Contacts of the helix formed by residues 305 - 317 (chain A) in PDB entry 4B92
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 ASN 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A ILE* 4.4 10.5 - - + +
303A ASP* 2.8 24.5 + - - +
304A THR* 1.3 79.2 - - - +
306A THR* 1.3 63.4 + - - +
307A SER 3.5 0.7 - - - -
308A THR* 3.6 11.7 + - + +
309A TYR* 3.0 23.2 + - + +
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Residues in contact with THR 306 (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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222A GLU* 5.0 1.6 + - - -
249A SER 3.4 25.4 - - - +
250A SER* 4.0 13.9 - - - -
251A ILE* 3.8 20.3 + - - +
275A HIS 5.3 0.7 - - - +
278A LEU 6.1 0.4 - - - -
301A ARG* 3.9 17.0 - - + +
303A ASP* 3.2 29.0 + - - +
304A THR 3.3 2.8 - - - -
305A ASN* 1.3 74.5 - - - +
307A SER* 1.3 66.3 + - - +
309A TYR* 3.0 3.6 + - - +
310A LEU* 2.9 31.3 + - + +
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Residues in contact with SER 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A HIS 3.7 13.7 - - - -
276A ALA 3.2 23.2 - - - +
277A THR* 3.7 24.5 + - - -
278A LEU 3.7 13.4 + - - -
279A THR* 4.5 8.2 - - - +
303A ASP 5.0 0.2 + - - -
304A THR 4.4 7.2 + - - -
306A THR* 1.3 78.0 - - - +
308A THR* 1.3 75.7 + - - +
310A LEU* 3.2 0.9 + - - +
311A MET* 2.9 20.6 + - - +
361A ARG* 5.6 2.3 + - - -
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Residues in contact with THR 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A THR 4.5 6.9 + - - -
305A ASN* 3.6 14.6 + - - +
307A SER* 1.3 85.7 + - - +
309A TYR* 1.3 58.5 + - - +
311A MET* 3.5 7.5 + - - +
312A SER* 3.1 29.0 + - - +
367A LYS* 4.0 24.6 - - - +
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Residues in contact with TYR 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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251A ILE* 3.6 47.1 - - + -
255A ASP* 2.5 26.8 + - - -
305A ASN* 3.0 18.4 + - + +
306A THR* 3.0 7.1 + - - +
308A THR* 1.3 75.9 - - - +
310A LEU* 1.3 63.7 + - + +
312A SER* 3.2 10.3 + - - -
313A LEU* 3.0 64.5 + - + +
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Residues in contact with LEU 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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248A VAL* 3.5 27.6 - - + +
249A SER* 3.7 20.6 - - - +
250A SER 3.9 24.0 - - - +
271A THR* 4.2 1.8 - - + +
275A HIS* 3.5 26.2 - - + +
276A ALA* 4.4 7.9 - - + -
306A THR* 2.9 25.5 + - + +
307A SER 3.8 3.8 - - - +
309A TYR* 1.3 73.9 - - + +
311A MET* 1.3 57.9 + - - +
313A LEU* 3.3 17.3 + - + +
314A LEU* 2.9 29.0 + - - +
319A LEU* 3.7 22.6 - - + +
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Residues in contact with MET 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ALA* 3.5 27.2 + - + +
277A THR* 3.8 8.7 - - + -
307A SER 2.9 12.1 + - - +
308A THR* 3.5 12.1 - - - +
310A LEU* 1.3 76.7 - - - +
312A SER* 1.3 55.9 + - - +
314A LEU* 3.3 13.9 + - - +
315A ALA* 3.0 27.9 + - - +
358A ILE* 4.0 12.3 - - + -
361A ARG* 3.8 28.0 - - + +
362A GLY* 3.8 8.5 - - - +
367A LYS* 3.9 27.6 - - + -
368A MET* 3.6 25.8 - - - -
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Residues in contact with SER 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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308A THR* 3.1 18.6 + - - +
309A TYR* 3.2 15.8 + - - -
311A MET* 1.3 75.4 - - - +
313A LEU* 1.3 63.7 + - - +
315A ALA* 3.3 9.2 + - - +
316A ASN* 2.9 28.7 + - - +
367A LYS* 4.1 15.7 - - - +
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Residues in contact with LEU 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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254A GLY* 3.9 25.4 - - - +
258A ALA* 6.0 1.3 - - + -
309A TYR* 3.0 60.9 + - + +
310A LEU* 3.4 19.3 - - + +
312A SER* 1.3 77.8 - - - +
314A LEU* 1.3 53.9 + - - +
316A ASN* 3.0 8.1 + - + +
317A ASP 2.7 31.0 + - - -
318A THR* 3.0 35.8 + - + +
319A LEU* 3.2 12.6 + - + -
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Residues in contact with LEU 314 (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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271A THR* 4.0 15.7 - - + -
276A ALA* 4.3 14.6 - - + -
310A LEU 2.9 11.9 + - - +
311A MET* 3.3 20.6 - - - +
313A LEU* 1.3 71.1 - - - +
315A ALA* 1.3 59.6 + - - +
316A ASN 3.1 1.1 - - - -
319A LEU* 3.4 30.3 - - + +
321A ILE 3.8 24.9 - - - +
322A VAL* 3.9 21.8 - - + -
358A ILE* 4.6 3.8 - - + -
368A MET* 4.4 6.7 - - + -
372A ARG* 2.7 34.7 + - - -
376A VAL* 3.6 19.8 - - + +
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Residues in contact with ALA 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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311A MET 3.0 12.6 + - - +
312A SER* 3.3 12.1 + - - +
314A LEU* 1.3 76.1 - - - +
316A ASN* 1.3 58.6 + - - +
367A LYS 3.2 28.0 - - - +
368A MET* 3.7 14.8 - - + +
372A ARG* 3.6 24.7 + - - +
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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
----------------------------------------------------------
312A SER 2.9 16.4 + - - +
313A LEU* 3.0 9.9 + - + +
315A ALA* 1.3 80.3 - - - +
317A ASP* 1.3 67.5 + - - +
318A THR* 2.6 22.3 + - - -
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Residues in contact with ASP 317 (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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261A LYS* 3.1 19.0 + - - +
313A LEU 2.7 7.3 + - - -
316A ASN* 1.3 78.1 - - - +
318A THR* 1.3 65.3 + - - +
319A LEU 3.1 3.4 - - - -
320A ASN* 2.6 29.6 + - - -
372A ARG* 3.1 39.6 + - - +
380A ASN* 3.9 4.4 + - - -
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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