Contacts of the helix formed by residues 293 - 300 (chain G) in PDB entry 3SRF
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 293 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291G VAL* 3.0 19.4 + - + +
292G ALA* 1.3 71.4 - - - +
294G GLY* 1.3 60.4 + - - +
296G LEU* 4.3 5.4 - - - -
297G GLY* 2.9 12.1 + - - -
305G VAL* 3.7 24.7 - - + +
309G GLN* 2.8 30.7 + - - +
325G CYS* 3.8 19.0 - - - -
326G ALA 2.9 24.8 + - - +
327G THR* 3.4 10.7 + - - -
328G GLN 4.0 0.6 + - - -
329G MET* 3.3 14.6 - - - +
346G ASP* 2.8 44.0 + - - -
341H ARG* 2.9 42.8 + - + -
342H ALA 3.9 9.3 - - - +
345H SER* 3.9 9.7 + - - -
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Residues in contact with GLY 294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177G ASP* 4.8 2.9 - - - +
293G ARG* 1.3 81.4 - - - +
295G ASP* 1.3 60.6 - - - +
297G GLY 3.5 0.2 + - - -
298G ILE* 3.4 8.8 - - - +
327G THR* 3.3 16.6 + - - -
328G GLN* 4.5 7.4 - - - -
534G PYR 3.0 17.2 + - - -
341H ARG* 3.1 26.6 + - - -
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Residues in contact with ASP 295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209G ASN* 3.1 24.0 + - - +
243G PHE* 3.6 19.7 - - + -
271G GLU* 2.9 28.6 - - + +
292G ALA 3.6 0.2 + - - -
294G GLY* 1.3 72.0 - - - +
296G LEU* 1.3 64.8 + - - +
298G ILE* 3.1 11.2 + - - +
299G GLU* 3.1 24.3 + - + +
533G MG 2.0 31.5 - - - -
534G PYR 3.0 7.7 + - - +
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Residues in contact with LEU 296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270G ILE 3.5 21.8 - - - +
271G GLU 3.3 9.0 + - - +
272G ASN 3.5 28.9 - - - +
276G VAL* 4.1 7.0 - - + -
291G VAL* 4.7 8.7 - - + -
292G ALA 3.1 18.1 + - - +
293G ARG* 4.1 3.8 - - - +
295G ASP* 1.3 77.0 - - - +
297G GLY* 1.3 56.7 + - - +
298G ILE 3.1 0.4 - - - -
299G GLU* 4.3 0.7 - - + -
300G ILE* 3.0 57.9 + - + +
305G VAL* 4.4 11.2 - - + -
308G ALA* 4.2 12.1 - - + -
312G MET* 3.9 25.8 - - + -
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Residues in contact with GLY 297 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293G ARG 2.9 11.3 + - - -
294G GLY 3.5 0.2 + - - -
295G ASP 3.2 0.6 - - - -
296G LEU* 1.3 74.4 - - - +
298G ILE* 1.3 58.4 + - - +
300G ILE 2.9 14.0 - - - +
301G PRO* 4.8 0.2 - - - +
302G ALA* 3.8 16.8 + - - +
305G VAL* 3.6 18.8 - - - +
338H ARG* 4.3 6.8 + - - -
341H ARG* 3.4 25.7 + - - -
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Residues in contact with ILE 298 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174G TYR* 3.8 22.3 - - + -
177G ASP* 3.8 30.1 - - - +
178G GLY* 3.8 13.7 - - - -
209G ASN* 3.4 30.3 - - + +
211G PRO* 3.4 19.9 - - - +
294G GLY 3.4 20.6 - - - +
295G ASP* 3.1 8.2 + - - +
297G GLY* 1.3 74.9 - - - +
299G GLU* 1.3 65.5 + - - +
300G ILE 3.4 2.1 - - - -
338H ARG* 3.7 21.8 - - - +
341H ARG* 3.5 9.4 - - - +
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Residues in contact with GLU 299 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209G ASN* 3.4 32.8 + - - +
210G LEU 4.0 18.4 + - - +
211G PRO* 4.1 20.3 - - - +
212G GLY 5.1 3.1 + - - -
243G PHE* 5.5 7.1 - - + -
271G GLU 3.2 27.6 - - - +
272G ASN* 3.9 26.5 - - + +
273G HIS* 4.5 8.1 + - - +
295G ASP* 3.1 10.6 + - + +
296G LEU* 3.2 3.1 + - - +
298G ILE* 1.3 80.5 - - - +
300G ILE* 1.3 62.6 + - + +
301G PRO* 4.9 0.3 - - - +
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Residues in contact with ILE 300 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273G HIS* 3.6 37.2 - - + -
296G LEU* 3.0 37.8 + - + +
297G GLY 2.9 19.1 - - - +
298G ILE 4.2 2.0 - - - -
299G GLU* 1.3 81.5 + - - +
301G PRO* 1.4 80.5 - - + +
304G LYS* 3.8 27.1 - - + -
305G VAL* 4.0 17.3 - - + +
308G ALA* 4.5 4.3 - - + -
34H ILE* 4.2 24.0 - - + -
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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