Contacts of the strand formed by residues 633 - 640 (chain A) in PDB entry 2Y6O
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 GLY 633 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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629A VAL* 3.8 1.6 - - - +
630A GLY 2.8 28.1 + - - +
631A GLU 3.4 2.4 - - - -
632A PHE* 1.3 86.5 - - - +
634A GLU* 1.3 62.1 + - - +
654A THR 3.4 10.8 - - - -
655A LEU 4.0 0.7 - - - -
656A LYS* 3.6 16.4 - - - +
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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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626A VAL* 3.8 29.3 - - + +
628A GLY 3.3 14.1 - - - +
629A VAL* 4.2 11.0 - - + +
632A PHE* 3.4 5.1 - - - -
633A GLY* 1.3 74.9 - - - +
635A VAL* 1.3 67.0 + - - +
636A CYS* 4.1 12.5 - - - -
652A ILE 3.8 0.7 - - - +
653A LYS* 3.4 4.0 - - - +
654A THR* 3.0 49.2 + - - +
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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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626A VAL* 3.7 3.1 - - - +
627A ILE* 2.8 40.2 + - + -
628A GLY* 2.9 19.7 + - - +
632A PHE* 4.0 17.5 - - + -
634A GLU* 1.3 79.2 - - - +
636A CYS* 1.3 73.7 + - - +
651A ALA* 4.3 7.0 - - + -
652A ILE 3.3 7.4 - - - +
653A LYS* 4.1 15.5 - - + -
1892A 1N1 4.2 33.7 - - + +
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Residues in contact with CYS 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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623A ILE* 3.7 30.7 - - + -
625A LYS 3.1 12.6 - - - +
626A VAL* 3.8 26.0 - - - -
627A ILE* 3.9 6.1 - - - -
634A GLU* 4.1 14.6 - - - -
635A VAL* 1.3 79.9 - - - +
637A SER* 1.3 60.4 + - - +
651A ALA* 3.3 5.9 - - - +
652A ILE* 2.8 41.5 + - + +
654A THR* 5.6 4.7 - - - -
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Residues in contact with SER 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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623A ILE* 3.9 1.4 - - - -
624A GLU* 2.9 27.8 + - - +
625A LYS* 2.9 37.4 + - - +
627A ILE* 3.8 10.4 - - - +
636A CYS* 1.3 78.2 - - - +
638A GLY* 1.3 59.5 + - - +
650A VAL 3.4 6.7 - - - -
652A ILE* 4.6 2.2 - - - -
701A TYR* 4.0 30.1 - - - -
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Residues in contact with GLY 638 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622A LYS 3.1 14.4 - - - -
624A GLU* 3.9 9.8 + - - -
637A SER* 1.3 77.8 - - - +
639A ARG* 1.3 72.9 + - - -
649A CYS* 3.4 3.3 - - - +
650A VAL* 2.9 33.4 + - - +
652A ILE* 4.2 8.0 - - - +
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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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620A CYS 3.5 1.0 - - - +
621A ILE* 3.5 6.8 - - - +
622A LYS* 2.9 50.9 + - + +
624A GLU* 2.7 54.8 + - - +
638A GLY* 1.3 85.5 - - - -
640A LEU* 1.3 59.7 - - - +
641A LYS* 4.2 0.4 - - + -
647A GLU* 3.2 42.7 + - + +
648A ILE 3.4 2.7 - - - -
649A CYS* 3.6 29.4 - - - +
650A VAL* 4.0 4.2 - - - +
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Residues in contact with LEU 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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616A ILE* 3.8 35.7 - - + -
620A CYS* 3.3 18.4 - - + +
621A ILE* 3.9 8.7 - - + -
639A ARG* 1.3 73.6 - - - +
641A LYS* 1.3 60.8 + - - +
642A VAL* 4.2 16.2 - - + -
646A ARG 4.2 1.6 - - - +
647A GLU* 3.4 2.6 - - - -
648A ILE* 2.9 46.8 + - + +
650A VAL* 3.7 20.8 - - + +
686A GLU* 4.0 33.0 - - + +
698A ILE* 4.9 1.6 - - + -
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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