Contacts of the helix formed by residues 311 - 316 (chain C) in PDB entry 6N0M
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 311 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129C VAL* 6.2 0.2 - - - -
133C MET* 4.2 18.3 - - - +
146C LEU 5.4 1.0 - - - +
310C PRO* 1.3 80.0 - - - +
312C MET* 1.3 70.4 + - + +
313C LEU* 2.9 14.1 + - - +
314C CYS* 3.2 21.7 + - - -
315C PHE* 4.0 14.6 - - - -
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Residues in contact with MET 312 (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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121C ALA* 3.9 16.3 - - + +
124C GLN* 3.8 43.7 - - + +
125C CYS 3.8 2.2 - - - -
126C SER* 3.8 30.1 - - - +
129C VAL* 3.8 32.1 - - + -
310C PRO* 3.5 25.7 - - + -
311C ASP* 1.3 90.6 - - + +
313C LEU* 1.3 56.8 + - - +
314C CYS 3.1 1.1 - - - -
315C PHE* 2.9 33.8 + - + +
316C VAL* 4.5 1.0 - - - +
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Residues in contact with LEU 313 (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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124C GLN* 3.9 25.8 - - - +
310C PRO* 3.5 31.9 - - + +
311C ASP 2.9 3.3 + - - +
312C MET* 1.3 76.4 - - - +
314C CYS* 1.3 55.5 + - - +
315C PHE 3.1 4.9 + - - -
316C VAL* 3.4 29.7 - - + +
319C PRO* 3.8 35.3 - - + +
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Residues in contact with CYS 314 (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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146C LEU 5.3 0.9 - - - -
147C LEU 3.8 17.0 - - - +
148C GLY* 3.0 13.7 - - - -
149C LEU* 2.5 36.2 + - - +
150C HIS* 4.4 9.8 + - + +
311C ASP* 3.2 26.9 + - - -
312C MET 3.0 0.8 + - - -
313C LEU* 1.3 75.6 - - - +
315C PHE* 1.3 62.6 + - - +
316C VAL 3.6 2.0 - - - -
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Residues in contact with PHE 315 (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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114C TYR* 3.3 38.6 - + - -
117C ILE* 3.9 26.7 - - + -
118C MET* 4.0 18.3 - - + +
121C ALA* 3.6 13.9 - - + -
129C VAL* 4.8 2.5 - - + -
133C MET* 4.3 17.0 - - + -
145C TRP 3.6 11.0 - - - -
146C LEU* 3.4 28.5 - - + -
148C GLY* 3.9 5.8 - - - -
149C LEU* 3.2 22.1 - - + +
160C SER* 4.6 1.4 + - - -
163C ASN* 5.1 1.4 + - - -
311C ASP* 4.0 19.5 - - - -
312C MET* 2.9 29.8 + - + +
314C CYS* 1.3 84.3 - - - +
316C VAL* 1.3 64.1 + - - +
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Residues in contact with VAL 316 (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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118C MET 4.6 0.2 - - - +
121C ALA* 3.6 34.1 - - + +
122C ARG* 3.7 27.6 - - - +
149C LEU* 3.7 6.7 - - - +
160C SER* 4.7 2.0 - - - -
163C ASN* 6.1 0.4 - - - +
312C MET 4.5 2.7 - - - +
313C LEU* 3.4 25.4 - - + +
314C CYS* 3.6 1.8 - - - -
315C PHE* 1.3 86.2 - - - +
317C GLU* 1.3 59.4 + - - +
318C ASP 4.0 0.7 + - - -
319C PRO* 3.6 37.7 - - + +
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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