Contacts of the strand formed by residues 635 - 640 (chain C) in PDB entry 1JZ3
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 635 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630C ARG 3.7 0.5 - - - +
631C LEU* 3.4 5.7 - - - +
632C SER* 2.9 34.8 + - - -
633C GLY 3.4 0.6 - - - -
634C GLN* 1.3 99.5 + - - +
636C ILE* 1.3 64.7 + - - +
637C GLU* 3.9 0.9 + - - +
679C LEU* 4.5 21.3 - - + -
680C ILE 3.5 17.3 - - - +
681C GLU* 4.0 13.9 + - + +
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Residues in contact with ILE 636 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629C PHE* 4.1 13.2 - - + -
630C ARG 3.5 8.1 - - - +
631C LEU* 4.0 15.0 - - + -
635C THR* 1.3 75.0 - - - +
637C GLU* 1.3 71.8 + - - +
638C VAL* 3.9 14.4 + - + -
652C LEU* 4.3 13.9 - - + -
654C TRP* 5.0 0.7 - - + -
678C GLN 3.6 1.4 - - - +
679C LEU* 3.6 2.6 - - - -
680C ILE* 2.8 45.5 + - + +
682C LEU* 3.6 31.4 - - + -
696C LEU* 4.3 7.4 - - + -
698C VAL* 3.8 25.4 - - + -
720C TRP* 4.5 8.7 - - + -
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Residues in contact with GLU 637 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628C GLN 3.6 0.5 - - - +
629C PHE* 3.2 6.8 - - - +
630C ARG* 2.7 82.7 + - + +
635C THR* 3.9 1.7 + - + +
636C ILE* 1.3 73.4 - - - +
638C VAL* 1.3 60.9 - - - +
639C THR* 3.9 7.7 + - - +
677C LYS* 2.7 45.9 + - + +
678C GLN 3.6 5.4 - - - +
679C LEU* 4.0 22.6 - - + +
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Residues in contact with VAL 638 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627C PHE* 4.0 26.5 - - + -
628C GLN 3.4 3.6 - - - -
629C PHE* 3.9 28.0 - - + -
636C ILE* 4.1 7.0 - - + +
637C GLU* 1.3 75.9 - - - +
639C THR* 1.3 63.5 + - - +
652C LEU* 4.6 2.5 - - + -
670C LEU* 4.1 21.8 - - + -
672C VAL* 4.2 7.4 - - + +
677C LYS* 3.1 4.9 - - - +
678C GLN* 2.8 40.6 + - + +
680C ILE* 3.9 27.6 - - + -
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Residues in contact with THR 639 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627C PHE* 3.4 7.8 - - - -
628C GLN* 2.8 47.9 + - + +
637C GLU* 3.9 8.3 + - - -
638C VAL* 1.3 77.2 - - - +
640C SER* 1.3 73.0 + - - +
641C GLU* 3.8 2.9 + - + -
675C GLN 4.8 4.0 - - - +
676C GLY 3.3 11.4 - - - +
677C LYS* 3.5 30.9 - - + +
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Residues in contact with SER 640 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626C PHE 3.7 4.0 - - - -
627C PHE* 4.0 12.2 - - - -
639C THR* 1.3 78.2 - - - +
641C GLU* 1.3 59.7 + - - +
642C TYR* 3.0 33.8 + - - +
645C ARG 4.7 1.0 + - - -
647C SER* 6.0 0.2 - - - -
672C VAL* 3.8 13.6 + - - +
673C ALA 3.4 23.7 + - - -
674C PRO* 3.9 1.4 - - - +
675C GLN* 3.2 27.1 + - - -
676C GLY 2.9 8.7 + - - -
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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