Contacts of the strand formed by residues 627 - 632 (chain B) 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 PHE 627 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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625B GLN* 3.9 12.0 + - - +
626B PHE* 1.3 84.9 - - + +
628B GLN* 1.3 70.1 + - - +
629B PHE* 3.6 31.4 - - + -
638B VAL* 3.8 21.8 - - + -
639B THR 3.3 8.1 - - - +
640B SER* 4.0 18.8 - - - -
642B TYR* 3.8 29.4 - + - -
647B SER* 3.8 26.2 - - - -
650B GLU* 3.9 21.1 - - + -
670B LEU* 4.0 10.5 - - + -
672B VAL* 4.6 4.7 - - + -
700B VAL* 4.2 19.5 - - + -
715B SER* 4.7 4.9 - - - -
716B ALA* 4.5 7.6 - - + -
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Residues in contact with GLN 628 (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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557B ARG* 3.3 20.5 + - - +
625B GLN 3.6 2.3 - - - +
627B PHE* 1.3 79.2 - - - +
629B PHE* 1.4 66.1 + - - +
637B GLU 3.5 0.4 - - - +
638B VAL* 3.4 4.3 - - - +
639B THR* 2.9 43.6 + - + +
641B GLU* 3.1 38.6 - - + +
8402B DMS 2.7 45.6 + - - +
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Residues in contact with PHE 629 (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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625B GLN* 4.1 14.6 - - - -
627B PHE* 3.6 24.2 - - + -
628B GLN* 1.4 79.4 - - - +
630B ARG* 1.3 69.8 + - - +
636B ILE* 4.3 7.0 - - + -
637B GLU* 3.0 7.2 - - - +
638B VAL* 4.0 26.0 - - + -
652B LEU* 3.7 24.0 - - + -
698B VAL* 4.1 13.5 - - + -
700B VAL* 3.8 21.5 - - + -
716B ALA* 4.4 3.6 - - + -
717B TRP 4.2 5.6 - - - -
718B GLN* 3.7 28.4 + - + +
720B TRP* 3.6 25.5 + + + -
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Residues in contact with ARG 630 (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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629B PHE* 1.3 79.2 - - - +
631B LEU* 1.3 63.1 + - - +
635B THR 3.7 0.3 - - - +
636B ILE* 3.4 5.5 - - - +
637B GLU* 2.5 82.1 + - + +
677B LYS* 4.2 6.9 - - - +
720B TRP* 4.1 7.0 - - - +
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Residues in contact with LEU 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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630B ARG* 1.3 79.1 - - - +
632B SER* 1.3 64.5 + - - +
633B GLY 3.8 20.2 - - - +
635B THR 3.1 15.0 - - - +
636B ILE* 3.8 21.1 - - + -
682B LEU* 4.8 3.8 - - + -
696B LEU* 4.0 11.9 - - + -
720B TRP* 3.7 39.7 - - + +
721B ARG 5.2 1.6 - - - +
722B LEU* 3.7 29.8 - - + -
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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
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631B LEU* 1.3 75.1 - - - +
633B GLY* 1.3 58.4 + - - +
634B GLN 3.0 0.7 + - - -
635B THR* 2.5 52.3 + - - -
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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