Contacts of the helix formed by residues 357 - 370 (chain A) in PDB entry 3Q29
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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351A ALA* 4.8 0.2 - - - -
356A GLN* 1.3 76.5 - - - +
358A VAL* 1.3 59.0 + - - +
359A ASP* 3.7 6.2 + - - +
360A GLU* 2.8 49.9 + - - +
361A ALA* 2.8 29.0 + - - +
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Residues in contact with VAL 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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190A LYS* 3.7 15.3 - - - +
193A LEU* 3.9 10.1 - - + -
194A THR* 3.6 33.2 - - + +
197A VAL* 3.7 35.4 - - + -
351A ALA* 4.2 7.8 - - + +
357A THR* 1.3 73.3 - - - +
359A ASP* 1.3 69.6 + - - +
361A ALA* 4.4 0.4 - - - -
362A LEU* 3.0 43.3 + - + +
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Residues in contact with ASP 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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185A ASP* 4.7 2.1 - - - +
190A LYS* 3.4 42.4 + - - +
357A THR* 3.3 7.0 + - - +
358A VAL* 1.3 79.1 - - - +
360A GLU* 1.3 57.9 + - + +
362A LEU* 4.0 0.9 - - - +
363A LYS* 3.0 30.7 + - - +
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Residues in contact with GLU 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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355A ARG 5.0 0.7 - - - +
356A GLN* 3.8 19.8 + - - +
357A THR* 2.8 48.1 + - - +
359A ASP* 1.3 77.0 - - + +
361A ALA* 1.3 65.0 + - - +
363A LYS* 3.5 9.7 + - - +
364A ASP* 3.1 27.9 + - - +
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Residues in contact with ALA 361 (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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193A LEU* 5.0 1.8 - - + -
347A ALA* 3.3 38.7 - - + +
351A ALA* 4.2 8.5 - - + -
356A GLN* 3.8 27.0 - - + +
357A THR 2.8 22.2 + - - +
358A VAL 3.8 2.9 - - - +
360A GLU* 1.3 73.9 - - - +
362A LEU* 1.3 56.9 + - - +
364A ASP* 3.6 2.8 + - - +
365A ALA 3.0 20.8 + - - -
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Residues in contact with LEU 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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162A ILE* 5.5 8.1 - - + -
184A VAL* 3.2 30.9 - - + +
185A ASP* 3.7 9.4 - - - +
189A ALA* 3.8 7.9 - - + +
190A LYS* 3.7 42.4 - - + +
193A LEU* 3.7 30.3 - - + -
344A VAL* 5.8 4.7 - - + -
347A ALA* 4.3 11.9 - - + -
348A VAL* 6.0 0.4 - - + -
358A VAL* 3.0 17.2 + - + +
359A ASP 4.2 1.1 - - - +
361A ALA* 1.3 73.0 - - - +
363A LYS* 1.3 57.8 + - - +
365A ALA* 3.6 6.1 - - + +
366A GLN* 2.7 36.6 + - - +
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Residues in contact with LYS 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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185A ASP* 3.4 19.7 + - - +
359A ASP 3.0 19.8 + - - +
360A GLU* 3.5 8.5 - - - +
362A LEU* 1.3 77.2 - - - +
364A ASP* 1.3 72.0 + - - +
366A GLN* 3.3 4.0 + - - +
367A THR* 3.1 28.7 + - - +
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Residues in contact with ASP 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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356A GLN* 3.0 26.7 + - - +
360A GLU* 3.1 12.1 + - - +
361A ALA* 3.9 4.3 - - - +
363A LYS* 1.3 89.1 - - - +
365A ALA* 1.3 61.6 + - - +
367A THR* 3.2 8.3 + - - -
368A ASN* 2.9 40.2 + - - +
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Residues in contact with ALA 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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184A VAL* 3.6 12.3 - - + -
343A ALA* 3.6 23.0 - - - +
344A VAL* 4.4 5.4 - - + -
347A ALA* 3.6 19.7 - - + -
361A ALA 3.0 18.5 + - - +
362A LEU* 3.6 8.7 - - + +
364A ASP* 1.3 72.3 - - - +
366A GLN* 1.3 59.8 + - - +
368A ASN* 4.8 0.2 - - - -
369A SER* 2.8 36.2 + - - -
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Residues in contact with GLN 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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180A LYS 5.9 0.2 + - - -
182A VAL* 2.9 38.8 + - - +
184A VAL* 3.1 34.4 + - + +
185A ASP* 3.1 30.3 - - + +
362A LEU 2.7 15.7 + - - +
363A LYS 3.3 10.1 - - - +
365A ALA* 1.3 76.1 - - - +
367A THR* 1.3 63.2 + - - +
369A SER* 3.8 3.1 - - - -
370A SER* 2.9 29.2 + - - +
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Residues in contact with THR 367 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A LYS* 3.1 17.0 + - - +
364A ASP* 3.6 10.9 + - - -
366A GLN* 1.3 81.7 - - - +
368A ASN* 1.3 67.4 + - - +
370A SER* 3.3 25.4 + - - +
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Residues in contact with ASN 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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339A ALA* 4.2 14.7 - - - +
343A ALA* 3.9 17.7 - - + +
364A ASP* 2.9 23.9 + - - +
365A ALA* 4.8 0.2 - - - -
367A THR* 1.3 84.2 - - - +
369A SER* 1.3 65.2 + - - +
370A SER 3.1 8.2 - - - +
372A MET* 5.9 3.5 - - - +
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Residues in contact with SER 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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170A PHE* 3.9 6.6 - - - -
182A VAL* 4.0 20.2 - - - -
184A VAL* 4.3 1.4 - - - +
336A GLN* 2.9 27.9 + - - +
339A ALA 4.4 0.2 - - - -
340A PHE* 3.5 35.3 + - - +
343A ALA* 3.5 15.0 - - - +
344A VAL* 4.1 4.3 - - - +
365A ALA 2.8 22.4 + - - -
366A GLN 3.8 4.5 - - - -
368A ASN* 1.3 75.8 - - - +
370A SER* 1.3 57.4 + - - +
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Residues in contact with SER 370 (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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179A ILE 5.0 5.3 + - - -
180A LYS* 6.0 1.0 - - - -
182A VAL* 3.8 19.6 - - - +
336A GLN* 3.1 8.8 + - - -
366A GLN* 2.9 17.7 + - - +
367A THR* 3.3 18.5 + - - +
368A ASN* 3.1 8.8 - - - +
369A SER* 1.3 80.7 - - - +
371A SER* 1.3 67.4 + - - +
372A MET 3.6 1.7 + - - -
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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