Contacts of the strand formed by residues 633 - 637 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554A GLY* 3.8 13.1 - - - +
555A PRO 4.9 2.8 - - - +
573A PRO* 3.3 29.2 - - - +
574A VAL 4.8 1.4 + - - -
589A SER* 4.1 7.3 - - - -
590A ARG 4.4 1.7 + - - -
631A THR 3.6 1.1 + - - -
632A GLU* 1.3 77.5 - - - +
634A THR* 1.3 61.5 + - - +
645A LEU* 3.3 35.4 - - - +
646A PHE 3.0 13.9 - - - -
647A MET* 3.9 11.2 - - - -
682A GLN* 6.0 2.4 - - - +
683A MET* 5.1 4.7 - - - +
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Residues in contact with THR 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A THR 4.9 7.4 + - - -
573A PRO* 4.4 3.4 - - - -
633A SER* 1.3 75.1 - - - +
635A VAL* 1.3 63.8 + - - +
645A LEU* 3.5 4.0 - - - -
646A PHE* 2.8 55.5 + - + +
683A MET* 3.8 27.8 - - + -
684A SER* 3.8 3.7 - - - -
685A ALA* 3.2 42.6 + - + +
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Residues in contact with VAL 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A THR 5.1 2.9 + - - +
558A GLY* 4.5 2.2 - - - -
559A ILE* 3.5 39.2 - - + +
571A LEU* 3.8 23.6 - - + +
573A PRO* 3.8 24.4 - - + +
591A VAL* 4.3 3.6 - - + -
634A THR* 1.3 75.8 + - - +
636A VAL* 1.3 71.0 + - - +
643A VAL* 3.5 28.3 - - + -
644A LYS 3.4 4.9 - - - +
645A LEU* 3.7 17.5 - - + -
685A ALA 4.2 4.9 - - - +
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Residues in contact with VAL 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A ILE* 3.9 7.9 - - - -
635A VAL* 1.3 82.6 - - - +
637A GLN* 1.3 67.8 + - - +
638A LEU* 4.0 0.6 + - + -
643A VAL* 3.5 2.9 - - - +
644A LYS* 2.8 32.8 + - + +
646A PHE* 3.8 26.7 - - + -
685A ALA* 3.4 31.0 - - + +
686A ILE* 4.1 3.6 - - - +
687A HIS* 3.7 31.2 - - + +
696A ILE* 3.9 21.3 - - + -
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Residues in contact with GLN 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A ILE* 3.5 9.0 - - + +
560A VAL 5.8 0.2 - - - +
561A LEU* 3.5 36.6 - - + +
562A ARG* 2.7 67.0 + - - +
563A ASN* 2.9 44.8 + - - -
564A GLY* 5.1 0.2 - - - -
636A VAL* 1.3 76.0 - - - +
638A LEU* 1.3 61.4 + - - +
641A GLY* 3.3 16.4 + - - +
642A ASP 3.4 12.6 - - - +
643A VAL* 4.3 1.6 - - + +
662A GLY* 6.0 0.2 - - - -
687A HIS* 3.3 9.6 - - - +
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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