Contacts of the helix formed by residues 297 - 312 (chain A) in PDB entry 2R6C
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 ARG 297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A SER 4.4 0.4 + - - -
296A ILE* 1.3 76.2 - - - +
298A VAL* 1.3 66.8 + - - +
299A SER* 3.4 15.9 - - - +
300A ASP* 3.1 36.9 + - - +
301A ILE* 3.4 9.4 + - - +
325A ILE* 4.2 0.2 - - - -
326A GLN* 3.8 52.0 + - + +
36B GLU 5.8 1.1 - - - -
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Residues in contact with VAL 298 (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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297A ARG* 1.3 67.4 - - - +
299A SER* 1.3 56.4 + - - +
300A ASP 2.8 6.5 + - - -
301A ILE* 2.8 27.0 + - + +
302A ARG* 2.9 15.7 + - + +
325A ILE* 3.6 26.5 - - + +
326A GLN 4.8 2.6 - - - +
342A ILE* 3.8 35.0 - - + -
345A SER* 3.5 33.2 - - - +
346A LEU* 4.4 14.8 - - + -
349A LEU* 5.6 1.3 - - + -
36B GLU* 4.7 6.5 - - + +
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Residues in contact with SER 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ARG* 4.0 20.4 - - - +
298A VAL* 1.3 77.0 - - - +
300A ASP* 1.3 62.7 + - - +
302A ARG* 3.7 3.5 - - - +
303A ALA* 3.0 26.9 + - - +
306A ARG* 5.5 0.2 + - - -
36B GLU* 3.3 54.1 + - - +
37B ILE* 5.2 4.9 - - - -
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Residues in contact with ASP 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE* 4.7 14.3 - - + +
297A ARG* 3.1 35.3 + - - +
298A VAL 2.8 2.0 + - - -
299A SER* 1.3 79.8 + - - +
301A ILE* 1.3 63.5 + - - +
302A ARG 3.2 1.1 - - - -
303A ALA* 3.8 8.0 - - - +
304A LYS* 3.0 41.2 + - - +
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Residues in contact with ILE 301 (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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238A PHE* 3.4 32.4 - - + -
240A LEU* 5.8 0.4 - - + -
296A ILE* 3.5 25.5 - - + +
297A ARG 3.4 5.8 + - - +
298A VAL* 2.8 11.7 + - + +
300A ASP* 1.3 72.9 - - - +
302A ARG* 1.3 59.6 + - - +
305A CYS* 3.0 33.3 + - - -
317A ILE* 4.5 0.2 - - + -
319A ILE* 3.8 34.3 - - + -
325A ILE* 3.4 31.6 - - + -
346A LEU* 4.7 2.0 - - + -
349A LEU* 3.8 21.8 - - + -
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Residues in contact with ARG 302 (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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298A VAL* 2.9 16.6 + - + +
299A SER 3.7 3.6 - - - +
301A ILE* 1.3 78.4 - - - +
303A ALA* 1.3 56.9 + - - +
305A CYS* 4.2 0.7 - - - +
306A ARG* 3.1 55.3 + - - +
345A SER* 2.7 31.7 + - - -
348A ALA* 3.6 8.7 + - - +
349A LEU* 3.3 39.0 - - + +
352A GLU* 2.9 23.2 + - - +
353A LEU* 5.8 0.4 - - + -
32B VAL* 3.5 18.1 - - - +
33B PRO* 4.9 10.0 - - - +
36B GLU* 2.6 39.2 + - - +
103B GLU* 5.9 0.7 - - - -
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Residues in contact with ALA 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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299A SER 3.0 19.4 + - - +
300A ASP* 3.3 11.9 + - - +
302A ARG* 1.3 75.5 - - - +
304A LYS* 1.3 65.7 + - + +
306A ARG* 3.4 13.9 + - - +
307A ARG* 3.3 35.9 + - - +
107B ARG* 5.5 9.4 - - - +
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Residues in contact with LYS 304 (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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238A PHE* 4.4 12.3 - - + -
291A ASP* 3.4 35.3 + - + +
293A THR* 3.5 15.4 + - - +
296A ILE* 5.4 4.1 - - + +
300A ASP* 3.0 30.0 + - - +
301A ILE 4.1 2.0 - - - +
303A ALA* 1.3 75.0 - - + +
305A CYS* 1.3 65.2 + - - +
307A ARG* 3.4 8.4 + - - +
308A LEU* 3.3 22.2 + - - +
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Residues in contact with CYS 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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236A ALA* 4.3 9.6 - - - -
238A PHE* 3.5 27.6 - - - -
301A ILE* 3.0 26.5 + - - +
302A ARG 4.2 2.5 - - - +
304A LYS* 1.3 77.9 - - - +
306A ARG* 1.3 61.9 + - - +
308A LEU* 3.3 8.8 + - - +
309A LYS* 3.2 22.5 + - - +
314A LEU* 4.3 6.4 - - + +
317A ILE* 3.6 28.7 - - + -
349A LEU* 4.6 2.0 - - + -
353A LEU* 3.7 21.6 - - + +
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Residues in contact with ARG 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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299A SER 5.5 0.4 + - - -
302A ARG* 3.1 61.3 + - - +
303A ALA* 3.6 12.0 - - - +
304A LYS 3.3 0.2 - - - -
305A CYS* 1.3 75.5 - - - +
307A ARG* 1.3 63.1 + - + +
309A LYS* 3.5 15.7 + - + +
310A GLN* 3.3 33.9 + - - +
352A GLU* 2.8 41.9 + - - +
353A LEU* 4.2 14.1 - - + +
33B PRO* 5.3 5.3 - - - +
103B GLU* 3.4 30.5 + - - -
107B ARG* 6.1 0.4 - - - +
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Residues in contact with ARG 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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303A ALA* 3.3 20.9 + - - +
304A LYS* 3.9 9.4 - - - +
305A CYS 3.3 0.6 - - - -
306A ARG* 1.3 79.5 - - + +
308A LEU* 1.3 63.5 + - - +
310A GLN* 3.7 9.0 + - - +
311A GLU* 3.5 27.5 + - - +
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Residues in contact with LEU 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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234A ASN* 5.0 2.5 - - + +
236A ALA* 4.4 13.5 - - + -
289A TYR* 3.9 55.2 - - + -
304A LYS 3.3 14.2 + - - +
305A CYS* 3.3 6.9 + - - +
307A ARG* 1.3 77.4 - - - +
309A LYS* 1.3 65.3 + - - +
311A GLU* 4.8 3.6 - - + -
312A SER* 3.1 29.5 + - - +
313A GLY 3.3 5.4 + - - +
314A LEU* 4.1 27.6 - - + -
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Residues in contact with LYS 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 CYS 3.2 11.7 + - - +
306A ARG* 3.6 13.9 - - + +
307A ARG 3.3 0.6 - - - -
308A LEU* 1.3 78.0 - - - +
310A GLN* 1.3 65.5 + - + +
312A SER 4.5 0.2 - - - -
313A GLY* 3.5 34.0 + - - +
314A LEU* 4.2 11.8 + - + +
352A GLU 5.0 2.2 - - - -
353A LEU* 3.2 45.9 + - + +
354A GLU* 5.3 4.5 - - - +
355A VAL* 5.6 1.3 - - + -
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Residues in contact with GLN 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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306A ARG* 3.3 36.8 + - - +
307A ARG* 3.7 9.5 + - - +
308A LEU 3.3 0.2 - - - -
309A LYS* 1.3 82.8 - - + +
311A GLU* 1.3 57.9 + - - +
312A SER 3.8 0.2 - - - -
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Residues in contact with GLU 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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307A ARG* 3.5 18.2 + - - +
308A LEU* 3.5 5.7 + - + +
309A LYS 3.4 0.2 - - - -
310A GLN* 1.3 81.7 - - - +
312A SER* 1.3 67.9 + - - +
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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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234A ASN* 3.2 19.4 + - - -
289A TYR* 3.8 17.4 + - - -
308A LEU* 3.1 17.0 + - - +
309A LYS 4.5 0.7 - - - -
310A GLN 3.8 0.6 - - - -
311A GLU* 1.3 88.1 + - - +
313A GLY* 1.3 58.2 + - - +
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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