Contacts of the helix formed by residues 297 - 312 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295E SER 4.4 0.2 + - - -
296E ILE* 1.3 77.3 - - - +
298E VAL* 1.3 64.7 + - - +
299E SER* 3.4 17.0 - - - +
300E ASP* 3.3 33.3 + - - +
301E ILE* 3.5 10.9 + - - +
326E GLN* 3.7 52.6 + - - +
36F GLU 6.0 1.3 - - - -
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Residues in contact with VAL 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297E ARG* 1.3 71.6 - - - +
299E SER* 1.3 68.6 + - - +
301E ILE* 2.9 17.7 + - + +
302E ARG* 2.9 18.8 + - + +
325E ILE* 3.6 24.7 - - + +
326E GLN 4.8 2.2 + - - +
341E GLU 5.6 0.2 - - - +
342E ILE* 3.7 35.0 - - + -
345E SER* 3.7 31.0 - - - +
346E LEU* 3.8 20.4 - - + -
349E LEU* 5.6 1.3 - - + -
36F GLU* 5.5 2.0 - - + +
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Residues in contact with SER 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297E ARG* 3.9 22.1 - - - +
298E VAL* 1.3 79.0 - - - +
300E ASP* 1.3 60.3 + - - +
302E ARG* 3.4 4.7 + - - +
303E ALA* 2.9 27.8 + - - +
36F GLU* 3.3 55.3 + - - +
37F ILE* 6.0 0.9 - - - -
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Residues in contact with ASP 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296E ILE* 4.6 16.1 - - + +
297E ARG* 3.3 33.4 + - - +
298E VAL 3.0 1.2 - - - -
299E SER* 1.3 80.2 + - - +
301E ILE* 1.3 65.4 + - - +
302E ARG 3.0 1.3 - - - -
303E ALA* 2.9 8.2 + - - +
304E LYS* 2.9 44.5 + - - +
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Residues in contact with ILE 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E PHE* 3.5 34.4 - - + -
240E LEU* 5.9 0.9 - - + -
296E ILE* 3.5 24.8 - - + +
297E ARG 3.8 7.6 - - - +
298E VAL* 2.9 12.5 + - + +
300E ASP* 1.3 72.7 - - - +
302E ARG* 1.3 57.5 + - - +
305E CYS* 3.0 32.3 + - - +
317E ILE* 4.5 0.2 - - + -
319E ILE* 3.7 33.0 - - + -
325E ILE* 3.5 28.7 - - + -
346E LEU* 4.6 2.2 - - + -
349E LEU* 3.8 22.2 - - + -
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Residues in contact with ARG 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298E VAL* 2.9 12.6 + - + +
299E SER 3.4 8.3 - - - +
301E ILE* 1.3 77.6 - - - +
303E ALA* 1.3 59.5 + - - +
305E CYS* 4.2 0.6 - - - +
306E ARG* 3.2 50.0 + - - +
345E SER* 2.6 33.7 + - - -
348E ALA* 3.6 14.6 + - - +
349E LEU* 3.2 39.3 - - + +
352E GLU* 2.8 25.0 + - - +
353E LEU* 6.3 0.2 - - + -
32F VAL* 3.5 22.0 - - - +
33F PRO* 5.3 6.0 - - - +
36F GLU* 2.7 34.3 + - - -
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Residues in contact with ALA 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299E SER 2.9 17.7 + - - +
300E ASP* 2.9 12.5 + - - +
302E ARG* 1.3 78.6 - - - +
304E LYS* 1.3 63.3 + - + +
306E ARG* 3.6 11.0 + - - +
307E ARG* 3.4 40.8 + - - +
107F ARG* 6.2 1.3 - - - +
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Residues in contact with LYS 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E PHE* 4.4 15.0 - - + -
291E ASP* 3.6 34.7 + - + +
293E THR* 3.7 11.7 + - - +
296E ILE* 5.6 3.3 - - + +
300E ASP* 2.9 33.9 + - - +
301E ILE 4.0 2.5 - - - +
303E ALA* 1.3 77.1 - - + +
305E CYS* 1.3 63.6 + - - +
307E ARG* 3.5 8.3 + - - +
308E LEU* 3.3 22.2 + - - +
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Residues in contact with CYS 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E ALA* 4.4 9.9 - - - -
238E PHE* 3.8 21.3 - - - -
301E ILE* 3.0 22.3 + - - +
302E ARG 4.4 2.0 - - - +
304E LYS* 1.3 74.3 - - - +
306E ARG* 1.3 64.5 + - - +
308E LEU* 3.5 5.1 + - - +
309E LYS* 3.1 23.4 + - - +
314E LEU* 3.7 10.3 - - + +
317E ILE* 3.2 36.1 - - + -
349E LEU* 4.6 2.0 - - + -
353E LEU* 3.6 19.0 - - + +
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Residues in contact with ARG 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302E ARG* 3.2 55.1 + - - +
303E ALA* 3.7 11.4 - - - +
304E LYS 3.3 0.4 - - - -
305E CYS* 1.3 78.1 - - - +
307E ARG* 1.3 64.6 + - + +
309E LYS* 3.4 16.1 + - - +
310E GLN* 3.5 30.9 + - - +
352E GLU* 2.8 43.7 + - - +
353E LEU* 4.2 16.1 - - + +
33F PRO* 4.8 10.3 - - - +
36F GLU* 5.5 0.6 + - - -
103F GLU* 3.6 27.1 + - - -
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Residues in contact with ARG 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303E ALA* 3.4 27.7 + - - +
304E LYS* 3.9 7.0 - - - +
305E CYS 3.3 0.2 - - - -
306E ARG* 1.3 80.6 - - + +
308E LEU* 1.3 63.3 + - - +
309E LYS 3.5 0.3 + - - -
310E GLN* 3.5 16.5 + - - +
311E GLU* 3.5 19.7 + - - +
107F ARG* 6.0 2.2 - - - +
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Residues in contact with LEU 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E ASN* 4.8 4.5 - - + +
236E ALA* 4.6 9.0 - - + -
289E TYR* 3.7 58.1 - - + -
304E LYS 3.3 14.1 + - - +
305E CYS* 3.5 6.0 + - - +
307E ARG* 1.3 75.9 - - - +
309E LYS* 1.3 65.8 + - - +
311E GLU* 3.9 4.7 - - + +
312E SER* 3.2 30.2 + - - +
313E GLY 3.3 5.9 + - - +
314E LEU* 4.3 23.8 - - + -
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Residues in contact with LYS 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305E CYS 3.1 13.6 + - - +
306E ARG* 3.5 13.2 - - - +
307E ARG 3.2 0.6 - - - -
308E LEU* 1.3 79.7 - - - +
310E GLN* 1.3 65.9 + - + +
311E GLU 3.4 0.5 + - - -
312E SER 3.8 0.3 + - - -
313E GLY* 3.4 37.4 + - - +
314E LEU* 4.1 14.4 + - + +
352E GLU 5.2 1.8 - - - +
353E LEU* 3.6 39.5 - - + +
354E GLU* 5.5 3.8 - - - +
355E VAL* 5.8 0.9 - - + -
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Residues in contact with GLN 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306E ARG* 3.5 35.0 + - - +
307E ARG* 3.5 9.8 + - - +
308E LEU 3.3 0.4 - - - -
309E LYS* 1.3 82.1 - - + +
311E GLU* 1.3 59.6 + - - +
312E SER 3.7 0.2 - - - -
542I GLU* 4.5 14.2 - - - +
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Residues in contact with GLU 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E ARG* 3.5 17.2 + - - +
308E LEU* 4.5 4.9 - - + +
309E LYS 3.3 0.4 - - - -
310E GLN* 1.3 80.2 - - + +
312E SER* 1.3 69.9 + - - +
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Residues in contact with SER 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E ASN* 3.2 20.9 + - - -
289E TYR* 3.9 17.7 + - - -
308E LEU* 3.2 17.5 + - - +
309E LYS 4.3 0.4 - - - -
310E GLN 3.7 0.8 - - - -
311E GLU* 1.3 88.6 + - - +
313E GLY* 1.3 59.1 + - - +
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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