Contacts of the helix formed by residues 229 - 234 (chain C) in PDB entry 7A62
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 VAL 229 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C ARG* 4.1 14.6 - - + +
156C ASP 5.9 0.4 - - - +
157C GLY 4.2 4.7 - - - +
158C ASP* 3.8 29.4 - - + -
225C ALA* 2.8 35.0 + - - +
227C PHE 3.6 0.2 - - - -
228C SER* 1.3 83.8 - - - +
230C LEU* 1.3 66.0 + - - +
231C ARG 3.3 0.9 - - - -
232C ILE* 3.0 13.5 + - - +
233C TYR* 3.3 30.9 - - + -
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Residues in contact with LEU 230 (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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154C PHE* 3.9 29.4 - - + -
158C ASP* 3.3 26.7 - - - +
159C CYS* 4.1 1.1 - - + +
160C SER* 3.9 22.0 - - - -
163C PHE* 3.7 41.7 - - + -
164C PHE* 4.5 4.3 - - + -
225C ALA 3.1 8.3 + - - +
226C PHE* 4.0 15.7 - - + +
229C VAL* 1.3 79.0 - - - +
231C ARG* 1.3 64.6 + - - +
233C TYR* 3.1 13.2 + - - -
234C LEU* 3.2 21.8 + - + +
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Residues in contact with ARG 231 (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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226C PHE* 2.8 40.0 + - + +
227C PHE* 2.5 63.5 + - - +
230C LEU* 1.3 73.1 - - - +
232C ILE* 1.3 84.9 + - - +
234C LEU* 3.3 14.8 + - - +
235C SER* 3.0 24.8 + - - +
354C ILE* 3.8 27.2 - - + +
362C PRO* 5.9 1.6 - - - +
363C LYS* 4.4 4.0 - - - +
374C LEU* 6.2 1.6 - - - +
375C GLU 4.2 17.0 + - - -
376C ALA* 4.6 8.7 + - - +
377C LYS* 5.9 5.3 - - - +
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Residues in contact with ILE 232 (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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92C TRP* 3.4 25.3 - - + -
95C GLY* 3.8 30.5 - - - +
228C SER 3.8 8.1 - - - +
229C VAL* 3.0 11.7 + - - +
231C ARG* 1.3 99.7 - - - +
233C TYR* 1.3 66.7 + - + +
235C SER* 3.3 21.1 + - - +
242C GLN* 5.5 6.5 - - - +
363C LYS* 3.7 36.1 - - + +
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Residues in contact with TYR 233 (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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50C ILE* 4.0 10.8 - - + -
88C MET* 3.3 45.1 - - - +
89C ALA* 4.4 4.7 - - - -
92C TRP* 3.9 15.0 - - + -
93C GLY 2.8 28.6 + - - -
94C LYS 3.3 4.2 - - - -
95C GLY* 4.3 7.2 - - - -
154C PHE* 3.8 43.8 - + + -
155C ARG* 3.1 47.9 + - + -
229C VAL* 3.3 30.1 - - + -
230C LEU* 3.1 6.9 + - - +
232C ILE* 1.3 83.8 - - + +
234C LEU* 1.3 60.7 + - - +
235C SER 3.2 1.3 - - - -
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Residues in contact with LEU 234 (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 MET* 4.0 4.7 - - - +
124C LEU* 3.7 28.9 - - + -
129C CYS* 4.2 13.2 - - - -
154C PHE* 4.4 9.2 - - + -
163C PHE* 4.1 24.9 - - + -
164C PHE* 4.5 5.6 - - + -
226C PHE* 4.9 7.0 - - + -
230C LEU* 3.2 32.1 + - + +
231C ARG* 3.3 9.3 + - - +
233C TYR* 1.3 78.3 - - - +
235C SER* 1.3 61.3 + - - +
261C GLY* 3.2 2.1 - - - -
262C GLY* 2.9 46.5 + - - +
263C SER* 5.3 3.4 - - - +
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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