Contacts of the helix formed by residues 362 - 367 (chain C) in PDB entry 4QGC
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 SER 362 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C THR* 3.4 11.8 - - - -
73C ARG* 3.8 9.1 + - - -
328C THR* 4.5 16.1 + - - +
332C GLU* 4.6 10.3 - - - -
360C MET* 3.7 19.8 + - - +
361C LEU* 1.3 71.5 - - - +
363C GLY* 1.3 67.4 + - - -
364C GLU* 2.7 13.9 + - - -
365C THR* 3.2 8.0 + - - -
366C ALA* 3.0 22.5 + - - +
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Residues in contact with GLY 363 (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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332C GLU* 4.9 2.2 + - - -
335C ILE* 3.7 18.8 - - - +
362C SER* 1.3 78.3 - - - +
364C GLU* 1.3 62.1 + - - +
365C THR 3.1 0.2 - - - -
366C ALA* 3.7 9.2 - - - -
367C LYS* 3.1 19.5 + - - +
368C GLY* 2.9 27.5 + - - -
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Residues in contact with GLU 364 (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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330C MET* 3.9 3.8 - - - +
331C LEU* 2.9 53.6 + - + +
332C GLU* 3.6 18.4 - - - +
334C MET* 4.7 5.2 - - + +
335C ILE* 3.8 13.6 - - + +
361C LEU* 3.6 17.0 - - + +
362C SER* 2.7 27.5 + - - -
363C GLY* 1.3 77.8 + - - +
365C THR* 1.3 59.4 + - - +
368C GLY* 4.1 7.8 - - - -
370C TYR 4.0 4.3 - - - +
371C PRO* 3.4 21.0 - - - +
374C ALA* 3.8 19.1 - - + -
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Residues in contact with THR 365 (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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49C CYS* 4.1 2.7 - - + -
50C THR 2.7 34.8 + - - -
54C ALA* 4.1 0.9 - - - +
55C SER* 2.6 32.2 + - - -
64C MET* 3.9 14.6 - - + -
361C LEU* 3.8 32.0 + - + -
362C SER 3.2 5.9 + - - -
364C GLU* 1.3 79.7 - - - +
366C ALA* 1.3 58.6 + - - +
367C LYS 3.6 0.4 - - - -
368C GLY 4.8 0.4 - - - -
371C PRO* 3.9 17.1 - - - +
374C ALA* 4.2 0.9 - - + -
375C VAL* 3.9 20.6 - - + -
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Residues in contact with ALA 366 (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 THR* 3.2 27.1 + - + -
52C GLY* 3.2 22.2 - - - +
53C PRO* 3.2 4.3 - - + +
54C ALA* 3.1 22.5 + - - -
362C SER 3.0 17.5 + - - +
363C GLY* 4.0 6.7 - - - -
365C THR* 1.3 78.7 - - - +
367C LYS* 1.3 62.8 + - + +
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Residues in contact with LYS 367 (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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53C PRO* 5.0 9.9 - - + -
54C ALA* 3.9 7.2 - - - +
207C LYS* 5.4 8.3 - - - +
335C ILE* 4.5 22.2 - - + +
363C GLY* 3.1 15.6 + - - +
366C ALA* 1.3 79.6 - - + +
368C GLY* 1.3 72.4 + - - +
369C ASP* 4.4 4.3 - - - +
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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