Contacts of the strand formed by residues 641 - 645 (chain N) in PDB entry 1ZYR
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 GLN 641 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636N GLN 5.0 0.3 - - - +
637N LEU* 3.2 29.8 - - + +
638N LYS* 2.5 70.9 + - - +
639N LEU 4.4 0.3 - - - +
640N HIS* 1.3 96.5 - - + +
642N CYS* 1.3 62.7 + - - +
716N PHE* 2.9 21.0 - - - -
717N GLN* 3.7 14.3 - - + +
719N VAL* 4.0 17.4 - - + +
729N HIS* 4.4 7.6 + - - +
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Residues in contact with CYS 642 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637N LEU* 3.7 6.7 - - - +
641N GLN* 1.3 79.2 - - - +
643N GLY* 1.3 67.8 + - - +
644N LEU* 3.4 9.6 + - - -
700N VAL* 4.4 14.4 - - - -
702N LEU* 3.8 22.7 - - + -
716N PHE* 3.4 30.5 - - + -
717N GLN 3.8 3.0 + - - -
718N PRO* 3.8 3.6 - - - +
719N VAL 3.5 16.1 + - - -
726N ILE* 4.9 3.1 - - - -
727N GLN 3.4 12.6 - - - +
728N LEU* 5.1 1.8 - - + +
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Residues in contact with GLY 643 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637N LEU* 3.6 7.8 - - - +
642N CYS* 1.3 71.4 - - - +
644N LEU* 1.3 56.6 + - - -
719N VAL* 3.7 12.6 - - - -
721N VAL* 4.1 4.9 - - - -
726N ILE* 3.3 13.3 - - - +
727N GLN* 2.8 59.1 + - - -
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Residues in contact with LEU 644 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642N CYS* 3.4 9.8 + - - +
643N GLY* 1.3 74.7 - - - +
645N PRO* 1.3 90.0 - - + +
646N LYS 2.8 4.9 + - - -
648N MET* 4.1 26.2 - - + -
649N ALA* 4.5 17.0 - - + +
652N LEU* 4.9 6.3 - - + -
653N PHE* 5.5 3.8 - - + -
695N ILE* 6.0 1.3 - - + -
700N VAL* 4.1 33.0 - - + -
702N LEU* 6.4 0.4 - - + -
718N PRO* 4.5 13.2 - - + -
719N VAL 3.0 13.1 + - - +
720N LEU* 3.5 6.1 - - + +
721N VAL* 3.4 16.4 + - - +
726N ILE* 4.6 9.4 - - + -
747N VAL* 4.7 13.0 - - + -
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Residues in contact with PRO 645 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005M MET* 3.1 24.9 - - + -
643N GLY 4.1 2.7 - - - +
644N LEU* 1.3 93.4 - - + +
646N LYS* 1.3 55.0 + - - +
647N ARG* 2.7 8.7 - - + +
648N MET* 2.4 29.5 + - + +
649N ALA 2.7 10.3 + - - -
721N VAL* 3.3 11.2 - - + +
723N GLY 3.8 6.5 - - - +
724N GLN* 2.6 33.2 - - - +
725N SER 3.6 8.7 - - - +
726N ILE* 3.8 14.1 - - + -
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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