Contacts of the strand formed by residues 650 - 655 (chain N) in PDB entry 1CZA
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 ASP 650 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595N ARG* 3.9 32.1 + - + +
596N MET 3.0 17.0 + - - +
597N PRO* 3.3 8.6 - - + +
598N LEU* 2.7 31.7 + - - -
638N ARG* 5.6 0.5 + - - -
649N LEU* 1.3 73.5 - - - +
651N VAL* 1.3 56.7 + - - +
652N VAL* 3.2 10.1 + - - +
909N VAL* 4.9 0.3 - - - +
912N ARG* 2.5 48.9 + - - -
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Residues in contact with VAL 651 (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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598N LEU* 3.6 25.8 - - + +
600N PHE* 4.7 2.2 - - + -
612N ASP* 4.1 3.1 - - - +
634N VAL* 3.7 30.1 - - + -
637N LEU* 4.0 25.1 - - + -
638N ARG* 3.0 41.6 + - + +
641N ILE* 4.6 12.8 - - + -
649N LEU* 3.7 7.9 + - + +
650N ASP* 1.3 73.5 + - - +
652N VAL* 1.3 62.3 - - - +
653N ALA 4.2 13.5 - - - +
912N ARG* 4.6 1.6 + - - -
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Residues in contact with VAL 652 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597N PRO* 4.0 7.9 - - + -
598N LEU 3.0 5.5 + - - -
611N LEU* 3.9 8.0 - - - +
612N ASP* 3.4 18.9 - - - +
650N ASP* 3.5 19.7 - - - +
651N VAL* 1.3 74.2 - - - +
653N ALA* 1.3 61.2 - - + +
905N THR* 3.7 34.5 - - + +
908N GLY* 3.8 11.4 - - - -
909N VAL* 3.8 26.9 - - + +
912N ARG* 3.3 28.0 - - - +
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Residues in contact with ALA 653 (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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598N LEU 3.7 2.3 + - - +
599N GLY* 3.6 1.1 - - - -
600N PHE* 2.7 34.7 + - - +
611N LEU* 3.3 31.6 - - + -
612N ASP* 4.1 2.4 - - - +
634N VAL* 5.2 0.2 - - - -
651N VAL* 3.5 7.7 - - - +
652N VAL* 1.3 86.2 - - + +
654N VAL* 1.3 57.0 + - - +
655N VAL* 4.1 13.0 - - + -
904N ILE* 4.2 7.2 - - + -
905N THR* 4.6 12.6 - - - +
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Residues in contact with VAL 654 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514N SER 4.9 0.9 - - - +
600N PHE* 3.2 15.0 - - + +
602N PHE* 3.9 23.3 - - + +
606N CYS* 5.1 5.2 - - + -
608N GLN* 3.3 38.9 + - - +
611N LEU* 2.9 16.2 + - - +
612N ASP* 4.4 0.6 - - - +
613N ALA 4.0 2.0 - - - +
614N GLY* 4.0 22.2 - - - +
633N VAL* 4.0 17.0 - - + -
634N VAL* 4.0 16.2 - - + -
653N ALA* 1.3 73.4 - - - +
655N VAL* 1.3 66.8 + - - +
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Residues in contact with VAL 655 (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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514N SER* 6.4 1.3 - - - -
516N VAL* 5.6 1.8 - - + -
599N GLY 5.5 0.4 - - - -
600N PHE 2.8 15.9 + - - +
601N THR* 3.2 17.0 - - - +
602N PHE 2.9 27.6 + - - -
608N GLN* 4.9 2.0 - - - -
611N LEU* 5.2 2.0 - - + -
653N ALA* 4.1 11.0 - - + +
654N VAL* 1.3 80.9 - - - +
656N ASN* 1.4 74.5 + - - +
659N VAL* 4.5 4.5 - - + -
660N GLY* 3.7 17.0 - - - +
901N ALA* 4.8 8.7 - - + +
904N ILE* 3.7 39.9 - - + -
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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