Contacts of the helix formed by residues 314 - 323 (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 ILE 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A TRP* 6.1 0.7 - - + -
161A SER* 3.2 10.1 - - - -
164A LEU* 3.6 3.5 - - - +
312A THR* 4.7 6.3 - - - +
313A ALA* 1.3 78.1 - - - +
315A TRP* 1.3 78.2 + - + +
316A ASN* 2.9 29.8 + - - +
317A SER* 3.0 21.4 + - - -
352A HIS 3.2 7.2 - - - +
353A THR* 3.3 41.7 - - + +
354A ALA* 3.9 8.5 - - + +
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Residues in contact with TRP 315 (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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14A LEU* 4.7 10.1 - - + +
22A ILE* 4.7 1.3 - - + -
43A TRP* 3.8 34.3 - + - -
161A SER* 3.3 5.4 + - - -
164A LEU* 4.3 0.4 - - - -
314A ILE* 1.3 84.3 - - + +
316A ASN* 1.3 90.1 + - + +
317A SER 2.9 6.5 + - - -
318A VAL 3.4 5.7 + - - -
321A ARG* 2.9 41.5 + - + +
322A LEU* 4.2 7.2 - - + -
331A ASP 4.0 5.4 - - - -
332A GLY* 4.0 28.0 - - - -
335A TRP* 3.7 27.6 - + + -
336A SER* 4.6 9.2 - - - -
348A PHE* 3.6 27.2 - + - -
352A HIS* 2.9 41.4 + - + +
353A THR* 4.2 6.6 - - + +
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Residues in contact with ASN 316 (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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43A TRP* 3.4 56.3 - - + +
314A ILE* 2.9 32.5 + - - +
315A TRP* 1.3 103.1 - - + +
317A SER* 1.3 62.5 + - - +
318A VAL 3.4 2.7 - - - -
319A LYS* 3.1 23.0 + - - +
322A LEU* 4.3 7.5 - - + +
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Residues in contact with SER 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 3.8 14.6 - - - +
141A ASP 5.7 0.3 + - - -
142A TYR* 3.7 31.3 + - - +
164A LEU* 4.2 9.4 - - - -
313A ALA* 3.9 17.7 - - - +
314A ILE 3.1 16.4 + - - -
315A TRP 2.9 1.8 + - - -
316A ASN* 1.3 80.0 + - - +
318A VAL* 1.3 62.1 + - - +
319A LYS* 3.2 24.3 + - - +
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 3.7 24.5 - - - +
142A TYR* 5.4 0.2 - - + -
163A GLN 4.2 7.0 - - - +
164A LEU* 3.8 20.0 - - + +
315A TRP 3.4 1.5 + - - +
316A ASN 4.5 1.3 - - - -
317A SER* 1.3 77.0 - - - +
319A LYS* 1.3 57.4 + - - +
320A GLU* 3.0 30.7 - - + +
321A ARG* 3.0 70.7 + - + +
322A LEU* 4.2 3.1 + - - +
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Residues in contact with LYS 319 (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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43A TRP* 4.9 4.9 - - - +
44A ASP* 3.3 26.8 + - - +
48A TYR* 3.1 28.7 + - + +
55A TYR* 3.3 34.5 - - + +
140A ARG* 4.8 2.4 - - + +
141A ASP* 5.2 14.6 - - + +
316A ASN* 3.1 22.0 + - - +
317A SER* 3.2 18.5 + - - +
318A VAL* 1.3 67.1 - - - +
320A GLU* 1.3 60.2 + - - +
321A ARG 2.9 5.8 - - - -
322A LEU* 2.9 44.0 + - + +
323A TYR* 3.6 10.0 - - - -
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Residues in contact with GLU 320 (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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52A PHE* 4.2 31.8 - - + -
55A TYR* 4.1 18.5 + - + -
56A LEU* 5.9 1.6 - - + -
140A ARG* 3.1 22.9 + - - -
318A VAL* 3.0 24.1 - - + +
319A LYS* 1.3 86.0 + - - +
321A ARG* 1.3 60.1 + - + +
322A LEU 3.1 1.8 + - - -
323A TYR* 3.4 20.0 + - - +
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Residues in contact with ARG 321 (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 ARG 4.9 0.2 + - - -
163A GLN* 3.2 41.0 + - - +
164A LEU* 4.0 5.1 - - - +
315A TRP* 2.9 50.5 + - + +
318A VAL* 3.0 39.0 + - + +
319A LYS 2.9 0.4 - - - -
320A GLU* 1.3 79.1 - - + +
322A LEU* 1.3 58.3 + - + +
323A TYR 3.3 5.1 + - - +
330A ASP* 4.6 0.2 - - - +
332A GLY* 3.2 18.7 - - - -
335A TRP* 3.0 72.8 + - + +
352A HIS* 4.4 3.2 + - - -
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Residues in contact with LEU 322 (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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41A SER* 4.3 4.5 - - - +
43A TRP* 4.0 18.6 - - + +
48A TYR* 4.6 5.6 - - + -
315A TRP* 4.2 11.2 - - + -
316A ASN 4.3 7.2 - - - +
318A VAL 4.5 2.7 - - - +
319A LYS* 2.9 46.7 + - + +
321A ARG* 1.3 82.6 - - - +
323A TYR* 1.3 55.9 + - + +
329A PHE* 3.5 25.1 - - + -
330A ASP* 2.6 36.7 + - - +
331A ASP* 3.0 38.0 + - - +
332A GLY* 3.4 6.1 - - - +
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Residues in contact with TYR 323 (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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48A TYR* 3.6 9.1 - + - +
49A PRO* 2.6 49.1 + - - +
50A GLU 3.7 1.3 - - - -
52A PHE* 3.4 57.2 - + + -
55A TYR* 3.6 26.7 - + + +
319A LYS 3.6 19.3 - - - -
320A GLU 3.4 12.6 + - - +
321A ARG* 3.3 4.9 - - - +
322A LEU* 1.3 81.5 - - + +
324A ASN* 1.3 68.5 + - - +
328A ILE 3.4 3.8 - - - +
329A PHE* 3.4 36.1 - + + -
330A ASP* 3.7 1.3 - - - -
334A GLN* 4.9 1.0 + - - -
335A TRP* 5.5 3.2 - - - +
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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