Contacts of the strand formed by residues 633 - 637 (chain A) in PDB entry 3BK0
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 TYR 633 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A EDO 3.5 27.8 + - - -
558A HIS* 4.0 9.0 - + - -
561A LEU* 4.2 14.1 - - + -
563A LEU* 3.3 27.2 - - + +
576A PHE* 5.0 3.5 - + - -
589A VAL* 3.6 25.6 - - + -
590A LYS 3.4 8.5 - - - -
591A SER* 3.8 20.6 - - - -
604A PHE* 4.6 0.2 - - - -
625A VAL* 3.6 7.6 - - - +
626A CYS* 2.8 45.4 + - + -
631A PRO* 3.4 41.1 + - + +
632A ILE* 1.3 83.6 - - - +
634A ILE* 1.3 63.2 + - - +
635A VAL* 4.5 1.3 - - + -
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Residues in contact with ILE 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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588A ALA 3.7 1.2 - - - +
589A VAL* 3.5 3.3 - - - -
590A LYS* 2.8 42.5 + - + +
604A PHE* 3.3 48.9 - - + +
605A LEU* 4.1 15.5 - - + -
607A GLU* 4.3 10.8 - - + -
608A ALA* 4.2 25.1 - - + +
622A LEU* 3.6 24.9 - - + -
624A GLY 3.9 2.9 - - - +
625A VAL* 4.6 1.1 - - + +
633A TYR* 1.3 76.8 - - - +
635A VAL* 1.3 63.3 + - - +
636A MET* 3.9 17.3 - - + +
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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
----------------------------------------------------------
556A LEU* 4.0 12.1 - - + -
561A LEU* 4.0 18.6 - - + -
580A LEU* 4.6 0.9 - - + -
587A VAL* 3.6 39.0 - - + -
588A ALA 3.4 3.1 - - - +
589A VAL* 4.5 6.7 - - + -
622A LEU* 3.4 5.0 - - - +
623A ILE* 2.8 38.5 + - + -
624A GLY 2.8 26.8 + - - +
626A CYS* 3.9 28.0 - - - -
633A TYR* 4.5 1.6 - - + +
634A ILE* 1.3 76.3 - - - +
636A MET* 1.3 56.8 + - - +
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Residues in contact with MET 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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575A VAL* 5.9 0.4 - - + -
587A VAL* 3.3 9.5 - - - +
588A ALA* 2.8 32.7 + - + +
589A VAL 5.3 0.2 - - - -
590A LYS* 3.8 29.6 - - + +
607A GLU* 4.0 23.3 - - - +
611A LEU* 4.3 7.0 - - + -
620A VAL* 3.9 13.7 - - + -
621A ARG 3.4 13.5 - - - +
622A LEU* 4.3 13.7 - - + -
623A ILE* 3.7 7.6 - - - +
634A ILE* 3.9 15.0 - - + +
635A VAL* 1.3 78.5 - - - +
637A GLU* 1.3 67.3 + - - +
700A SER* 5.3 0.2 - - - -
826A STU 3.8 37.2 - - + -
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Residues in contact with GLU 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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586A LEU 4.6 1.3 - - - -
588A ALA* 3.8 0.4 - - - +
619A ILE 3.9 0.9 - - - +
620A VAL* 3.5 13.0 - - + -
621A ARG* 2.8 63.0 + - + +
623A ILE* 3.6 17.3 - - + +
636A MET* 1.3 73.6 - - - +
638A LEU* 1.3 62.6 + - - +
639A VAL* 4.1 14.4 - - + +
698A LYS* 3.2 30.8 + - - +
826A STU 2.9 24.6 + - - -
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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