Contacts of the strand formed by residues 637 - 642 (chain A) in PDB entry 3QIK
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 PHE 637 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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628A ILE* 3.8 12.1 - - + -
634A ASP* 4.2 16.5 + - - +
635A TYR* 3.6 23.1 + + + +
636A GLY* 1.3 81.9 + - - +
638A ASP* 1.3 74.7 + - - +
639A ILE* 3.6 23.1 - - + -
648A VAL* 4.4 3.1 - - + -
650A SER* 3.2 15.9 - - - +
651A VAL* 4.2 3.6 - - + +
652A GLN* 4.8 0.9 - - - +
657A ALA* 4.3 1.1 - - + -
662A LEU* 3.4 29.2 - - + -
668A ILE* 4.0 9.9 - - + -
688A LEU* 4.2 16.3 - - + +
698A LEU* 3.5 33.7 - - + -
700A LEU* 3.9 11.2 - - + -
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Residues in contact with ASP 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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634A ASP* 6.0 1.3 - - - -
637A PHE* 1.3 78.6 - - - +
639A ILE* 1.3 70.5 + - - +
648A VAL* 3.5 9.0 - - - +
649A LYS* 2.8 41.9 + - + +
650A SER* 3.0 28.4 + - - +
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Residues in contact with ILE 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 PHE* 3.6 24.5 - - + -
638A ASP* 1.3 83.7 + - - +
640A GLU* 1.3 63.4 + - - +
646A VAL* 3.9 7.2 - - + -
647A VAL 3.3 11.4 - - - +
648A VAL* 4.6 0.4 - - - -
649A LYS* 3.8 10.8 - - - +
668A ILE* 3.7 20.0 - - + -
681A PHE* 3.6 30.0 - - + -
684A VAL* 3.9 20.0 - - + -
685A GLU* 4.1 16.7 - - + +
688A LEU* 3.8 23.1 - - + +
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Residues in contact with GLU 640 (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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639A ILE* 1.3 76.0 - - - +
641A GLU* 1.3 68.2 + - - +
642A LYS* 5.3 1.9 - - + +
646A VAL* 3.6 3.1 - - - -
647A VAL* 2.9 53.5 + - + +
648A VAL 4.6 0.5 - - - +
649A LYS* 3.8 41.7 + - + +
681A PHE* 3.7 13.1 - - - -
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Residues in contact with GLU 641 (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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640A GLU* 1.3 80.6 - - - +
642A LYS* 1.3 62.6 + - - +
643A ASN 3.9 16.2 - - - +
644A LYS* 4.3 11.3 - - - +
645A ALA 3.5 12.6 - - - +
646A VAL* 5.6 0.7 - - + -
681A PHE* 3.6 47.1 + - + +
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Residues in contact with LYS 642 (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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640A GLU* 4.0 3.3 + - + +
641A GLU* 1.3 73.6 - - - +
643A ASN* 1.3 63.1 + - - +
645A ALA* 2.8 39.5 + - - +
647A VAL* 4.1 25.4 - - + -
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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