Contacts of the helix formed by residues 302 - 313 (chain A) in PDB entry 2A79
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 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A GLN* 5.5 1.6 - - - +
296A ALA* 4.1 1.1 - - - -
301A CYS* 1.3 80.1 - - - +
303A LEU* 1.3 63.0 + - - +
304A PRO* 3.0 7.4 - - - +
305A GLN* 2.9 29.2 + - - +
306A LEU* 3.2 16.6 + - - +
332A GLU* 2.6 37.6 + - + +
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Residues in contact with LEU 303 (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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219A MET* 5.8 0.9 - - - -
251A VAL* 3.1 28.5 - - + +
252A SER 4.3 11.4 - - - +
253A GLY* 4.4 2.2 - - - +
289A LEU* 3.5 33.4 - - + +
292A LEU* 3.9 28.5 - - + +
293A GLN* 3.5 30.7 + - + +
296A ALA* 4.0 7.9 - - - +
302A THR* 1.3 68.6 - - - +
304A PRO* 1.4 74.6 - - + +
306A LEU* 3.0 19.5 + - + +
307A ALA* 2.9 21.1 + - + +
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Residues in contact with PRO 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 4.2 15.3 - - + -
251A VAL 4.8 2.2 - - - +
252A SER* 4.1 19.5 - - - +
302A THR* 3.0 11.4 - - - +
303A LEU* 1.4 93.2 - - + +
305A GLN* 1.3 63.3 + - - +
307A ALA* 3.0 4.9 + - + +
308A ILE* 2.8 30.5 + - - +
332A GLU* 3.1 20.0 - - - +
333A ASN* 3.7 19.7 - - - +
1001A NAP 3.9 17.3 - - + +
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Residues in contact with GLN 305 (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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301A CYS* 3.2 12.5 - - + +
302A THR* 2.9 42.8 + - - +
303A LEU 3.3 0.6 - - - -
304A PRO* 1.3 75.0 - - - +
306A LEU* 1.3 58.6 + - - +
308A ILE* 4.6 0.9 - - - -
309A ALA* 2.9 33.1 + - - +
331A MET 4.9 0.4 + - - -
332A GLU* 2.6 43.5 + - + +
333A ASN* 4.8 1.3 - - - +
335A GLY* 3.7 15.2 - - - -
336A ALA* 3.3 24.1 - - - +
339A VAL* 3.9 10.8 - - + -
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A MET* 4.5 11.7 - - + -
292A LEU* 4.1 18.6 - - + +
295A ILE* 4.7 4.7 - - + -
296A ALA* 4.4 10.3 - - + +
299A LEU* 4.2 18.8 - - + -
301A CYS* 4.5 6.9 - - - -
302A THR 3.2 10.5 + - - +
303A LEU* 3.0 29.7 + - + +
305A GLN* 1.3 80.2 - - - +
307A ALA* 1.3 52.4 + - - +
309A ALA* 3.6 1.4 - - - +
310A TRP* 2.6 35.9 + - - +
339A VAL* 4.5 9.9 - - + -
343A LEU* 4.0 24.2 - - + +
351A ILE* 4.4 19.3 - - + -
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Residues in contact with ALA 307 (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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219A MET* 3.9 15.5 - - + +
245A PRO 4.3 7.4 - - - +
246A LEU* 4.2 11.4 - - + -
251A VAL* 3.6 30.3 - - + -
303A LEU* 2.9 10.0 + - + +
304A PRO* 3.6 6.5 - - + +
306A LEU* 1.3 77.8 - - - +
308A ILE* 1.3 63.1 + - - +
310A TRP* 3.0 12.0 + - - +
311A CYS* 2.9 27.3 + - - -
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Residues in contact with ILE 308 (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 LEU* 3.9 26.9 - - + -
245A PRO* 4.1 7.0 - - + -
246A LEU* 3.7 20.4 - - + -
304A PRO 2.8 21.9 + - - +
307A ALA* 1.3 69.8 - - - +
309A ALA* 1.3 64.7 + - - +
311A CYS* 2.8 26.7 + - - +
312A LEU* 3.4 7.2 + - + +
320A VAL* 4.8 4.0 - - + -
322A LEU* 3.4 27.8 - - + -
333A ASN* 3.4 37.9 - - + +
336A ALA* 3.4 20.0 - - + -
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Residues in contact with ALA 309 (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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305A GLN 2.9 21.4 + - - +
306A LEU 3.8 2.7 - - - +
308A ILE* 1.3 77.7 - - - +
310A TRP* 1.3 63.0 + - - +
312A LEU* 3.2 8.0 + - - +
313A ARG 3.1 17.7 + - - -
336A ALA* 3.2 25.8 - - - +
339A VAL* 3.8 15.3 - - + -
340A LEU* 3.5 11.1 - - + +
343A LEU* 3.4 16.3 - - + +
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Residues in contact with TRP 310 (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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217A TYR* 3.9 11.2 - + - -
218A HIS 3.6 6.1 - - - -
219A MET* 3.4 59.7 - - + -
222A ARG* 3.4 32.1 - - + +
226A GLU* 3.3 17.9 - - - -
306A LEU* 2.6 19.7 + - + +
307A ALA 3.0 14.3 + - - +
309A ALA* 1.3 74.9 - - - +
311A CYS* 1.3 65.4 + - - +
313A ARG* 2.8 83.3 + - - +
343A LEU* 4.1 12.1 - - + +
348A VAL* 4.8 9.8 + - + +
351A ILE* 4.3 23.7 - - + +
352A ASP* 5.8 1.2 + - - -
355A LEU* 4.8 3.1 - - + -
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Residues in contact with CYS 311 (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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217A TYR* 3.5 57.6 - - + -
218A HIS* 4.2 10.1 - - - -
245A PRO* 4.4 15.9 - - - -
307A ALA* 2.9 15.8 + - - -
308A ILE* 2.8 13.0 + - - +
310A TRP* 1.3 80.5 - - - +
312A LEU* 1.3 57.3 + - - +
313A ARG* 3.7 0.5 + - - +
314A ASN* 4.5 2.4 + - - +
317A VAL* 3.5 17.7 - - - +
320A VAL* 3.5 20.9 - - + -
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Residues in contact with LEU 312 (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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40A ARG* 4.5 14.5 + - - +
51A CYS* 3.5 46.7 - - + +
52A LEU* 3.8 26.9 - - + -
308A ILE* 3.4 9.6 + - + +
309A ALA* 3.2 10.8 + - - +
311A CYS* 1.3 73.9 - - - +
313A ARG* 1.3 66.4 + - - +
314A ASN 2.9 14.5 + - - +
317A VAL* 4.3 19.2 - - + +
319A SER* 4.5 0.4 - - - -
320A VAL* 3.9 18.4 - - + +
336A ALA* 5.9 1.1 - - + -
337A ILE* 5.3 5.8 - - + -
340A LEU* 4.2 20.7 - - + +
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Residues in contact with ARG 313 (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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217A TYR* 3.2 13.4 + - - -
222A ARG* 3.6 5.5 - - - +
226A GLU* 3.1 27.9 + - - -
309A ALA 3.1 10.3 + - - +
310A TRP* 2.8 87.4 + - - +
311A CYS 3.4 0.6 - - - -
312A LEU* 1.3 77.2 - - - +
314A ASN* 1.3 80.6 + - - +
315A GLU* 3.9 2.9 + - - +
340A LEU* 4.0 9.4 - - - -
343A LEU* 4.1 15.0 - - + -
348A VAL* 4.0 28.6 - - + +
352A ASP* 5.7 0.4 + - - -
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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