Contacts of the helix formed by residues 296 - 308 (chain C) in PDB entry 3OP5
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 296 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151C ARG* 3.6 28.0 - - - +
255C LEU* 4.2 9.4 - - + -
286C MET* 4.9 0.9 - - - +
290C PHE* 3.5 36.1 - - + -
294C ASN 3.7 4.0 - - - +
295C ALA* 1.4 82.6 - - + +
297C GLY* 1.3 65.6 + - - +
298C GLU* 3.2 24.9 - - - +
299C ILE* 3.1 26.8 + - + +
300C ALA* 3.7 5.0 + - - +
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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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151C ARG* 4.3 2.8 - - - +
295C ALA 3.3 6.5 + - - -
296C PRO* 1.3 69.9 - - - +
298C GLU* 1.3 60.1 + - - +
300C ALA* 3.4 8.8 + - - +
301C LYS* 3.1 38.9 + - - +
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Residues in contact with GLU 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ARG* 2.8 48.4 + - - +
155C LEU* 3.7 32.2 - - + +
255C LEU* 5.9 0.2 - - - +
296C PRO* 3.4 11.6 - - - +
297C GLY* 1.3 71.3 + - - -
299C ILE* 1.4 67.1 + - + +
301C LYS* 4.3 3.6 - - - -
302C TYR* 2.8 32.0 + - - +
323C ILE* 3.3 37.3 - - + +
324C LEU* 4.6 2.9 - - + +
326C GLN* 5.8 0.2 - - + -
327C GLY* 3.6 15.0 - - - +
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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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154C VAL* 5.0 3.1 - - + -
155C LEU* 5.2 2.7 - - + -
248C GLY 5.3 0.2 - - - +
251C MET* 3.9 36.6 - - + -
252C ILE* 4.0 28.5 - - + -
255C LEU* 3.8 29.6 - - + -
286C MET* 4.0 16.8 - - + -
290C PHE* 4.5 3.6 - - + -
296C PRO* 3.1 24.7 + - + +
298C GLU* 1.4 86.6 - - + +
300C ALA* 1.3 56.9 + - - +
302C TYR* 3.4 5.1 + - - +
303C MET* 2.9 37.5 + - + +
324C LEU* 5.2 2.0 - - + -
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Residues in contact with ALA 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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282C ILE* 4.1 10.5 - - + +
286C MET* 4.0 29.3 - - + -
295C ALA* 6.4 0.4 - - + -
296C PRO 3.7 3.2 + - - +
297C GLY* 3.4 12.0 + - - +
299C ILE* 1.3 78.1 - - - +
301C LYS* 1.4 56.7 + - + +
303C MET* 3.3 2.9 + - - +
304C GLU* 2.9 37.5 + - + +
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Residues in contact with LYS 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C GLY* 3.1 25.7 + - - +
298C GLU* 3.8 7.6 - - - +
300C ALA* 1.4 75.0 - - + +
302C TYR* 1.3 53.9 + - - +
304C GLU* 3.4 7.1 + - - +
305C THR* 2.7 37.6 + - - -
323C ILE* 3.8 22.4 - - + +
326C GLN* 6.4 1.6 - - + -
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Residues in contact with TYR 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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162C LEU* 4.5 16.8 - - + -
244C LEU* 2.6 43.1 + - - +
247C LEU* 3.6 18.1 - - + +
248C GLY* 3.7 8.1 - - - -
251C MET* 3.5 30.7 - - + -
298C GLU 2.8 19.1 + - - +
299C ILE* 3.5 6.5 - - - +
301C LYS* 1.3 76.7 - - - +
303C MET* 1.4 67.7 + - - +
305C THR* 3.3 4.2 + - - -
306C VAL* 3.1 46.1 + - + +
320C LEU* 3.7 29.2 - - + -
323C ILE* 3.8 13.6 - - + +
324C LEU* 4.4 15.5 - - + -
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Residues in contact with MET 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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245C GLU* 5.0 8.1 - - + +
248C GLY* 3.8 26.7 - - - +
249C TYR* 3.8 34.1 - - + -
251C MET* 5.4 0.2 - - - -
252C ILE* 4.1 5.8 - - + -
282C ILE* 3.6 22.7 - - + +
285C LEU* 3.9 19.7 - - + -
286C MET* 4.4 12.1 - - + -
299C ILE* 2.9 27.5 + - + +
300C ALA 3.3 4.7 + - - +
302C TYR* 1.4 81.5 - - - +
304C GLU* 1.4 57.2 + - - +
306C VAL* 3.5 5.8 + - - +
307C LYS* 3.0 29.1 + - - +
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Residues in contact with GLU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C ILE* 3.7 32.7 + - + +
283C ALA 5.2 1.6 + - - -
300C ALA* 2.9 24.3 + - + +
301C LYS* 3.7 7.6 - - - +
303C MET* 1.4 74.2 - - - +
305C THR* 1.3 62.7 + - - +
307C LYS* 3.5 19.4 + - - +
308C LEU* 3.4 27.0 + - + +
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Residues in contact with THR 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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301C LYS 2.7 21.8 + - - -
302C TYR 3.3 4.9 + - - -
304C GLU* 1.3 74.8 - - - +
306C VAL* 1.4 63.3 + - - +
308C LEU* 3.2 26.2 + - + +
309C LEU* 3.7 10.6 + - + +
316C LEU* 5.8 0.7 - - + +
319C ASN* 3.5 26.1 + - - +
320C LEU* 3.9 21.8 - - + -
323C ILE* 3.4 11.9 - - + +
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Residues in contact with VAL 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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241C ARG* 3.7 27.1 - - + +
244C LEU* 3.8 19.1 - - + -
245C GLU* 3.9 21.3 - - + +
279C ARG* 5.1 0.5 + - - -
302C TYR* 3.1 40.8 + - + +
303C MET* 4.0 7.4 - - - +
305C THR* 1.4 72.1 - - - +
307C LYS* 1.3 63.2 + - - +
309C LEU* 3.1 29.6 + - + +
320C LEU* 4.2 11.0 - - + -
366C EDO 6.0 1.2 - - - -
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Residues in contact with LYS 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ARG* 2.8 85.5 + - + +
280C GLU* 3.4 26.2 + - - +
282C ILE* 3.8 13.3 - - + +
303C MET 3.0 18.6 + - - +
304C GLU* 3.5 20.5 + - - +
305C THR 3.3 0.2 - - - -
306C VAL* 1.3 76.6 - - - +
308C LEU* 1.4 60.8 + - + +
309C LEU 3.4 2.1 + - - +
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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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304C GLU 3.4 15.0 + - - +
305C THR* 3.2 18.9 + - + +
307C LYS* 1.4 76.0 - - + +
309C LEU* 1.3 61.9 + - - +
310C ASP* 3.6 2.6 + - - +
313C GLU* 3.5 9.7 - - - +
367C EDO 3.8 7.4 + - - -
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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