Contacts of the helix formed by residues 332 - 342 (chain A) in PDB entry 2O0K
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 GLY 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ILE* 4.2 3.4 - - - -
315A TRP* 4.0 12.9 - - - -
321A ARG 3.2 23.6 - - - -
322A LEU* 3.4 6.3 - - - +
330A ASP* 3.1 8.2 + - - -
331A ASP* 1.3 77.9 - - - +
333A TRP* 1.3 62.0 + - - +
334A GLN 3.2 2.2 - - - -
335A TRP* 3.9 2.2 - - - -
336A SER* 2.8 29.7 + - - -
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Residues in contact with TRP 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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10A ASP* 4.0 15.5 - - + +
11A PHE 3.8 10.8 + - - -
12A HIS* 2.7 61.3 + - + -
15A ASN* 4.1 7.6 - - - -
22A ILE* 3.4 32.3 - - + -
23A LYS 3.7 6.3 - - - -
24A HIS* 3.3 63.0 + + + -
25A PRO* 4.0 7.9 - - + -
330A ASP* 3.2 21.6 + - + +
331A ASP 3.4 1.8 + - - -
332A GLY* 1.3 76.3 - - - +
334A GLN* 1.3 63.1 + - + +
336A SER* 3.0 4.3 + - - -
337A ILE* 3.4 20.9 + - + +
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Residues in contact with GLN 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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323A TYR 4.9 0.6 + - - -
324A ASN* 3.5 14.0 + - + +
325A ASP* 2.9 59.1 + - - +
326A GLU 4.9 0.2 + - - -
330A ASP* 2.8 19.2 + - - +
333A TRP* 1.3 76.0 - - + +
335A TRP* 1.3 60.2 + - - +
336A SER 3.2 2.7 - - - -
337A ILE* 3.9 6.4 - - + +
338A GLN* 2.9 58.1 + - + +
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Residues in contact with TRP 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A TRP* 3.7 28.3 - + + -
320A GLU 5.5 0.2 - - - -
321A ARG* 3.0 75.2 - - + +
323A TYR 5.5 2.9 - - - +
324A ASN* 5.7 0.8 - - - +
330A ASP* 4.6 0.4 + - - -
332A GLY* 3.5 4.2 + - - +
334A GLN* 1.3 79.9 - - - +
336A SER* 1.3 59.1 + - - +
338A GLN* 4.0 12.0 - - + +
339A THR* 2.4 54.2 + - + -
348A PHE* 3.6 22.2 - + - -
352A HIS* 3.6 31.2 - + - -
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Residues in contact with SER 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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12A HIS* 2.6 37.7 + - - -
14A LEU* 4.0 17.0 - - - -
22A ILE* 4.2 2.1 - - - +
315A TRP* 4.6 5.8 - - - -
332A GLY 2.8 18.6 + - - -
335A TRP* 1.3 83.2 - - - +
337A ILE* 1.3 64.1 + - - +
339A THR* 3.9 0.6 - - - -
340A ILE* 2.9 33.0 + - - +
348A PHE* 4.2 15.3 - - - -
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Residues in contact with ILE 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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11A PHE* 4.0 9.6 - - + +
12A HIS* 3.1 38.8 - - + +
13A PRO* 3.7 15.9 - - + -
333A TRP* 3.4 27.3 + - + +
334A GLN* 3.4 8.4 + - + +
336A SER* 1.3 80.9 + - - +
338A GLN* 1.3 67.1 + - + +
340A ILE* 3.6 6.0 - - - +
341A ASN* 3.0 46.4 + - - +
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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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325A ASP* 3.2 28.4 + - - +
334A GLN* 2.9 46.1 + - + +
335A TRP* 4.0 10.3 - - - +
337A ILE* 1.3 78.2 - - + +
339A THR* 1.3 63.5 + - - +
341A ASN* 3.0 11.4 + - - +
342A GLY* 2.9 22.0 + - - -
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Residues in contact with THR 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 TRP* 2.4 44.8 + - + -
336A SER 3.9 3.6 - - - -
338A GLN* 1.3 78.6 - - - +
340A ILE* 1.3 53.2 + - - +
342A GLY* 3.5 7.2 + - - +
343A SER* 2.7 28.8 + - - +
348A PHE* 3.9 18.2 - - + -
352A HIS* 3.8 25.6 - - + +
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Residues in contact with ILE 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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13A PRO* 3.7 35.4 - - + -
14A LEU* 4.4 16.8 - - + +
336A SER* 2.9 29.3 + - - +
337A ILE* 3.6 3.4 - - - +
339A THR* 1.3 74.3 - - - +
341A ASN* 1.3 63.9 + - - +
343A SER* 2.7 27.0 + - - -
344A SER* 2.9 30.0 + - - +
345A LEU* 4.0 12.3 - - + +
348A PHE* 3.7 37.7 - - + -
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Residues in contact with ASN 341 (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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13A PRO* 5.4 3.5 - - - +
337A ILE* 3.0 37.5 + - - +
338A GLN* 3.0 9.9 + - - +
340A ILE* 1.3 81.6 - - - +
342A GLY* 1.3 57.0 + - - +
343A SER* 3.0 8.5 + - - +
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Residues in contact with GLY 342 (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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338A GLN 2.9 14.4 + - - -
339A THR* 3.8 4.3 - - - -
340A ILE 3.1 0.6 - - - -
341A ASN* 1.3 75.4 - - - +
343A SER* 1.3 62.2 + - - +
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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