Contacts of the helix formed by residues 582 - 588 (chain C) in PDB entry 2CKJ
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 ALA 582 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580C HIS* 2.5 18.9 + - + +
581C LEU* 1.3 72.3 - - + +
583C ALA* 1.3 61.6 + - - -
584C ASP 3.2 3.4 - - - -
585C MET* 3.6 23.1 + - + +
586C GLN* 3.0 33.4 + - - +
794C ARG* 3.7 26.0 - - - +
757D GLU* 5.2 1.1 - - - +
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Residues in contact with ALA 583 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C ALA* 3.6 30.8 - - + +
111C SER* 4.3 20.8 - - - +
579C PRO* 5.7 1.8 - - + -
580C HIS* 2.9 20.6 + - + +
581C LEU 3.8 0.2 - - - -
582C ALA* 1.3 77.9 - - - +
584C ASP* 1.3 64.5 + - - +
586C GLN* 3.7 10.1 - - - +
587C ALA* 2.9 24.3 + - - +
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Residues in contact with ASP 584 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C THR* 4.0 17.5 - - + +
98C LEU* 4.0 22.7 - - + +
103C GLU* 5.2 1.7 - - - +
106C ALA* 3.6 21.3 - - - +
107C LYS* 5.1 5.9 + - - +
582C ALA 3.2 1.0 - - - -
583C ALA* 1.3 77.2 - - - +
585C MET* 1.3 57.3 + - + +
587C ALA* 3.0 6.1 + - - +
588C SER* 2.7 36.4 + - - -
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Residues in contact with MET 585 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C THR* 4.1 22.2 - - + +
581C LEU 4.0 7.0 - - - +
582C ALA* 3.6 33.9 - - + +
584C ASP* 1.3 79.7 - - + +
586C GLN* 1.3 63.9 + - - +
588C SER* 3.7 7.9 - - - -
589C GLY 3.4 1.0 + - - -
590C GLU* 3.2 29.5 + - + -
591C ALA* 3.2 17.4 + - + +
794C ARG* 6.2 0.2 - - - +
757D GLU* 3.3 40.6 - - + +
758D ALA* 4.1 14.6 - - + -
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Residues in contact with GLN 586 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C SER* 3.4 14.6 + - - +
112C GLN 3.0 20.1 + - - +
113C CYS 3.9 8.6 + - - -
114C GLY* 3.1 30.4 - - - +
117C THR* 4.3 2.7 - - - -
118C PRO* 4.2 9.2 - - - +
580C HIS* 4.0 15.7 + - - -
582C ALA* 3.0 34.2 + - + +
583C ALA* 3.7 5.6 - - - +
584C ASP 3.1 0.2 - - - -
585C MET* 1.3 74.8 - - - +
587C ALA* 1.3 59.2 + - - +
588C SER 3.2 4.2 + - - -
589C GLY* 3.3 11.1 + - - -
591C ALA* 3.9 17.8 - - + +
593C TYR* 4.5 2.7 - - - +
794C ARG* 3.7 28.1 - - - +
1038C GLU* 6.1 1.2 - - - +
1040C GLY* 6.1 0.2 - - - -
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Residues in contact with ALA 587 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C VAL* 4.2 7.8 - - - +
98C LEU* 6.1 0.7 - - + -
102C GLN* 3.2 45.5 + - + +
105C ILE* 4.2 8.1 - - + -
106C ALA* 4.3 5.4 - - + -
111C SER* 5.6 0.9 - - - +
117C THR* 3.5 23.3 - - + +
118C PRO* 5.5 0.9 - - - -
121C VAL* 4.3 6.4 - - + +
583C ALA 2.9 17.5 + - - +
584C ASP* 3.0 4.2 + - - +
586C GLN* 1.3 74.9 - - - +
588C SER* 1.3 60.1 + - - +
589C GLY 3.3 0.6 + - - -
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Residues in contact with SER 588 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C VAL* 4.3 9.6 - - - +
89C GLU* 4.7 8.0 - - - +
92C GLY 4.3 11.6 - - - +
93C SER* 5.4 0.2 - - - -
94C THR* 4.2 1.3 - - - +
98C LEU* 4.1 19.7 - - - -
102C GLN* 3.6 15.0 + - - +
584C ASP 2.7 15.9 + - - -
585C MET* 3.4 1.8 + - - -
586C GLN 3.1 0.6 - - - -
587C ALA* 1.3 82.1 - - - +
589C GLY* 1.3 56.3 + - - +
590C GLU* 2.7 48.3 + - - +
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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