Contacts of the helix formed by residues 297 - 312 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137D ASP* 5.1 14.4 - - - +
138D VAL* 5.4 11.7 - - - +
141D ASP* 2.6 36.3 + - - +
296D ILE* 1.3 76.3 - - - +
298D VAL* 1.3 67.5 + - - +
299D SER* 3.4 4.5 - - - +
300D ASP* 3.2 35.4 + - - +
301D ILE* 3.5 9.7 + - - +
325D ILE* 4.4 0.7 - - - -
326D GLN* 3.4 55.9 + - - +
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Residues in contact with VAL 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D ILE 4.1 0.4 + - - -
297D ARG* 1.3 73.9 - - - +
299D SER* 1.3 56.7 + - - +
300D ASP 2.8 1.4 + - - -
301D ILE* 2.8 28.6 + - + +
302D ARG* 2.9 16.3 + - + +
325D ILE* 3.9 13.0 - - + +
326D GLN 4.6 1.5 + - - +
342D ILE* 3.6 45.1 - - + -
345D SER* 3.2 33.7 - - - +
346D LEU* 4.1 17.7 - - + -
349D LEU* 5.7 1.8 - - + -
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Residues in contact with SER 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A MET* 5.7 3.3 - - - +
141D ASP* 2.3 34.3 + - - -
144D ASP* 4.1 18.2 - - - -
297D ARG* 4.2 7.1 - - - +
298D VAL* 1.3 77.0 - - - +
300D ASP* 1.3 61.4 + - - +
302D ARG* 3.7 15.8 - - - +
303D ALA* 2.9 27.7 + - - +
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Residues in contact with ASP 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D ASP* 4.8 0.7 - - - +
296D ILE* 4.7 15.2 - - + +
297D ARG* 3.2 35.3 + - + +
298D VAL 2.8 1.4 + - - -
299D SER* 1.3 79.0 + - - +
301D ILE* 1.3 65.3 + - - +
302D ARG 3.2 0.7 - - - -
303D ALA* 3.8 8.1 - - - +
304D LYS* 3.2 38.1 + - + +
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Residues in contact with ILE 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D PHE* 3.5 32.7 - - + -
240D LEU* 5.8 0.7 - - + -
296D ILE* 3.5 24.2 - - + +
297D ARG 3.5 6.9 + - - +
298D VAL* 2.8 11.3 + - + +
300D ASP* 1.3 73.9 - - - +
302D ARG* 1.3 59.3 + - - +
305D CYS* 2.9 37.0 + - - -
317D ILE* 4.4 0.4 - - + -
319D ILE* 3.7 34.5 - - + -
325D ILE* 3.4 31.4 - - + -
346D LEU* 4.8 2.2 - - + -
349D LEU* 3.8 22.7 - - + -
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Residues in contact with ARG 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A MET* 4.5 15.2 - - - -
298D VAL* 2.9 16.8 + - + +
299D SER* 3.7 12.0 - - - +
301D ILE* 1.3 76.5 - - - +
303D ALA* 1.3 63.0 + - - +
305D CYS* 4.1 1.0 - - - +
306D ARG* 3.1 49.4 + - - +
345D SER* 2.8 43.8 + - - +
348D ALA* 3.5 14.5 - - - +
349D LEU* 3.3 44.1 - - + +
352D GLU* 2.8 29.6 + - - +
353D LEU* 6.3 0.2 - - + -
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Residues in contact with ALA 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A MET* 6.5 0.9 - - + -
299D SER 2.9 19.6 + - - +
300D ASP* 4.2 11.7 - - - +
301D ILE 3.4 0.2 - - - -
302D ARG* 1.3 73.3 - - - +
304D LYS* 1.3 67.5 + - + +
306D ARG* 3.4 15.7 + - - +
307D ARG* 3.3 38.9 + - - +
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Residues in contact with LYS 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D PHE* 4.6 11.7 - - + -
291D ASP* 3.1 35.9 + - + +
293D THR* 3.7 11.7 + - - +
296D ILE* 5.8 2.5 - - + +
300D ASP* 3.2 26.3 + - - +
301D ILE 4.0 2.0 - - - +
303D ALA* 1.3 76.8 - - + +
305D CYS* 1.3 65.9 + - - +
306D ARG 3.3 0.3 + - - -
307D ARG* 3.3 12.4 + - - +
308D LEU* 3.2 21.8 + - - +
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Residues in contact with CYS 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D ALA* 4.4 8.5 - - - -
238D PHE* 3.5 29.4 - - - -
301D ILE* 2.9 25.8 + - - +
302D ARG 4.2 2.2 - - - +
304D LYS* 1.3 77.3 - - - +
306D ARG* 1.3 61.6 + - - +
308D LEU* 3.4 8.8 + - - +
309D LYS* 3.2 22.5 + - - +
314D LEU* 4.2 6.4 - - + +
317D ILE* 3.6 28.7 - - + -
349D LEU* 4.5 2.5 - - + -
353D LEU* 3.7 22.6 - - + +
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Residues in contact with ARG 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A MET* 3.3 54.6 + - - +
302D ARG* 3.1 44.5 + - - +
303D ALA* 3.4 15.3 - - - +
304D LYS 3.2 0.2 - - - -
305D CYS* 1.3 76.7 - - - +
307D ARG* 1.3 62.3 + - + +
309D LYS* 3.4 16.5 + - + +
310D GLN* 3.3 30.3 + - - +
352D GLU* 2.9 41.3 + - - +
353D LEU* 4.2 15.4 - - + +
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Residues in contact with ARG 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D ALA* 3.3 26.0 + - - +
304D LYS* 3.3 12.8 + - - +
306D ARG* 1.3 81.5 - - + +
308D LEU* 1.3 61.0 + - - +
310D GLN* 3.7 10.7 + - - +
311D GLU* 3.5 26.2 + - - +
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Residues in contact with LEU 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ASN* 5.2 1.6 - - + -
236D ALA* 4.3 21.1 - - + -
289D TYR* 3.9 52.9 - - + -
304D LYS 3.2 14.2 + - - +
305D CYS* 3.7 7.2 - - - +
306D ARG 3.3 0.2 - - - -
307D ARG* 1.3 78.1 - - - +
309D LYS* 1.3 64.2 + - - +
311D GLU* 5.0 2.7 - - + -
312D SER* 3.1 31.0 + - - +
313D GLY 3.4 5.5 + - - -
314D LEU* 4.4 17.3 - - + +
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Residues in contact with LYS 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D CYS 3.2 12.6 + - - +
306D ARG* 3.6 11.7 - - - +
307D ARG 3.3 0.4 - - - -
308D LEU* 1.3 78.0 - - - +
310D GLN* 1.3 66.3 + - + +
313D GLY* 3.4 37.2 + - - +
314D LEU* 4.1 11.2 - - + +
352D GLU 5.1 2.2 - - - +
353D LEU* 3.5 44.9 - - + +
354D GLU* 5.5 2.7 - - - -
355D VAL* 5.9 0.9 - - + -
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Residues in contact with GLN 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D ARG* 3.3 34.3 + - - +
307D ARG* 3.7 10.7 + - - +
308D LEU 3.4 0.2 - - - -
309D LYS* 1.3 83.7 - - + +
311D GLU* 1.3 60.6 + - + +
312D SER 3.6 0.2 - - - -
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Residues in contact with GLU 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D ARG* 3.5 16.3 + - - +
308D LEU* 3.5 4.2 + - + +
309D LYS 3.4 0.4 - - - -
310D GLN* 1.3 80.7 - - + +
312D SER* 1.3 66.6 + - - +
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Residues in contact with SER 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D ASN* 3.0 20.9 + - - -
289D TYR* 3.9 18.3 + - - -
308D LEU* 3.1 19.1 + - - +
309D LYS 4.5 0.2 - - - -
310D GLN 3.6 0.8 - - - -
311D GLU* 1.3 88.0 + - - +
313D GLY* 1.3 57.6 + - - +
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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