Contacts of the helix formed by residues 304 - 310 (chain C) in PDB entry 3D38
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 ASP 304 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144C TYR* 4.6 2.9 - - - +
146C ARG* 3.5 13.8 - - - +
179C TYR* 2.6 42.9 + - - +
190C PHE* 4.1 6.9 - - + -
194C LEU* 4.0 17.7 - - + -
239C SER* 4.8 2.5 - - - +
274C VAL* 4.5 3.8 - - - -
302C GLN 4.2 0.8 + - - -
303C ALA* 1.3 75.3 - - - +
305C CYS* 1.3 66.1 + - - +
306C ARG* 2.8 25.9 + - - +
307C THR* 3.0 26.9 + - - -
404C HEC 3.7 11.8 - - - +
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Residues in contact with CYS 305 (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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194C LEU* 4.5 8.3 - - - -
236C ILE* 4.3 16.4 - - - -
239C SER* 3.8 17.4 + - - +
240C LEU* 4.1 6.1 - - + -
304C ASP* 1.3 73.8 - - - +
306C ARG* 1.3 65.6 - - - +
308C CYS* 3.3 4.5 + - - +
309C HIS* 3.0 26.7 + - - +
404C HEC 1.8 83.9 - - + +
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Residues in contact with ARG 306 (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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144C TYR* 3.4 41.3 - - + -
154C LEU* 3.5 28.0 - - - +
179C TYR* 3.8 25.5 + - - -
235C SER* 4.6 0.4 + - - -
238C ASP* 3.3 30.9 + - - +
239C SER* 3.4 48.7 + - - +
304C ASP* 2.8 11.9 + - - +
305C CYS* 1.3 80.3 - - - +
307C THR* 1.3 63.5 + - - +
308C CYS 2.9 0.3 + - - -
310C GLN* 2.5 45.9 + - - +
311C GLY* 4.8 3.8 - - - +
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Residues in contact with THR 307 (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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134C THR 3.7 4.0 - - - +
135C CYS* 3.9 28.1 - - + -
142C PRO* 4.8 9.0 - - + -
144C TYR* 2.7 31.2 + - + +
145C VAL* 5.3 3.1 - - + -
302C GLN 4.4 0.2 + - - -
303C ALA* 3.4 19.5 - - + -
304C ASP* 3.0 33.2 + - - -
305C CYS 3.2 0.2 - - - -
306C ARG* 1.3 74.2 - - - +
308C CYS* 1.3 60.1 + - - +
310C GLN* 2.9 24.1 + - - -
402C HEC 4.3 4.9 - - + -
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Residues in contact with CYS 308 (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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134C THR* 3.6 18.2 - - + +
135C CYS* 3.7 20.6 - - - -
137C ARG* 3.2 17.5 + - - -
304C ASP 4.4 0.2 + - - -
305C CYS 3.3 2.6 + - - -
306C ARG 3.1 0.6 - - - -
307C THR* 1.3 81.4 - - - +
309C HIS* 1.3 64.7 + - - +
310C GLN* 3.4 0.4 - - - +
315C PRO* 3.1 14.4 - - + +
402C HEC 4.4 1.1 - - - -
404C HEC 1.8 71.3 - - + -
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Residues in contact with HIS 309 (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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34C ARG* 4.6 0.7 + - - -
137C ARG* 4.6 2.1 + - - -
239C SER 3.6 12.8 - - - +
240C LEU* 3.3 11.0 - - + +
305C CYS 3.0 23.7 + - - +
306C ARG 2.9 1.2 + - - -
308C CYS* 1.3 74.3 - - - +
310C GLN* 1.3 75.5 + - - +
311C GLY 3.2 0.4 - - - -
312C VAL* 2.9 32.6 + - - +
313C THR 2.9 25.8 + - - -
315C PRO* 3.5 16.9 - - + +
316C LEU 4.7 0.7 + - - -
404C HEC 2.1 83.8 + + - -
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Residues in contact with GLN 310 (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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31C LYS* 4.7 1.6 - - - +
34C ARG* 3.1 38.6 + - - +
134C THR 3.5 12.5 + - - -
135C CYS 3.7 7.1 + - - -
137C ARG* 3.1 39.8 + - - +
143C PRO* 3.8 9.5 - - - +
144C TYR* 3.6 27.3 - - + +
306C ARG* 2.5 39.0 + - - +
307C THR 2.9 18.2 + - - -
308C CYS 3.4 12.3 - - - +
309C HIS* 1.3 74.0 - - - +
311C GLY* 1.3 58.0 + - - +
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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