Contacts of the helix formed by residues 297 - 312 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C SER 4.4 0.2 + - - -
296C ILE* 1.3 78.5 - - - +
298C VAL* 1.3 66.1 + - - +
299C SER* 3.3 13.7 - - - +
300C ASP* 3.1 41.7 + - - +
301C ILE* 3.4 4.3 + - - +
325C ILE* 4.5 0.4 - - - -
326C GLN* 3.6 51.3 + - - +
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Residues in contact with VAL 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C ILE 4.0 0.4 + - - -
297C ARG* 1.3 68.2 - - - +
299C SER* 1.3 64.3 + - - +
300C ASP 2.9 5.4 - - - -
301C ILE* 2.9 17.7 + - + +
302C ARG* 2.9 18.2 + - + +
325C ILE* 3.5 24.0 - - + -
326C GLN 4.8 1.7 + - - +
342C ILE* 3.7 34.8 - - + -
345C SER* 3.7 30.5 - - - +
346C LEU* 4.0 20.9 - - + -
349C LEU* 5.6 1.8 - - + -
60D ASP* 5.9 2.5 - - - +
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Residues in contact with SER 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ARG* 3.3 12.8 - - - +
298C VAL* 1.3 77.3 - - - +
300C ASP* 1.3 66.4 + - - +
302C ARG* 3.9 13.7 - - - +
303C ALA* 3.1 26.2 + - - +
32D VAL* 5.3 1.0 - - - +
35D SER* 5.1 13.6 + - - -
36D GLU* 5.4 0.2 - - - +
56D LEU* 5.3 11.6 - - - +
60D ASP* 5.3 9.5 + - - -
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Residues in contact with ASP 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C ILE* 4.6 16.0 - - + +
297C ARG* 3.1 34.2 + - - +
298C VAL 2.9 1.0 + - - -
299C SER* 1.3 82.8 + - - +
301C ILE* 1.3 63.3 + - - +
302C ARG 3.2 1.1 - - - -
303C ALA* 4.0 7.0 - - - +
304C LYS* 3.2 40.4 + - + +
36D GLU* 5.3 8.8 - - - +
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Residues in contact with ILE 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C PHE* 3.5 32.4 - - + -
240C LEU* 5.9 0.7 - - + -
296C ILE* 3.6 28.5 - - + -
297C ARG 3.4 5.3 + - - +
298C VAL* 2.9 10.3 + - + +
300C ASP* 1.3 77.6 - - - +
302C ARG* 1.3 57.2 + - - +
305C CYS* 3.1 31.6 + - - -
317C ILE* 4.5 0.7 - - + -
319C ILE* 3.6 35.7 - - + -
325C ILE* 3.6 26.9 - - + -
346C LEU* 4.9 1.1 - - + -
349C LEU* 3.9 20.9 - - + -
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Residues in contact with ARG 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C VAL* 2.9 17.3 + - + +
299C SER* 3.9 12.4 - - - +
301C ILE* 1.3 78.3 - - - +
303C ALA* 1.3 61.4 + - - +
305C CYS 4.2 0.2 - - - -
306C ARG* 2.9 55.1 + - - +
345C SER* 3.0 41.6 + - - -
348C ALA* 3.4 25.7 + - - +
349C LEU* 3.6 35.3 - - + +
352C GLU* 3.0 23.0 + - - +
32D VAL* 4.5 5.6 - - + -
59D ALA 4.8 9.4 + - - -
61D ARG 5.5 0.2 + - - -
62D GLY 5.4 1.4 + - - -
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Residues in contact with ALA 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C SER 3.1 19.4 + - - +
300C ASP* 4.0 9.0 - - - +
301C ILE 3.2 0.2 - - - -
302C ARG* 1.3 76.7 - - - +
304C LYS* 1.3 66.6 + - + +
306C ARG* 3.3 4.2 + - - +
307C ARG* 3.3 20.7 + - - +
32D VAL* 3.7 13.7 - - + -
35D SER* 5.9 0.2 - - - +
36D GLU* 3.3 45.1 - - + +
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Residues in contact with LYS 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C PHE* 4.7 11.9 - - + -
291C ASP* 3.4 37.3 + - + +
293C THR* 3.6 11.5 + - - +
296C ILE* 5.4 4.7 - - + +
300C ASP* 3.2 25.7 + - - +
301C ILE 4.3 1.6 - - - +
303C ALA* 1.3 80.5 - - + +
305C CYS* 1.3 62.7 + - - +
307C ARG* 3.3 13.3 + - - +
308C LEU* 3.1 22.3 + - - +
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Residues in contact with CYS 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C ALA* 4.3 10.1 - - - -
238C PHE* 3.5 28.0 - - - -
301C ILE* 3.1 22.4 + - - +
302C ARG 4.4 2.5 - - - +
304C LYS* 1.3 77.5 - - - +
306C ARG* 1.3 63.1 + - - +
308C LEU* 3.5 8.4 + - - +
309C LYS* 3.3 18.0 + - - +
314C LEU* 4.1 6.0 - - + +
317C ILE* 3.5 29.2 - - + -
349C LEU* 4.8 1.3 - - + -
353C LEU* 3.7 25.5 - - + +
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Residues in contact with ARG 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C ARG* 2.9 66.5 + - - +
303C ALA 3.5 5.6 - - - +
304C LYS 3.2 0.6 - - - -
305C CYS* 1.3 79.0 - - - +
307C ARG* 1.3 62.7 + - + +
309C LYS* 3.4 17.4 + - + +
310C GLN* 3.7 26.7 + - - +
352C GLU* 2.4 46.0 + - - +
353C LEU* 4.1 13.8 - - + +
29D ALA* 4.3 17.9 + - - +
32D VAL* 2.6 51.2 - - - +
33D PRO* 5.3 3.4 - - - -
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Residues in contact with ARG 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ALA 3.3 12.8 + - - +
304C LYS* 3.3 14.0 + - - +
306C ARG* 1.3 80.3 - - + +
308C LEU* 1.3 61.3 + - - +
309C LYS 3.2 0.7 + - - -
310C GLN* 3.3 17.8 + - - +
311C GLU* 3.4 19.6 + - - +
33D PRO* 4.9 4.6 - - - +
36D GLU* 2.4 44.2 + - - +
37D ILE* 5.0 4.8 - - - +
103D GLU* 3.7 25.6 + - - -
107D ARG* 5.2 3.6 - - - +
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Residues in contact with LEU 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C ASN* 5.1 2.7 - - + -
236C ALA* 4.2 22.4 - - + -
289C TYR* 3.7 58.3 - - + +
304C LYS 3.1 14.0 + - - +
305C CYS* 3.9 7.0 - - - +
307C ARG* 1.3 80.3 - - - +
309C LYS* 1.3 62.2 + - - +
311C GLU* 4.0 4.0 - - + +
312C SER* 3.3 26.5 + - - +
313C GLY 3.3 7.1 + - - +
314C LEU* 4.4 17.9 - - + +
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Residues in contact with LYS 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C CYS 3.3 12.4 + - - +
306C ARG* 3.5 13.9 - - + +
307C ARG 3.1 1.0 - - - -
308C LEU* 1.3 79.6 - - - +
310C GLN* 1.3 66.5 + - + +
311C GLU 3.5 0.3 + - - -
312C SER 4.0 0.3 + - - -
313C GLY* 3.5 36.1 + - - +
314C LEU* 4.2 9.8 + - + +
352C GLU 5.0 2.5 - - - +
353C LEU* 3.4 43.3 - - + +
354C GLU* 5.4 4.5 - - - +
355C VAL* 5.9 0.7 - - + -
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Residues in contact with GLN 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C ARG* 3.7 32.9 + - - +
307C ARG* 3.3 9.3 + - - +
309C LYS* 1.3 82.6 - - + +
311C GLU* 1.3 59.3 - - + +
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Residues in contact with GLU 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307C ARG* 3.4 17.7 + - - +
308C LEU* 4.6 3.6 - - + +
309C LYS 3.3 0.6 - - - -
310C GLN* 1.3 80.9 - - - +
312C SER* 1.3 67.9 + - - +
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Residues in contact with SER 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C ASN* 3.3 16.8 + - - -
289C TYR* 3.9 18.7 + - - -
308C LEU* 3.3 17.1 + - - +
309C LYS 4.4 0.4 - - - -
310C GLN 3.7 0.8 - - - -
311C GLU* 1.3 89.3 + - - +
313C GLY* 1.3 58.8 + - - +
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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