Contacts of the strand formed by residues 633 - 639 (chain A) in PDB entry 3SHW
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
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Residue Dist Surf HB Arom Phob DC
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521A ILE* 3.7 31.0 - - + -
522A ARG 3.7 2.2 - - - -
523A THR* 4.2 9.0 - - + -
525A PHE* 3.9 11.4 - + - -
537A PHE* 4.0 11.6 - + - -
557A TRP* 3.8 25.4 - + - -
574A ILE* 3.7 11.7 - - + +
575A PRO* 2.5 50.3 + - - +
576A ASN 3.8 6.1 - - - -
577A LYS* 3.1 43.7 + - + +
580A ALA* 3.5 22.1 - - + +
631A PRO* 3.4 9.9 - - - +
632A ALA* 1.3 87.0 - - + +
634A GLU* 1.3 60.3 + - - +
635A ARG 4.2 1.0 + - - -
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Residues in contact with GLU 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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521A ILE* 3.1 5.1 - - - -
522A ARG* 2.6 58.9 + - - +
524A HIS* 2.7 36.6 + - + +
630A PHE* 4.2 12.0 - - + -
631A PRO* 4.3 12.6 - - + -
633A TYR* 1.3 73.9 - - - +
635A ARG* 1.3 71.9 + - - +
636A VAL* 3.4 14.0 + - - +
722A TYR* 3.5 11.3 + - - -
801A SER* 2.6 29.8 + - - +
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Residues in contact with ARG 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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441A ASN* 5.4 3.2 - - - +
479A ILE* 3.9 26.9 - - - +
482A GLU* 4.9 6.9 + - - -
519A PHE* 3.5 44.4 - - - +
520A TYR 3.6 4.9 - - - +
521A ILE* 3.9 9.2 - - - -
557A TRP* 6.1 0.4 - - - -
577A LYS* 6.6 0.2 - - - -
633A TYR 4.2 1.5 + - - +
634A GLU* 1.3 75.3 - - - +
636A VAL* 1.3 63.3 + - - +
801A SER* 3.5 4.3 - - - -
802A GLU* 3.5 62.0 + - + +
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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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520A TYR* 3.0 35.8 + - + +
521A ILE 3.7 19.5 - - - +
522A ARG* 3.8 23.3 - - + +
542A VAL* 4.2 5.4 - - + -
634A GLU* 3.5 28.7 - - - +
635A ARG* 1.3 80.0 - - - +
637A VAL* 1.3 70.9 + - - +
799A TRP* 3.7 23.3 - - + -
800A VAL 3.0 13.0 - - - +
801A SER* 4.5 0.7 - - - +
802A GLU* 4.9 1.1 - - - +
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Residues in contact with VAL 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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520A TYR* 5.5 5.4 - - + -
636A VAL* 1.3 80.8 - - - +
638A LEU* 1.3 63.1 - - - +
639A ARG* 3.5 41.0 + - + +
798A VAL 3.4 0.5 - - - +
799A TRP* 3.4 11.0 - - - -
800A VAL* 2.9 25.2 + - - +
801A SER 3.9 18.8 - - - +
802A GLU* 3.9 26.2 - - + +
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Residues in contact with LEU 638 (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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566A HIS* 4.0 27.4 - - + -
637A VAL* 1.3 71.1 - - - +
639A ARG* 1.3 75.0 + - - +
797A LEU* 3.8 42.2 - - + -
798A VAL 3.5 10.5 - - - +
799A TRP* 3.4 46.3 - - + +
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Residues in contact with ARG 639 (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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637A VAL* 3.5 39.6 - - + +
638A LEU* 1.3 86.1 + - - +
640A GLU* 1.3 66.2 + - - +
797A LEU* 3.4 10.2 - - - -
798A VAL* 2.7 44.1 + - - +
800A VAL* 4.3 21.8 - - + -
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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