Contacts of the helix formed by residues 314 - 324 (chain C) in PDB entry 6C9G
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 LEU 314 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C HIS* 3.7 15.0 - - + +
169C LYS* 3.6 44.9 - - + +
172C LEU* 3.7 21.5 - - + -
291C LEU* 3.6 27.1 - - + -
292C VAL* 6.0 0.2 - - + -
296C VAL 4.2 9.2 - - - +
297C HIS* 3.1 39.3 + - + +
313C SER* 1.3 74.2 - - - +
315C SER* 1.3 57.9 + - - +
317C ILE* 3.1 5.7 + - - +
318C LEU* 2.9 36.0 + - + +
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Residues in contact with SER 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ILE* 4.5 8.5 - - - +
150C HIS* 5.5 0.2 - - - -
168C HIS* 3.6 32.1 + - - -
297C HIS* 4.5 1.2 - - - -
313C SER* 2.7 22.4 + - - -
314C LEU* 1.3 79.8 - - - +
316C ASP* 1.3 55.6 + - - +
318C LEU* 4.3 2.8 - - - +
319C GLN* 3.1 29.3 + - - +
1103C AMP 3.2 30.3 + - - -
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Residues in contact with ASP 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C ILE* 4.1 11.6 - - + +
198C GLY* 3.6 27.8 - - - +
199C THR* 4.6 0.5 + - - -
311C ILE 3.7 0.7 - - - +
312C VAL* 4.6 0.9 - - + -
313C SER* 3.0 29.9 + - - +
314C LEU 3.1 0.6 - - - -
315C SER* 1.3 78.2 + - - +
317C ILE* 1.3 58.4 + - - +
319C GLN* 3.1 14.5 + - - +
320C ALA* 3.0 26.3 + - - +
1103C AMP 2.6 44.8 + - - -
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Residues in contact with ILE 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C LEU* 4.6 15.0 - - + -
197C ILE* 4.5 4.3 - - + -
284C LEU* 4.6 11.4 - - + -
287C ILE* 4.3 7.6 - - + -
288C ILE* 3.7 41.5 - - + -
291C LEU* 3.6 31.9 - - + -
312C VAL* 3.8 17.7 - - + -
313C SER 3.2 8.5 + - - +
314C LEU* 3.1 8.4 + - - +
316C ASP* 1.3 73.1 - - - +
318C LEU* 1.3 62.1 + - - +
320C ALA* 3.1 10.1 + - + +
321C LEU* 3.0 35.3 + - + +
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Residues in contact with LEU 318 (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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32C MET* 5.1 2.5 - - + +
141C VAL* 4.2 20.3 - - + +
144C LEU* 5.4 1.6 - - + -
145C ILE* 4.5 2.2 - - + -
168C HIS* 3.9 46.0 - - + +
171C ILE* 4.4 20.0 - - + -
172C LEU* 4.1 36.6 - - + +
175C LEU* 5.0 10.8 - - + -
314C LEU* 2.9 17.6 + - + +
315C SER* 4.3 3.6 - - - +
317C ILE* 1.3 77.6 - - + +
319C GLN* 1.3 54.2 + - - +
321C LEU* 4.1 6.0 - - + +
322C VAL* 2.7 39.1 + - - +
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Residues in contact with GLN 319 (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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145C ILE* 3.6 34.5 - - + +
315C SER 3.1 21.7 + - - +
316C ASP* 3.1 13.4 + - - +
318C LEU* 1.3 76.1 - - - +
320C ALA* 1.3 61.4 + - - +
322C VAL* 3.2 21.9 - - + +
323C LEU* 3.3 20.0 + - + +
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Residues in contact with ALA 320 (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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197C ILE* 3.9 31.6 - - + -
284C LEU* 5.5 0.7 - - + -
316C ASP 3.0 11.5 + - - +
317C ILE* 3.1 10.5 + - - +
319C GLN* 1.3 78.8 - - - +
321C LEU* 1.3 65.6 + - + +
324C THR* 2.8 45.7 + - - +
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Residues in contact with LEU 321 (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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26C SER* 4.6 5.5 + - - -
28C TYR* 4.1 31.6 - - + +
29C THR* 3.2 20.6 + - - -
32C MET* 3.5 15.4 - - + +
172C LEU* 4.9 5.4 - - + -
175C LEU* 4.7 13.2 - - + -
179C ILE* 4.2 24.5 - - + -
187C PHE* 6.2 2.9 - - + -
188C MET* 5.4 1.8 - - - -
284C LEU* 4.5 21.5 - - + -
288C ILE* 4.3 6.5 - - + -
317C ILE* 3.0 29.3 + - + +
318C LEU* 4.1 7.0 - - + +
320C ALA* 1.3 79.8 - - + +
322C VAL* 1.3 58.6 + - - +
323C LEU 4.8 0.2 - - - -
324C THR* 4.7 2.9 - - - -
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Residues in contact with VAL 322 (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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29C THR* 3.2 14.0 + - - +
32C MET* 3.7 8.7 - - + +
138C PHE* 3.3 36.7 - - + -
141C VAL* 3.7 22.7 - - + -
142C SER* 4.3 12.6 - - - +
145C ILE* 3.8 12.8 - - + -
318C LEU 2.7 24.1 + - - +
319C GLN* 3.2 21.3 - - + +
321C LEU* 1.3 74.3 - - - +
323C LEU* 1.3 66.0 + - + +
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Residues in contact with LEU 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C SER* 4.7 2.1 - - - -
29C THR* 4.6 3.1 + - - -
319C GLN* 3.3 21.2 + - + +
322C VAL* 1.3 86.0 - - + +
324C THR* 1.3 74.5 + - - +
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Residues in contact with THR 324 (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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25C ASN 5.3 0.5 - - - +
26C SER* 3.5 28.5 + - - -
187C PHE* 3.3 43.8 - - + -
320C ALA* 2.8 33.3 + - - +
321C LEU* 4.8 3.8 - - + -
323C LEU* 1.3 86.0 - - - +
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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