Contacts of the strand formed by residues 661 - 669 (chain A) 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 LYS 661 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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657A ALA* 3.1 1.7 - - - -
658A LEU* 2.7 66.6 + - + +
659A ASP* 3.5 18.8 + - - +
660A GLY* 1.3 72.4 - - - +
662A PRO* 1.3 73.0 - - + +
663A LEU* 3.4 7.3 + - + +
690A SER* 5.3 4.3 + - - -
691A ALA 5.3 3.4 + - - -
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Residues in contact with PRO 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A MET* 3.8 22.7 - - + -
656A VAL 3.9 5.6 - - - +
657A ALA* 4.0 2.7 - - + -
660A GLY 3.1 11.2 - - - +
661A LYS* 1.3 87.0 - - + +
663A LEU* 1.3 65.4 + - - +
664A ALA 5.2 0.2 - - - +
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Residues in contact with LEU 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A VAL* 2.9 14.0 + - + +
658A LEU* 4.4 15.7 - - + +
661A LYS* 3.4 12.8 + - + +
662A PRO* 1.3 83.1 - - - +
664A ALA* 1.3 65.9 + - - +
686A PRO* 3.2 40.7 - - + +
688A PRO* 3.7 26.7 - - + -
694A LEU* 4.0 10.8 - - + -
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Residues in contact with ALA 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654A TRP* 3.5 15.3 - - + -
655A MET* 3.2 4.5 - - - +
656A VAL* 2.8 27.3 + - + -
662A PRO* 5.2 0.4 - - - +
663A LEU* 1.3 83.4 - - - +
665A SER* 1.3 64.6 + - - +
685A LEU* 4.1 16.6 - - + -
686A PRO* 4.2 9.0 - - + -
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Residues in contact with SER 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653A HIS* 5.2 7.7 - - - -
654A TRP* 2.9 35.9 - - - -
655A MET* 3.7 14.3 - - - +
664A ALA* 1.3 80.0 - - - +
666A GLY* 1.3 58.1 + - - +
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Residues in contact with GLY 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653A HIS* 3.4 10.2 + - - -
654A TRP* 2.8 48.8 + - - +
665A SER* 1.3 77.0 - - - +
667A GLU* 1.3 64.7 + - - -
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Residues in contact with GLU 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651A LEU* 4.0 26.0 - - + +
652A LEU 3.1 11.4 - - - +
653A HIS* 3.6 28.9 + - + +
654A TRP* 4.0 1.4 + - - +
666A GLY* 1.3 78.5 - - - +
668A VAL* 1.3 68.3 + - - +
669A PRO* 4.7 0.9 - - - +
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Residues in contact with VAL 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651A LEU* 4.4 2.9 - - - -
652A LEU* 2.7 41.7 + - + +
654A TRP* 4.7 14.8 - - + +
667A GLU* 1.3 80.7 - - - +
669A PRO* 1.3 85.6 - - + +
678A GLN* 4.3 3.6 - - - +
680A ILE* 4.0 40.4 - - + -
681A GLU 6.0 0.2 - - - +
682A LEU* 5.7 0.7 - - + -
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Residues in contact with PRO 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650A GLU 4.5 1.1 - - - +
651A LEU* 4.2 11.2 - - + -
667A GLU 4.7 0.7 - - - +
668A VAL* 1.3 108.4 - - + +
670A LEU* 1.3 61.8 + - - +
671A ASP* 4.0 2.7 + - + +
678A GLN* 3.2 10.2 + - - -
8425A DMS 5.4 12.1 - - + -
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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