Contacts of the helix formed by residues 230 - 235 (chain A) in PDB entry 4F5G
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 GLY 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A GLY* 3.8 6.7 - - - -
228A GLY 3.7 0.8 - - - -
229A ARG* 1.3 78.6 - - - +
231A LEU* 1.3 61.2 + - - -
232A GLU 3.4 2.0 - - - -
233A GLU* 4.0 5.4 - - - +
234A ASP* 2.8 33.5 + - - -
325A ARG* 3.7 22.4 - - - +
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Residues in contact with LEU 231 (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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91A LEU* 4.3 8.3 - - + -
225A GLN* 3.0 62.2 + - + +
226A GLY* 3.9 4.5 - - - +
230A GLY* 1.3 73.9 - - - +
232A GLU* 1.3 68.0 + - + +
235A ALA 3.4 8.0 + - - -
257A ASN* 4.9 2.0 - - - +
314A ARG* 4.1 12.3 - - - +
317A TRP* 3.6 35.7 - - + -
318A GLU* 4.0 22.0 - - + +
321A LEU* 3.7 18.8 - - + -
325A ARG* 4.8 1.4 - - - +
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Residues in contact with GLU 232 (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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90A GLU 5.1 1.0 - - - +
91A LEU* 4.4 3.5 - - - +
94A GLY* 4.6 5.6 - - - -
95A LYS 5.6 0.5 + - - -
225A GLN* 5.1 0.2 + - - -
230A GLY 3.4 0.2 - - - -
231A LEU* 1.3 84.7 - - + +
233A GLU* 1.3 66.2 + - + +
235A ALA* 3.1 13.5 + - - +
236A GLU* 3.4 11.7 + - - +
239A ARG* 2.7 48.1 + - - +
314A ARG* 5.9 0.7 + - - -
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Residues in contact with GLU 233 (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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229A ARG* 3.2 79.6 + - + +
230A GLY* 3.4 5.6 + - - +
231A LEU 3.4 0.2 - - - -
232A GLU* 1.3 79.4 - - + +
234A ASP* 1.3 58.7 + - - +
236A GLU* 3.1 36.3 + - - +
237A GLY 4.8 0.2 + - - -
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Residues in contact with ASP 234 (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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189A GLY 3.5 20.8 - - - +
190A CYS* 3.6 25.0 - - - +
222A ILE* 4.0 7.1 - - - +
224A TYR 3.6 1.7 - - - +
225A GLN* 4.1 5.6 - - + -
226A GLY* 2.7 29.0 + - - +
227A PHE 3.1 0.9 + - - -
228A GLY* 2.8 23.9 + - - -
229A ARG* 2.7 27.6 + - - +
230A GLY 2.8 23.9 + - - +
231A LEU 4.0 2.0 - - - +
233A GLU* 1.3 74.2 - - - +
235A ALA* 1.3 58.9 + - - +
236A GLU 3.3 0.6 + - - -
237A GLY 4.6 1.4 + - - -
238A LEU* 5.2 0.7 + - - +
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Residues in contact with ALA 235 (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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92A LEU* 3.7 9.2 - - - +
222A ILE* 4.8 4.3 - - + -
225A GLN* 3.5 25.4 - - - +
231A LEU 3.4 2.4 + - - -
232A GLU 3.1 8.0 + - - +
233A GLU 3.1 1.2 - - - -
234A ASP* 1.3 74.2 - - - +
236A GLU* 1.3 65.4 + - - +
237A GLY 3.2 2.9 - - - -
238A LEU* 3.3 9.7 + - + +
239A ARG* 2.8 49.4 + - - +
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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