Contacts of the strand formed by residues 630 - 636 (chain A) in PDB entry 4NPJ
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 THR 630 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623A LEU* 4.8 0.2 - - - -
626A SER* 4.0 6.2 - - - -
627A GLU* 3.2 13.1 + - - +
628A ASP* 2.9 22.3 + - - +
629A MET* 1.3 75.3 - - - +
631A VAL* 1.3 78.2 + - - +
632A SER* 5.2 5.6 - - - -
649A LYS* 5.3 5.4 - - + -
650A ILE 3.2 13.2 - - - +
651A ALA* 3.2 22.8 - - + +
653A ARG* 4.1 4.0 + - - -
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Residues in contact with VAL 631 (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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618A VAL* 5.8 2.5 - - + -
622A GLN* 5.3 3.1 - - + +
623A LEU* 3.7 23.6 - - + -
626A SER* 3.6 21.3 - - - +
630A THR* 1.3 82.3 - - - +
632A SER* 1.3 61.0 + - - +
633A GLN* 5.0 7.6 - - - +
635A PHE* 3.9 27.4 - - + -
648A MET 4.2 0.5 - - - +
649A LYS* 3.5 1.0 - - - -
650A ILE* 2.8 40.6 + - + +
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Residues in contact with SER 632 (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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630A THR* 5.2 4.7 - - - -
631A VAL* 1.3 75.9 - - - +
633A GLN* 1.3 65.3 + - - +
647A LYS* 6.0 2.9 - - - +
648A MET 3.4 6.0 + - - -
649A LYS* 3.5 34.9 - - - +
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Residues in contact with GLN 633 (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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631A VAL* 5.0 6.9 - - + +
632A SER* 1.3 79.2 + - - +
634A ARG* 1.3 79.6 + - - +
635A PHE* 3.3 47.5 - - + +
636A GLN 5.5 0.4 - - - +
647A LYS* 3.6 6.7 - - - +
648A MET 3.2 29.8 + - - +
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Residues in contact with ARG 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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544A SER* 4.2 5.7 + - - -
545A ALA* 3.9 3.6 - - - +
546A ARG* 3.5 63.6 - - - +
633A GLN* 1.3 90.6 + - - +
635A PHE* 1.3 59.8 + - - +
636A GLN 4.2 0.5 + - - -
645A THR* 3.1 33.8 + - + -
646A ILE 3.6 5.2 - - - -
647A LYS* 3.5 54.5 - - + +
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Residues in contact with PHE 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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616A LEU* 3.5 39.3 - - + -
618A VAL* 4.8 13.7 - - + -
622A GLN* 6.0 1.1 - - - -
631A VAL* 3.9 23.1 - - + -
633A GLN* 3.3 51.8 - - + +
634A ARG* 1.3 72.3 - - - +
636A GLN* 1.3 61.5 + - - +
637A LEU 3.5 0.2 + - - -
645A THR* 3.1 9.1 - - - -
646A ILE* 2.7 44.1 + - + +
648A MET* 4.1 18.4 - - + -
650A ILE* 4.0 21.3 - - + -
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Residues in contact with GLN 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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616A LEU* 3.3 21.6 - - - +
634A ARG 4.2 1.4 + - - -
635A PHE* 1.3 71.4 - - - +
637A LEU* 1.3 69.0 + - - +
638A SER 4.0 0.7 + - - -
642A PRO* 6.0 1.0 - - - +
643A ASN* 5.1 10.9 - - - +
644A SER 3.9 11.7 - - - +
645A THR* 4.1 10.0 - - + +
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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