Contacts of the helix formed by residues 293 - 304 (chain C) in PDB entry 3R2A
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 PRO 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 GLU 4.0 4.3 - - - +
292C LEU* 1.3 98.9 - - + +
294C LEU* 1.3 65.7 + - - +
295C ASP* 3.0 4.7 - - + +
296C ASP* 3.1 16.4 + - - +
297C GLN* 3.3 8.1 + - - +
384C SER* 4.1 26.5 - - - +
385C ASN* 5.7 2.9 - - - +
388C GLU* 4.1 8.3 - - - +
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Residues in contact with LEU 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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457B ALA* 4.7 14.4 - - + +
459B HIS* 4.3 7.0 - - + +
460B GLN* 3.7 40.6 - - + +
292C LEU 3.0 5.6 + - - -
293C PRO* 1.3 72.3 - - - +
295C ASP* 1.3 69.0 + - - +
297C GLN* 3.2 34.1 + - - +
298C VAL* 3.3 10.3 + - + +
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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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293C PRO* 3.0 4.9 - - + -
294C LEU* 1.3 88.9 - - - +
296C ASP* 1.3 64.3 + - - +
298C VAL* 3.4 15.8 + - - +
299C ILE* 3.6 16.4 + - + +
384C SER* 5.7 1.3 - - - +
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Residues in contact with ASP 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C LEU* 4.6 14.5 - - + +
293C PRO* 3.1 24.0 + - + +
295C ASP* 1.3 76.2 - - - +
297C GLN* 1.3 66.5 + - - +
299C ILE* 2.9 20.4 + - - +
300C LEU* 3.1 18.0 + - + +
383C LEU* 3.9 16.0 - - + +
384C SER* 1.8 49.2 + - - -
385C ASN* 4.0 12.6 + - - +
389C VAL* 4.5 6.3 - - + +
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Residues in contact with GLN 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B HIS* 2.6 39.8 + - - +
289C PHE* 2.7 52.9 + - + +
290C SER* 3.1 20.9 + - - +
292C LEU* 2.9 27.0 + - + -
293C PRO 3.5 8.5 - - - +
294C LEU* 3.3 17.8 - - - +
296C ASP* 1.3 78.5 - - - +
298C VAL* 1.3 61.1 + - - +
300C LEU* 4.6 1.6 - - - -
301C LEU* 3.1 27.9 + - - +
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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
----------------------------------------------------------
454B MET* 5.0 13.0 - - + -
456B GLU* 4.0 40.3 - - + +
457B ALA* 4.4 8.1 - - + +
459B HIS* 4.6 7.0 - - + -
294C LEU* 3.3 10.4 + - + +
295C ASP* 3.8 12.8 - - - +
296C ASP 3.1 0.8 - - - -
297C GLN* 1.3 82.2 - - - +
299C ILE* 1.3 65.1 + - + +
301C LEU* 4.2 3.3 - - - +
302C ARG* 3.1 41.6 + - + +
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Residues in contact with ILE 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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295C ASP* 3.6 14.6 + - + +
296C ASP* 2.9 9.9 + - - +
298C VAL* 1.3 78.4 - - + +
300C LEU* 1.3 55.7 + - - +
302C ARG* 3.3 23.4 - - + +
303C ALA* 2.7 40.4 + - + +
380C SER* 3.8 22.0 - - - -
381C LYS 3.8 17.5 - - - +
382C GLY* 3.5 34.1 - - - +
383C LEU* 3.9 13.5 - - + +
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Residues in contact with LEU 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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289C PHE* 4.3 15.9 - - + -
292C LEU* 4.1 26.2 - - + -
296C ASP* 3.1 15.2 + - + +
297C GLN 4.0 3.6 - - - +
299C ILE* 1.3 77.8 - - - +
301C LEU* 1.3 68.9 + - - +
303C ALA* 3.7 3.0 - - - +
304C GLY* 3.1 19.6 + - - -
375C LEU* 3.8 29.2 - - + +
376C PHE* 4.3 13.0 - - + -
377C ASN* 3.7 23.8 - - + +
380C SER* 3.9 7.9 - - - +
383C LEU* 3.8 20.2 - - + -
389C VAL* 4.6 7.4 - - + -
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Residues in contact with LEU 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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456B GLU* 4.8 11.0 - - + -
459B HIS* 4.4 15.7 - - + -
279C LEU* 3.9 28.7 - - + +
280C VAL* 3.5 36.8 - - + -
283C ALA* 3.7 26.5 - - + -
289C PHE* 3.9 9.9 - - + -
297C GLN 3.1 18.4 + - - +
298C VAL* 4.2 2.5 - - - +
300C LEU* 1.3 81.6 - - - +
302C ARG* 1.3 63.3 + - - +
304C GLY 3.8 0.9 - - - -
305C TRP* 3.1 25.1 + - + +
308C LEU* 5.5 0.9 - - + -
375C LEU* 4.2 12.1 - - + -
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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
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445B THR* 3.6 29.5 + - - +
447B ILE* 4.0 10.9 - - - +
448B ASP* 5.0 16.5 + - + +
451B LEU* 5.7 5.4 - - + +
454B MET* 4.8 17.4 - - - +
456B GLU* 4.0 17.9 + - - +
298C VAL* 3.1 32.7 + - + +
299C ILE* 3.3 29.3 - - - +
301C LEU* 1.3 81.1 - - - +
303C ALA* 1.3 67.3 + - - +
305C TRP* 3.5 20.4 - - + +
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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
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445B THR* 4.4 23.0 - - + +
447B ILE* 4.6 7.4 - - - +
299C ILE* 2.7 29.2 + - + +
300C LEU* 3.7 3.4 - - - +
302C ARG* 1.3 77.8 - - + +
304C GLY* 1.3 57.2 + - - +
305C TRP 3.4 1.9 + - - -
306C ASN* 4.7 1.7 + - - +
377C ASN* 5.7 3.6 - - + +
380C SER* 3.8 21.5 - - - +
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Residues in contact with GLY 304 (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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300C LEU 3.1 11.8 + - - -
301C LEU 3.8 2.5 - - - -
303C ALA* 1.3 77.3 - - - +
305C TRP* 1.3 63.9 + - - +
306C ASN 3.3 2.8 + - - -
307C GLU* 3.4 11.4 + - - +
308C LEU* 3.0 37.4 + - - +
374C VAL* 5.2 10.1 - - - -
375C LEU* 5.8 1.6 - - - -
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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