Contacts of the helix formed by residues 2558 - 2566 (chain B) in PDB entry 6X34
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 ALA2558 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2501B ALA* 4.9 2.7 - - + +
2504B VAL* 3.7 25.5 - - + +
2505B LEU* 3.8 28.0 - - + +
2554B TYR 3.8 1.8 + - - -
2557B LEU* 1.3 81.4 - - + +
2559B VAL* 1.3 66.4 + - - +
2561B PRO* 3.5 10.7 - - - +
2562B LEU* 3.1 24.6 + - - +
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Residues in contact with VAL2559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2504B VAL* 4.7 6.1 - - + -
2527B PHE* 4.0 30.3 - - + -
2554B TYR* 3.5 51.6 - - + +
2555B LEU* 3.3 16.2 + - + +
2558B ALA* 1.3 76.0 - - - +
2560B LEU* 1.3 68.8 + - + +
2562B LEU* 3.2 20.8 + - + +
2563B ILE* 3.3 8.1 + - - +
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Residues in contact with LEU2560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2555B LEU* 2.9 23.0 + - + +
2556B CYS* 3.8 12.1 - - - +
2559B VAL* 1.3 77.6 - - + +
2561B PRO* 1.3 70.6 - - + +
2563B ILE* 3.1 16.0 + - + +
2564B THR* 3.3 16.0 + - - +
2587B VAL* 6.0 4.0 - - + -
2603B VAL* 3.7 22.2 - - + +
2604B ILE* 3.7 43.7 - - + -
2607B CYS* 3.7 29.3 - - + +
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Residues in contact with PRO2561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2556B CYS 4.0 12.3 - - - +
2557B LEU 3.5 18.2 - - - +
2558B ALA* 3.5 17.5 - - - +
2559B VAL 3.8 0.2 - - - +
2560B LEU* 1.3 94.1 - - + +
2562B LEU* 1.3 58.7 + - - +
2564B THR* 2.6 23.3 + - + +
2565B LYS* 3.3 12.1 + - - +
2603B VAL* 4.3 7.9 - - + -
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Residues in contact with LEU2562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2504B VAL* 5.2 7.9 - - + +
2507B LEU* 4.4 20.9 - - + -
2508B ASP* 4.1 26.9 - - + -
2512B GLY* 5.9 4.0 - - - -
2527B PHE* 4.8 22.4 - - + -
2558B ALA 3.1 18.9 + - - +
2559B VAL* 3.3 8.1 - - + +
2560B LEU 3.1 1.0 - - - -
2561B PRO* 1.3 76.4 - - - +
2563B ILE* 1.3 63.0 + - - +
2565B LYS* 3.4 8.4 + - + +
2566B CYS* 3.2 23.8 + - + +
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Residues in contact with ILE2563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2559B VAL 3.3 7.7 + - - +
2560B LEU* 3.1 10.1 + - + +
2562B LEU* 1.3 76.3 - - - +
2564B THR* 1.3 64.8 + - - +
2566B CYS* 3.3 14.4 + - - +
2567B ALA* 3.4 12.6 + - - +
2570B PHE* 6.2 1.5 - - + -
2607B CYS* 4.4 19.5 - - - -
2611B LEU* 4.4 15.2 - - + +
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Residues in contact with THR2564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2560B LEU 3.3 10.2 + - - +
2561B PRO* 2.6 30.9 + - + +
2563B ILE* 1.3 77.2 - - + +
2565B LYS* 1.3 58.2 + - - +
2567B ALA* 3.4 17.2 + - - +
2568B PRO* 5.0 0.3 - - - +
2606B GLU* 4.0 16.8 - - + +
2607B CYS* 4.5 8.1 - - - -
2610B ALA* 3.7 30.1 - - + +
2611B LEU* 5.7 0.2 - - + -
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Residues in contact with LYS2565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2561B PRO 3.3 9.7 + - - +
2562B LEU* 3.8 13.2 - - + +
2563B ILE 3.3 0.2 - - - -
2564B THR* 1.3 81.7 + - - +
2566B CYS* 1.3 56.0 + - - +
2567B ALA 3.3 3.3 + - - -
2568B PRO* 4.0 9.7 - - - +
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Residues in contact with CYS2566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2562B LEU* 3.2 19.4 + - + +
2563B ILE* 3.3 8.6 + - - +
2564B THR 3.3 0.2 - - - -
2565B LYS* 1.3 75.2 - - - +
2567B ALA* 1.3 62.8 + - - +
2568B PRO* 3.5 2.9 - - - -
2569B LEU* 3.4 16.7 + - + -
2570B PHE* 3.1 24.5 + - + +
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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