Contacts of the helix formed by residues 258 - 263 (chain A) in PDB entry 5L0U
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 HIS 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A ILE* 4.1 29.8 + - + +
177A TYR* 3.6 23.8 - + - -
187A PHE* 3.3 30.8 - + - -
190A ASP* 5.6 3.6 - - - -
257A VAL* 1.3 74.9 - - - +
259A LEU* 1.3 72.5 + - - +
260A VAL* 3.1 32.2 + - + +
261A ASP* 2.9 37.9 + - - +
262A HIS* 3.0 10.7 + - - -
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Residues in contact with LEU 259 (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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177A TYR* 3.0 27.1 + - + +
181A LEU* 4.6 4.3 - - + -
187A PHE* 3.8 17.0 - - + -
191A LEU* 3.9 10.4 - - + +
257A VAL 3.5 0.2 + - - -
258A HIS* 1.3 73.4 + - - +
260A VAL* 1.3 62.3 + - - +
262A HIS* 3.0 45.5 + - + +
279A ARG* 4.3 4.3 - - + -
282A HIS* 3.7 42.0 - - + +
283A LEU* 4.0 17.7 - - + -
286A CYS* 4.0 2.8 - - - -
404A 660 3.5 31.0 - - - +
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A PHE* 4.2 8.5 - - + -
190A ASP* 3.9 35.0 - - + +
191A LEU* 4.0 9.6 - - + -
194A SER* 2.7 33.7 + - - -
198A TRP* 5.6 0.7 + - - -
258A HIS* 3.1 33.5 + - + +
259A LEU* 1.3 76.1 - - - +
261A ASP* 1.3 73.7 + - - +
262A HIS 3.2 1.4 + - - -
263A CYS* 3.5 6.3 + - - +
264A LYS 5.1 0.2 + - - -
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Residues in contact with ASP 261 (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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208A TYR* 5.0 0.2 - - - -
257A VAL* 3.7 17.9 - - + +
258A HIS* 2.9 29.4 + - - +
260A VAL* 1.3 87.4 - - - +
262A HIS* 1.3 62.3 + - - +
263A CYS 3.3 1.1 - - - -
264A LYS* 4.1 21.9 - - - +
265A TYR* 4.2 6.6 - - - -
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Residues in contact with HIS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A TYR* 4.0 27.7 - + - -
209A PHE* 5.7 1.1 - - - -
210A ARG* 4.3 18.2 + - + +
257A VAL* 3.3 31.0 - - + +
258A HIS 3.0 17.2 + - - -
259A LEU* 3.0 37.5 + - + +
261A ASP* 1.3 78.1 - - - +
263A CYS* 1.3 61.9 + - - +
264A LYS 3.2 3.1 - - - -
265A TYR* 3.1 19.5 + - - -
268A LEU* 3.4 31.1 - - + +
279A ARG* 5.2 5.2 + - - -
283A LEU* 4.1 14.6 - - + -
286A CYS* 4.1 2.2 - - - -
404A 660 4.2 6.6 + - - -
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Residues in contact with CYS 263 (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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191A LEU* 3.9 11.4 - - - -
194A SER* 3.3 42.0 - - - +
195A ALA 4.5 1.1 - - - -
198A TRP* 3.7 3.5 - - + +
203A LYS* 2.8 27.3 + - - +
259A LEU 4.1 0.4 - - - -
260A VAL 3.5 6.0 + - - +
261A ASP 3.3 1.8 - - - -
262A HIS* 1.3 77.2 - - - +
264A LYS* 1.3 60.4 + - - +
265A TYR 3.1 2.6 + - - -
286A CYS* 2.0 61.9 - - + +
288A SER* 3.6 3.2 + - - -
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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