Contacts of the helix formed by residues 655 - 661 (chain A) in PDB entry 1CEZ
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 ILE 655 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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620A TRP* 4.0 13.5 - - + -
650A VAL 3.4 7.2 + - - +
651A LEU* 3.9 8.5 - - + +
654A THR* 1.3 70.7 - - - +
656A GLN* 1.3 69.1 + - - +
658A ALA* 2.9 4.7 + - - +
659A ILE* 2.9 41.3 + - + +
667A PHE* 3.4 42.8 - - + -
670A PRO* 3.3 31.4 - - + +
673A ALA* 3.8 11.0 - - + -
674A ALA* 3.4 32.1 - - + +
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Residues in contact with GLN 656 (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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379A ARG* 3.5 32.0 + - - +
651A LEU* 2.8 42.6 + - + +
652A GLU* 3.9 10.1 - - + +
655A ILE* 1.3 74.2 - - - +
657A PRO* 1.3 62.6 - - + +
659A ILE* 3.1 18.5 + - - +
660A ASP* 2.5 53.5 + - - +
670A PRO* 6.3 0.6 - - - +
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Residues in contact with PRO 657 (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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632A ARG* 5.3 0.7 - - - +
652A GLU 3.3 15.9 - - - +
653A ASP* 3.2 20.4 - - - +
654A THR* 3.1 21.3 - - - +
656A GLN* 1.3 96.7 - - + +
658A ALA* 1.3 58.3 + - - +
660A ASP* 3.9 8.3 - - + +
661A SER* 3.0 25.7 + - - -
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Residues in contact with ALA 658 (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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623A TYR* 4.0 25.6 - - + +
654A THR 3.1 14.9 + - - +
655A ILE* 2.9 12.0 + - - +
657A PRO* 1.3 74.3 - - - +
659A ILE* 1.3 68.5 + - - +
661A SER* 2.9 21.0 + - - -
663A LYS* 2.9 21.6 + - + +
664A GLY* 4.1 15.0 - - - +
667A PHE* 4.8 0.9 - - + -
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Residues in contact with ILE 659 (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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379A ARG* 5.6 3.6 - - - +
655A ILE* 2.9 37.7 + - + +
656A GLN* 3.4 22.9 - - - +
658A ALA* 1.3 76.1 - - - +
660A ASP* 1.3 65.5 + - - +
662A GLY* 3.1 14.4 + - - +
663A LYS 3.1 11.4 + - - +
664A GLY* 4.0 20.2 - - - +
665A LEU* 6.3 2.5 - - + -
667A PHE 4.9 4.0 - - - +
670A PRO* 4.0 19.3 - - + -
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Residues in contact with ASP 660 (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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379A ARG* 3.0 37.2 + - - +
656A GLN* 2.5 57.3 + - - +
657A PRO* 3.9 8.1 - - + +
659A ILE* 1.3 74.1 - - - +
661A SER* 1.3 57.8 + - - +
662A GLY 3.3 1.6 + - - -
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Residues in contact with SER 661 (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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657A PRO 3.0 14.5 + - - -
658A ALA* 2.9 20.5 + - - -
660A ASP* 1.3 76.4 - - - +
662A GLY* 1.3 56.0 + - - +
663A LYS* 3.3 9.4 + - - +
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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