Contacts of the helix formed by residues 357 - 369 (chain A) in PDB entry 4Z4H
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 THR 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A ARG* 5.6 1.3 - - - +
355A LYS 5.3 1.6 - - - +
356A LEU* 1.3 72.1 - - - +
358A ASP* 1.3 57.9 + - - +
359A ASN* 3.4 7.0 + - - +
360A GLN* 3.0 42.2 + - - +
361A THR* 2.7 35.1 + - - -
3D A 4.5 0.2 - - - -
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Residues in contact with ASP 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A LEU 5.2 0.2 - - - +
357A THR* 1.3 76.8 - - - +
359A ASN* 1.3 63.9 + - - +
362A SER* 3.0 23.7 + - - -
3D A 2.8 41.2 + - - +
4D U 3.3 29.9 + - - +
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Residues in contact with ASN 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LEU 5.5 0.4 - - - -
357A THR* 3.4 6.9 + - - +
358A ASP* 1.3 81.5 - - - +
360A GLN* 1.3 59.4 + - - +
362A SER* 3.3 7.9 + - - -
363A THR* 2.9 33.2 + - - -
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Residues in contact with GLN 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LEU* 3.3 31.8 - - + +
193A GLY 2.7 29.5 + - - -
194A GLY* 4.0 5.7 - - - -
196A ARG* 3.4 35.5 + - - +
356A LEU* 3.4 14.7 - - + +
357A THR* 3.0 45.6 + - - +
359A ASN* 1.3 73.3 - - + +
361A THR* 1.3 60.3 + - - +
363A THR* 3.3 7.7 + - - -
364A MET* 2.9 28.9 + - - +
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Residues in contact with THR 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LEU* 3.8 16.7 + - - +
357A THR 2.7 25.0 + - - -
358A ASP 3.6 5.6 - - - -
360A GLN* 1.3 76.7 - - - +
362A SER* 1.3 62.6 + - - +
364A MET* 2.9 19.8 + - + +
365A ILE* 2.9 24.7 + - + +
7B U 5.4 0.7 - - - +
3D A 3.5 29.1 + - + +
4D U 3.1 27.6 - - - +
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Residues in contact with SER 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A ASP 3.0 15.4 + - - -
359A ASN* 3.3 10.3 + - - -
361A THR* 1.3 74.0 - - - +
363A THR* 1.3 61.8 + - - +
365A ILE* 3.5 2.3 + - - +
366A ARG* 3.2 40.6 + - - +
4D U 3.3 26.9 + - - -
5D G 3.2 20.0 + - - -
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Residues in contact with THR 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ASN* 6.4 0.4 - - + -
191A PRO 3.7 15.3 - - - +
192A LEU* 3.4 27.4 + - + -
198A VAL* 5.4 0.7 - - + -
359A ASN* 2.9 20.0 + - - +
360A GLN* 3.5 6.9 - - - -
361A THR 3.1 0.2 - - - -
362A SER* 1.3 72.3 - - - +
364A MET* 1.3 65.0 - - - +
366A ARG* 3.4 10.0 + - - +
367A ALA* 3.0 25.8 + - + +
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Residues in contact with MET 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LEU* 3.5 34.3 - - + -
198A VAL* 3.6 28.0 - - + -
221A ALA* 4.9 2.5 - - - +
222A THR* 4.1 9.2 - - - -
223A ALA* 3.8 24.2 - - + +
356A LEU* 3.8 13.0 - - + -
360A GLN 2.9 11.1 + - - +
361A THR* 2.9 13.2 + - + +
363A THR* 1.3 77.6 - - - +
365A ILE* 1.3 66.5 + - + +
367A ALA* 3.3 3.2 + - - +
368A THR* 3.1 38.1 + - + +
7B U 5.2 8.1 - - - +
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Residues in contact with ILE 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A THR* 2.9 25.4 + - + +
362A SER 3.7 6.1 - - - +
364A MET* 1.3 79.5 - - + +
366A ARG* 1.3 59.0 + - + +
368A THR* 3.3 4.3 + - - +
369A ALA* 2.9 43.2 + - + +
6B A 5.4 3.6 - - + +
7B U 3.5 40.4 - - + +
4D U 3.4 33.2 - - - +
5D G 4.1 31.2 - - - +
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Residues in contact with ARG 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A SER* 3.2 31.2 + - - +
363A THR* 3.7 7.2 - - - +
365A ILE* 1.3 78.6 - - + +
367A ALA* 1.3 63.8 + - - +
368A THR 3.3 0.7 + - - -
369A ALA* 3.9 11.2 + - - +
370A ARG* 4.9 0.9 + - - -
5D G 4.8 22.5 + - - -
6D U 5.8 2.0 + - - -
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Residues in contact with ALA 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ASN* 4.0 23.5 + - + +
198A VAL* 4.6 10.5 - - + -
200A PHE* 4.0 9.7 - - + -
363A THR* 3.0 19.6 + - + +
364A MET* 3.7 7.6 - - - +
365A ILE 3.2 0.4 - - - -
366A ARG* 1.3 77.1 - - - +
368A THR* 1.3 66.2 + - + +
370A ARG* 3.1 21.2 + - - -
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Residues in contact with THR 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A VAL* 4.5 0.9 - - + -
200A PHE* 4.1 9.4 - - + -
221A ALA* 3.5 32.8 - - + -
364A MET* 3.1 30.8 + - - +
365A ILE* 3.8 3.8 + - - -
367A ALA* 1.3 84.8 - - + +
369A ALA* 1.3 69.1 + - - +
370A ARG* 3.4 19.8 + - - +
375A ARG* 5.9 0.9 + - - -
7B U 4.6 17.7 + - - +
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Residues in contact with ALA 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A ILE* 2.9 27.2 + - + +
366A ARG* 3.9 8.4 + - - +
367A ALA 3.8 0.6 - - - -
368A THR* 1.3 76.1 + - - +
370A ARG* 1.3 73.9 + - - +
757A GLN* 4.0 17.0 - - - +
5D G 5.7 2.9 - - - +
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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