Contacts of the helix formed by residues 330 - 340 (chain A) in PDB entry 4M83
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 GLN 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A PHE* 5.9 4.2 - - - +
305A HIS* 2.9 54.4 - - + +
306A ALA* 3.8 5.1 - - - +
325A PRO* 3.3 11.1 - - + +
326A GLN* 2.4 38.3 + - - +
327A ALA* 3.0 25.3 + - - +
328A VAL 3.3 4.2 + - - -
329A ASP* 1.3 103.1 + - + +
331A PHE* 1.3 56.9 + - - +
332A GLY 3.5 1.6 - - - -
333A ASN* 3.2 4.9 + - - +
334A ALA* 2.7 36.7 + - - +
1401A UDP 5.4 0.2 + - - -
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Residues in contact with PHE 331 (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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325A PRO* 4.3 19.3 - - + -
326A GLN 4.6 4.0 - - - -
327A ALA* 3.4 33.2 - - - -
328A VAL* 3.4 27.6 - - - -
330A GLN* 1.3 76.8 - - - +
332A GLY* 1.3 53.7 + - - +
334A ALA* 3.1 3.9 + - - +
335A ASP* 2.8 42.3 + - - +
345A LYS* 4.9 7.5 + - - +
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Residues in contact with GLY 332 (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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330A GLN 3.5 0.2 - - - -
331A PHE* 1.3 76.1 - - - +
333A ASN* 1.3 54.4 + - - +
335A ASP* 3.0 11.0 + - - +
336A MET* 2.7 47.8 + - - +
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Residues in contact with ASN 333 (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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196A LEU* 4.4 16.0 - - + +
306A ALA* 3.1 29.5 + - + +
307A GLY 3.9 1.2 - - - -
308A ALA* 3.8 21.6 - - - +
311A SER* 4.0 10.5 + - - +
329A ASP 3.3 14.6 + - - +
330A GLN 3.2 5.5 + - - +
332A GLY* 1.3 73.7 - - - +
334A ALA* 1.3 58.5 + - - +
336A MET* 3.2 21.0 + - - +
337A LEU* 2.9 34.3 + - - +
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Residues in contact with ALA 334 (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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306A ALA* 3.9 7.3 - - + +
323A ALA* 3.7 29.6 - - + +
325A PRO* 4.2 20.2 - - + -
330A GLN 2.7 19.7 + - - +
331A PHE 3.4 4.0 - - - +
333A ASN* 1.3 74.5 - - - +
335A ASP* 1.3 57.7 + - - +
337A LEU* 3.4 2.9 + - - +
338A GLN* 2.9 29.7 + - - +
344A ARG 5.9 0.2 - - - -
345A LYS* 4.4 12.8 + - + +
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Residues in contact with ASP 335 (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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331A PHE* 2.8 24.7 + - - +
332A GLY* 3.0 11.5 + - - +
334A ALA* 1.3 73.1 - - - +
336A MET* 1.3 59.7 + - + +
338A GLN* 3.0 11.4 - - - +
339A GLY* 2.9 23.7 + - - -
345A LYS* 3.3 32.7 + - - +
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Residues in contact with MET 336 (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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134A LEU* 5.6 3.1 - - + -
195A ALA 4.3 11.7 - - - +
196A LEU* 3.1 42.6 - - + +
197A GLN 3.9 2.7 - - - +
198A PRO* 3.7 33.2 - - + -
332A GLY* 2.7 27.0 + - - +
333A ASN* 3.5 24.5 - - - +
335A ASP* 1.3 73.8 - - + +
337A LEU* 1.3 65.6 + - - +
339A GLY* 3.1 3.3 + - - +
340A LEU* 2.9 29.7 + - - +
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Residues in contact with LEU 337 (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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196A LEU* 4.1 11.0 - - + +
304A THR* 4.9 1.8 - - + -
306A ALA* 4.3 12.8 - - + -
311A SER* 3.8 22.4 - - - +
315A LEU* 3.8 39.0 - - + -
321A MET* 3.8 27.6 - - + -
323A ALA* 4.6 7.9 - - + -
333A ASN 2.9 20.9 + - - +
334A ALA* 3.8 4.9 - - - +
336A MET* 1.3 74.1 - - - +
338A GLN* 1.3 64.5 + - - +
340A LEU* 3.3 11.7 + - + -
342A VAL* 3.4 22.3 + - + +
343A ALA* 3.7 17.5 + - + -
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Residues in contact with GLN 338 (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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334A ALA 2.9 16.3 + - - +
335A ASP* 3.0 20.6 - - - +
337A LEU* 1.3 75.0 - - - +
339A GLY* 1.3 59.9 + - - +
341A GLY* 2.8 23.6 + - - -
342A VAL 4.2 0.2 + - - -
343A ALA* 3.3 23.9 + - - +
344A ARG* 4.4 7.3 - - - +
345A LYS* 3.6 28.3 + - + +
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Residues in contact with GLY 339 (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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335A ASP 2.9 17.9 + - - -
336A MET* 3.1 5.3 + - - -
338A GLN* 1.3 76.5 - - - +
340A LEU* 1.3 58.9 + - - +
341A GLY* 3.0 1.8 + - - -
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Residues in contact with LEU 340 (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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195A ALA* 3.8 35.9 - - + +
196A LEU* 4.9 0.9 - - + -
315A LEU* 4.4 3.6 - - + -
336A MET 2.9 19.5 + - - +
337A LEU* 3.5 28.0 - - + +
338A GLN 3.1 0.6 + - - -
339A GLY* 1.3 76.7 - - - +
341A GLY* 1.3 59.9 + - - +
342A VAL* 3.5 15.2 + - + +
372A ARG* 3.8 21.6 + - - +
376A ILE* 3.6 32.5 - - + +
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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