Contacts of the helix formed by residues 293 - 300 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291C VAL* 3.0 26.7 + - + -
292C ALA* 1.3 70.1 - - - +
294C GLY* 1.3 56.6 + - - +
296C LEU* 3.9 7.0 - - - -
297C GLY 2.7 29.6 + - - -
305C VAL* 3.7 24.4 - - + +
309C GLN* 2.9 27.4 + - - +
325C CYS* 3.9 10.0 - - - -
326C ALA 2.7 27.9 + - - +
327C THR* 3.1 18.2 + - - -
329C MET* 3.5 11.0 - - - +
346C ASP* 2.7 42.8 + - - -
341D ARG* 2.9 46.0 + - + +
342D ALA 3.9 0.4 - - - +
345D SER* 4.2 5.5 - - - -
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Residues in contact with GLY 294 (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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177C ASP* 4.8 4.9 - - - -
292C ALA 3.3 1.8 - - - -
293C ARG* 1.3 77.4 - - - +
295C ASP* 1.3 60.9 + - - +
297C GLY 3.6 0.2 + - - -
298C ILE* 3.4 9.3 - - - +
327C THR* 3.4 21.9 + - - +
328C GLN* 4.5 2.9 - - - -
534C PYR 3.5 15.7 - - - -
341D ARG* 2.8 32.5 + - - -
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Residues in contact with ASP 295 (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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209C ASN* 3.3 23.2 + - - +
243C PHE* 3.3 22.2 - - + -
271C GLU* 3.5 26.5 - - + +
292C ALA 3.8 2.2 + - - -
294C GLY* 1.3 73.1 - - - +
296C LEU* 1.3 60.2 + - - +
298C ILE* 3.1 10.5 + - - +
299C GLU* 2.9 32.4 + - + +
533C MG 2.7 25.0 - - - -
534C PYR 3.7 6.8 + - - +
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Residues in contact with LEU 296 (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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270C ILE 3.7 22.2 - - - +
271C GLU 3.4 16.4 + - - -
272C ASN 4.7 0.7 - - - +
276C VAL* 4.2 18.2 - - + -
291C VAL* 4.3 13.0 - - + -
292C ALA 3.2 18.7 + - - +
293C ARG* 3.5 7.2 - - - +
295C ASP* 1.3 76.6 - - - +
297C GLY* 1.3 58.8 + - - +
298C ILE 3.1 0.2 - - - -
299C GLU 3.8 0.2 - - - -
300C ILE* 3.0 66.0 + - + +
305C VAL* 4.3 9.9 - - + -
308C ALA* 4.4 8.1 - - + -
312C MET* 3.9 24.7 - - + -
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Residues in contact with GLY 297 (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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293C ARG 2.7 14.1 + - - -
295C ASP 3.2 0.2 - - - -
296C LEU* 1.3 71.9 - - - +
298C ILE* 1.3 60.5 + - - +
300C ILE 3.0 12.4 - - - +
302C ALA* 3.8 10.2 + - - +
305C VAL* 3.6 17.9 - - - +
338D ARG* 3.0 18.9 + - - -
341D ARG* 3.5 22.9 - - - -
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Residues in contact with ILE 298 (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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174C TYR* 3.8 27.3 - - + -
177C ASP* 3.6 13.7 - - - +
178C GLY* 3.5 31.0 - - - +
209C ASN* 3.4 43.1 - - + +
211C PRO* 3.4 13.8 - - - +
294C GLY 3.4 18.6 - - - +
295C ASP* 3.1 9.6 + - - +
297C GLY* 1.3 77.4 - - - +
299C GLU* 1.3 62.4 + - - +
300C ILE 3.3 5.0 + - - +
338D ARG* 4.1 7.4 + - - +
341D ARG* 3.5 10.1 - - - +
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Residues in contact with GLU 299 (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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209C ASN* 3.1 24.4 + - - +
210C LEU 3.6 22.0 + - - +
211C PRO* 3.7 33.5 - - - +
212C GLY 5.3 0.9 + - - -
243C PHE* 5.5 6.3 - - + -
271C GLU 3.4 19.1 - - - +
272C ASN* 3.9 24.4 - - + +
273C HIS* 4.7 5.5 - - - +
295C ASP* 2.9 21.4 + - + +
296C LEU 4.1 1.6 - - - +
298C ILE* 1.3 76.6 - - - +
300C ILE* 1.3 63.0 + - + +
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Residues in contact with ILE 300 (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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272C ASN 4.7 0.2 - - - -
273C HIS* 3.9 43.3 - - + +
296C LEU* 3.0 40.2 + - + +
297C GLY 3.0 19.2 - - - +
298C ILE 3.9 4.0 - - - -
299C GLU* 1.3 81.9 - - - +
301C PRO* 1.4 78.1 - - + +
304C LYS* 3.8 27.4 - - + -
305C VAL* 4.2 11.4 - - + +
308C ALA* 4.6 2.2 - - + -
34D ILE* 3.9 22.4 - - + -
338D ARG* 5.0 0.5 + - - -
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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