31.2 - - + +
686B ILE* 4.1 2.7 - - - +
687B HIS* 3.6 34.5 - - + +
696B ILE* 4.1 18.4 - - + -
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Residues in contact with GLN 637 (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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559B ILE* 3.5 9.0 - - + +
561B LEU* 3.4 33.1 - - + +
562B ARG* 2.7 68.9 + - - +
563B ASN* 2.9 45.8 + - - -
636B VAL* 1.3 76.2 - - - +
638B LEU* 1.3 62.4 + - - +
641B GLY* 3.6 13.9 + - - +
642B ASP 3.4 11.4 - - - +
643B VAL* 4.2 7.0 - - + +
687B HIS* 3.6 7.3 - - - -
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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