Contacts of the helix formed by residues 2361 - 2365 (chain F) 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 LYS2361 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2304F ALA* 5.0 10.8 - - + -
2357F LEU 4.2 6.2 + - - +
2358F LEU 3.0 19.3 + - - +
2359F ILE 3.2 2.0 - - - -
2360F ARG* 1.3 80.0 - - + +
2362F PRO* 1.3 68.1 - - + +
2363F GLU* 3.4 5.7 + - + +
2364F CYS* 3.5 18.3 + - + +
2365F PHE* 4.2 0.5 - - - -
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Residues in contact with PRO2362 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D PHE* 6.5 1.3 - - + -
196D MET* 6.3 5.2 - - + -
2359F ILE 4.7 3.1 - - - +
2360F ARG 3.9 7.0 - - - +
2361F LYS* 1.3 82.8 - - - +
2363F GLU* 1.3 64.8 + - + +
2364F CYS 3.2 1.0 + - - -
2365F PHE* 3.6 25.9 + - + +
2366F GLY 5.5 0.7 - - - +
2370F ARG 5.7 7.5 - - - -
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Residues in contact with GLU2363 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2304F ALA* 4.3 24.4 - - + +
2307F GLY* 5.5 5.2 - - - +
2308F LEU* 5.6 7.6 - - + -
2361F LYS* 3.3 3.9 - - + -
2362F PRO* 1.3 80.7 - - + +
2364F CYS* 1.3 63.3 + - - +
2365F PHE 3.3 9.2 - - - +
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Residues in contact with CYS2364 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2300F VAL* 5.0 6.1 - - + +
2303F LEU* 5.0 8.8 - - + +
2304F ALA* 4.1 27.1 - - + +
2333F LEU* 6.0 1.4 - - - +
2357F LEU 5.8 0.4 - - - +
2358F LEU* 3.3 52.0 - - + +
2361F LYS* 3.5 11.3 + - + +
2362F PRO 3.2 1.0 - - - -
2363F GLU* 1.3 74.8 - - - +
2365F PHE* 1.3 84.0 + - - +
2426F PHE* 5.0 8.5 - - - -
2430F LEU* 4.9 7.4 - - - +
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Residues in contact with PHE2365 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2358F LEU* 3.5 55.9 - - + -
2359F ILE* 4.3 17.7 - - + -
2361F LYS 4.2 3.1 - - - -
2362F PRO* 3.6 19.3 + - + +
2363F GLU* 3.3 11.7 - - - +
2364F CYS* 1.3 87.5 - - - +
2366F GLY* 1.3 69.9 + - - +
2367F PRO* 3.7 2.8 - - - +
2369F LEU* 4.4 8.5 - - + +
2370F ARG* 5.9 4.9 - - + -
2426F PHE* 5.5 2.0 - - - -
2430F LEU* 4.3 15.9 - - + -
2434F LEU* 3.9 25.4 - - + -
2461F LEU* 4.9 22.0 - - + -
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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