Contacts of the helix formed by residues 367 - 374 (chain C) in PDB entry 4C1M
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 ALA 367 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C THR* 3.5 11.4 - - - +
241C SER 4.2 1.6 + - - -
244C PRO* 3.8 11.0 - - - +
363C ARG 3.7 6.7 - - - +
364C VAL* 3.0 31.2 + - + +
365C PHE 3.0 1.7 - - - +
366C PHE* 1.3 76.1 - - - +
368C SER* 1.3 63.2 + - - +
369C TRP* 3.1 22.9 - - - +
370C ARG* 3.0 25.1 + - + +
371C VAL 4.1 0.3 + - - -
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Residues in contact with SER 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C CYS* 3.4 21.6 + - - +
230C ILE* 3.4 8.0 + - - +
231C PRO 2.7 28.9 + - - -
233C PHE* 3.5 28.2 - - - -
241C SER* 4.6 4.1 + - - -
244C PRO* 5.7 0.2 - - - -
247C THR* 5.7 2.0 - - - -
366C PHE 3.1 4.4 + - - -
367C ALA* 1.3 75.3 - - - +
369C TRP* 1.3 62.6 + - - +
370C ARG 3.1 0.2 - - - -
371C VAL* 3.1 20.0 + - - +
372C VAL* 3.2 14.9 + - - +
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Residues in contact with TRP 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C CYS 4.9 2.2 - - - -
224C THR* 3.4 27.0 + - - -
225C ASN* 3.4 39.7 - - + +
228C ALA* 3.7 10.8 - - + -
230C ILE* 3.7 32.3 + - + +
363C ARG 5.0 1.0 + - - -
367C ALA* 3.5 16.5 - - - +
368C SER* 1.3 81.9 + - - +
370C ARG* 1.3 88.4 + - + +
372C VAL 3.8 0.9 - - - +
373C LEU* 2.7 38.6 + - + +
374C GLU* 3.4 36.1 - - + -
1630C NAG 3.6 35.7 - - - -
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Residues in contact with ARG 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C PRO* 4.5 8.3 - - + -
343C MET* 4.1 8.1 - - + -
345C ARG* 3.9 14.9 + - - +
356C ASN* 5.6 3.6 - - - +
359C VAL* 3.6 23.1 - - - +
363C ARG* 3.2 37.8 + - - +
364C VAL* 3.8 21.0 - - - +
367C ALA* 3.0 17.4 + - + +
369C TRP* 1.3 106.1 - - + +
371C VAL* 1.3 64.6 + - - +
374C GLU* 2.8 76.8 + - - +
376C GLY 4.6 1.0 + - - +
380C ILE* 5.3 2.8 - - + +
409C GLN* 5.9 0.2 - - - +
1630C NAG 5.0 3.8 + - - +
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Residues in contact with VAL 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C ASP* 5.8 0.2 - - - +
210C LEU* 4.1 18.0 - - + +
233C PHE* 4.3 13.2 - - + -
244C PRO* 3.7 32.5 - - + +
247C THR* 4.0 21.8 - - + -
248C SER* 5.1 0.4 - - - +
251C THR* 5.5 0.4 - - - +
368C SER* 3.1 12.4 + - - +
370C ARG* 1.3 76.6 - - - +
372C VAL* 1.3 61.2 + - - +
376C GLY* 3.0 37.4 + - - -
377C ILE* 3.8 27.4 - - + -
380C ILE* 4.3 5.8 - - + -
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Residues in contact with VAL 372 (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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203C PHE* 3.6 47.2 - - + +
204C GLN 5.5 2.9 - - - +
210C LEU* 4.1 18.6 - - + +
213C PHE* 4.3 9.4 - - + -
230C ILE* 3.9 23.3 - - + -
233C PHE* 3.8 21.5 - - + -
368C SER 3.2 15.0 + - - +
369C TRP 4.1 2.0 - - - +
371C VAL* 1.3 79.2 - - - +
373C LEU* 1.3 65.1 + - + +
375C GLY 5.2 0.9 + - - -
376C GLY 5.4 0.2 + - - -
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Residues in contact with LEU 373 (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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203C PHE* 4.5 12.8 - - + -
228C ALA* 3.7 22.4 - - + +
230C ILE* 4.3 9.9 - - + -
369C TRP* 2.7 25.4 + - + +
372C VAL* 1.3 91.0 - - + +
374C GLU* 1.3 61.0 + - + +
375C GLY 3.8 2.5 + - - -
1630C NAG 3.2 32.3 - - - +
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Residues in contact with GLU 374 (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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345C ARG* 2.7 46.1 + - - +
353C MET* 4.0 14.8 - - + +
356C ASN* 5.6 4.0 + - - +
369C TRP* 3.4 31.9 - - + -
370C ARG* 2.8 48.4 + - - +
373C LEU* 1.3 81.5 - - - +
375C GLY* 1.3 56.6 + - - +
376C GLY 4.0 2.3 + - - +
379C PRO* 5.1 0.5 - - - +
380C ILE* 6.0 0.2 - - - +
1630C NAG 5.1 1.0 - - - +
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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