Contacts of the strand formed by residues 630 - 636 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623B LEU* 4.6 0.4 - - - -
626B SER* 3.8 7.7 - - - -
627B GLU 3.2 14.1 + - - +
628B ASP* 2.7 24.7 + - - +
629B MET* 1.3 75.9 - - - +
631B VAL* 1.3 77.1 + - - +
632B SER* 4.9 1.6 - - - +
649B LYS* 4.2 25.4 - - + -
650B ILE 3.2 16.8 - - - +
651B ALA* 3.3 17.8 - - + +
653B ARG* 4.2 3.3 + - - -
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Residues in contact with VAL 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618B VAL* 6.0 1.8 - - + -
622B GLN* 5.3 3.1 - - + +
623B LEU* 3.5 24.9 - - + +
626B SER* 3.6 20.2 - - - +
630B THR* 1.3 81.2 - - - +
632B SER* 1.3 61.2 + - - +
633B GLN* 4.2 11.2 - - - +
635B PHE* 4.1 24.7 - - + -
648B MET 4.0 1.4 - - - +
649B LYS* 3.6 1.0 - - - -
650B ILE* 2.9 40.0 + - + +
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Residues in contact with SER 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B THR* 5.3 1.3 - - - -
631B VAL* 1.3 75.9 - - - +
633B GLN* 1.3 64.8 + - - +
647B LYS* 5.0 8.7 + - - +
648B MET 3.4 6.5 + - - -
649B LYS* 3.6 32.4 - - - +
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Residues in contact with GLN 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631B VAL* 4.2 10.6 - - - +
632B SER* 1.3 77.2 + - - +
634B ARG* 1.3 72.6 + - - +
635B PHE* 3.4 40.7 - - + +
647B LYS* 3.6 10.7 - - - +
648B MET 3.2 30.1 + - - +
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Residues in contact with ARG 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A LYS* 6.3 0.4 - - - +
546B ARG* 3.0 51.6 - - - +
633B GLN* 1.3 87.0 + - - +
635B PHE* 1.3 61.4 + - - +
636B GLN* 4.1 3.6 + - - +
645B THR* 4.0 26.5 - - + +
646B ILE 3.7 3.1 - - - -
647B LYS* 4.2 43.4 - - + +
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Residues in contact with PHE 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616B LEU* 3.7 36.1 - - + -
618B VAL* 4.3 24.5 - - + -
622B GLN* 5.8 1.8 - - - -
631B VAL* 4.1 22.2 - - + -
633B GLN* 3.4 48.9 - - + +
634B ARG* 1.3 72.7 - - - +
636B GLN* 1.3 62.0 + - - +
637B LEU 3.8 0.2 + - - -
645B THR* 3.1 5.7 - - - -
646B ILE* 2.9 42.6 + - + +
648B MET* 4.0 25.4 - - + -
650B ILE* 4.1 10.8 - - + -
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Residues in contact with GLN 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616B LEU* 3.6 18.7 - - - +
634B ARG 4.1 3.1 + - - +
635B PHE* 1.3 73.4 - - - +
637B LEU* 1.3 64.2 + - - +
638B SER* 3.5 6.6 + - - -
643B ASN* 6.3 1.3 - - - -
644B SER 3.7 5.8 - - - +
645B THR* 4.4 14.0 - - + +
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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