Contacts of the strand formed by residues 628 - 632 (chain D) in PDB entry 3P23
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 628 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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608D PHE* 3.9 30.1 - + + -
613D VAL* 3.9 31.5 - - + +
616D LEU* 6.3 3.1 - - + -
626D ILE* 3.7 21.6 + - + +
627D ARG* 1.3 75.7 - - - +
629D PHE* 1.3 69.9 + - - +
630D CYS* 3.6 2.6 - - - +
640D ILE* 4.4 11.0 - - + -
641D ALA 3.6 5.6 - - - +
642D ILE* 3.1 32.1 - - + -
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Residues in contact with PHE 629 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591D PHE* 3.7 34.2 - + + -
594D ARG* 4.5 27.8 - - - -
596D VAL* 3.8 27.1 - - + -
627D ARG* 4.4 29.4 - - + -
628D TYR* 1.3 75.7 - - - +
630D CYS* 1.3 61.5 + - - +
641D ALA* 3.0 20.6 + - + +
643D GLU* 3.5 42.6 - - + -
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Residues in contact with CYS 630 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568D LYS* 4.3 11.4 - - - +
569D ILE* 4.1 21.3 - - - -
591D PHE* 3.3 37.5 - - + -
628D TYR* 3.6 2.4 - - - -
629D PHE* 1.3 81.9 - - - +
631D THR* 1.3 66.0 + - - +
632D GLU* 4.2 11.9 - - - -
640D ILE* 3.8 3.3 - - - +
641D ALA* 3.1 27.9 + - - +
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Residues in contact with THR 631 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569D ILE* 5.1 0.9 - - - -
608D PHE* 5.0 15.3 - - + -
610D ASP* 6.6 0.2 - - - -
630D CYS* 1.3 77.7 - - - +
632D GLU* 1.3 79.7 + - - +
633D LYS* 5.5 0.2 - - - +
638D GLN* 3.8 20.1 + - - +
639D TYR 2.6 22.4 + - - -
640D ILE* 4.0 11.9 - - - +
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Residues in contact with GLU 632 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566D VAL* 2.9 27.5 - - + +
567D GLY 2.9 22.8 - - - +
568D LYS* 2.9 31.8 + - - -
569D ILE* 3.8 19.2 + - + +
630D CYS* 4.2 2.8 - - - -
631D THR* 1.3 83.7 + - - +
633D LYS* 1.3 67.3 + - - +
638D GLN* 3.7 0.5 - - - +
639D TYR* 2.7 41.1 + - + +
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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