Contacts of the helix formed by residues 302 - 316 (chain C) in PDB entry 2OQH
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 LEU 302 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 3.6 40.4 - - + -
16C PRO 5.1 1.8 - - - +
17C LEU* 4.4 12.1 - - + -
31C GLU* 3.6 26.5 - - + +
33C ARG* 4.8 1.6 - - + -
49C GLU* 3.1 23.8 + - - +
300C GLY 4.1 0.7 - - - +
301C GLU* 1.3 77.5 - - - +
303C GLY* 1.3 69.4 + - - +
304C ILE 3.3 0.3 + - - -
305C ALA 3.4 0.9 + - - -
306C THR* 2.8 25.6 + - - -
326C MSE 5.3 1.1 - - - +
327C TYR* 3.9 9.4 - - + -
330C HIS* 3.8 32.8 - - + +
332C ASP 5.8 0.9 - - - +
333C ASP* 3.5 12.6 - - - +
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Residues in contact with GLY 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLU* 3.9 0.2 + - - -
302C LEU* 1.3 69.8 - - - +
304C ILE* 1.3 63.2 + - - +
306C THR* 3.8 1.7 - - - -
307C ALA* 3.0 23.4 + - - +
327C TYR* 3.6 14.9 - - - -
333C ASP* 2.6 26.5 + - - -
335C ILE* 3.5 21.5 - - - +
338C LEU* 3.8 5.3 - - - +
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Residues in contact with ILE 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C VAL* 4.6 8.1 - - + -
47C TRP* 3.9 28.5 - - + +
48C GLY* 3.9 0.7 - - - +
49C GLU* 3.3 34.0 + - + +
102C VAL* 5.0 1.6 - - + -
303C GLY* 1.3 72.3 - - - +
305C ALA* 1.3 65.2 + - - +
307C ALA* 3.0 18.4 + - - +
308C ALA* 3.1 12.0 + - - +
333C ASP* 5.5 0.8 + - - -
334C ILE* 3.7 28.9 - - + -
335C ILE* 3.8 19.7 - - + +
353C LEU* 3.9 12.3 - - + +
355C VAL* 4.6 7.0 - - + -
357C VAL* 3.8 20.4 - - + -
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Residues in contact with ALA 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ARG* 3.5 10.1 - - - +
49C GLU* 2.8 34.9 + - - +
102C VAL* 6.0 0.2 - - - -
272C TYR* 2.7 36.1 + - + +
301C GLU* 3.4 25.8 - - + -
302C LEU 3.9 0.2 - - - +
304C ILE* 1.3 74.5 - - - +
306C THR* 1.3 61.9 + - - +
308C ALA 3.2 1.4 + - - -
309C HIS* 3.2 14.4 + - - +
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Residues in contact with THR 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C GLU* 3.5 23.8 + - - +
302C LEU 2.8 29.0 + - - -
303C GLY 3.8 2.9 - - - -
305C ALA* 1.3 69.7 - - - +
307C ALA* 1.3 59.6 + - - +
309C HIS* 3.1 9.0 + - + +
310C LEU* 2.8 32.0 + - + +
325C SER* 4.9 4.2 + - - +
327C TYR* 3.8 11.5 - - + +
338C LEU* 3.8 14.8 - - + -
345C LEU* 3.7 29.4 - - + -
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Residues in contact with ALA 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C GLY 3.0 13.8 + - - +
304C ILE 3.0 10.0 + - - +
306C THR* 1.3 76.7 - - - +
308C ALA* 1.3 63.5 + - - +
310C LEU* 3.3 11.8 + - - +
311C ALA* 3.1 21.8 + - - +
338C LEU* 4.2 3.8 - - + +
348C PRO* 4.3 10.8 - - + +
353C LEU* 4.0 20.1 - - + +
355C VAL* 3.7 26.7 - - + -
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Residues in contact with ALA 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C VAL* 3.8 30.5 - - + -
271C VAL* 5.5 1.3 - - + -
272C TYR* 3.3 24.0 - - + +
277C ILE* 4.6 8.8 - - + +
304C ILE 3.1 7.8 + - - +
305C ALA 3.4 0.7 - - - +
307C ALA* 1.3 76.5 - - - +
309C HIS* 1.3 64.7 + - + +
311C ALA* 3.0 15.3 + - - +
312C VAL* 3.1 16.7 + - - +
353C LEU* 3.8 13.4 - - + +
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Residues in contact with HIS 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C ASP* 3.4 20.7 + - - -
271C VAL* 3.1 47.8 + - + +
272C TYR* 3.6 16.5 - + - -
296C LEU* 3.7 25.7 - - + +
297C HIS 3.8 17.3 + - - -
301C GLU* 4.2 16.8 + - - +
305C ALA 3.2 6.5 + - - +
306C THR* 3.1 12.4 + - + +
308C ALA* 1.3 80.7 - - - +
310C LEU* 1.3 57.0 + - + +
312C VAL* 3.0 8.1 + - + +
313C VAL* 2.9 30.8 + - - +
323C ILE* 5.4 7.2 - - + +
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Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C VAL* 3.6 39.5 - - + -
306C THR* 2.8 38.7 + - + +
307C ALA* 3.7 5.2 - - - +
309C HIS* 1.3 70.6 - - + +
311C ALA* 1.3 65.8 + - - +
313C VAL* 4.0 2.8 - - + +
314C SER* 2.9 27.8 + - - -
323C ILE* 4.9 4.9 - - + -
338C LEU* 4.0 13.7 - - + -
345C LEU* 3.8 26.7 - - + +
346C ARG 3.8 20.6 - - - +
347C VAL* 4.0 8.0 - - + +
348C PRO* 4.2 14.8 - - + -
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Residues in contact with ALA 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C VAL* 4.1 28.5 - - + -
117C THR* 3.4 26.0 + - - +
120C LEU* 4.0 4.9 - - + +
277C ILE* 6.0 0.2 - - + -
307C ALA 3.1 11.5 + - - +
308C ALA* 3.0 13.0 + - - +
310C LEU* 1.3 76.1 - - - +
312C VAL* 1.3 62.8 + - - +
314C SER* 3.5 2.3 + - - -
315C SER* 3.1 24.4 + - - -
347C VAL* 4.5 2.6 - - + +
353C LEU* 5.2 2.2 - - + -
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Residues in contact with VAL 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C LEU* 4.3 5.2 - - + -
271C VAL* 4.2 22.4 - - + -
277C ILE* 4.2 23.3 - - + +
280C THR* 3.9 21.8 - - + +
281C LYS* 4.6 7.0 - - + -
296C LEU* 4.9 4.0 - - + -
308C ALA 3.1 13.2 + - - +
309C HIS* 3.0 8.5 + - - +
311C ALA* 1.3 77.3 - - - +
313C VAL* 1.3 64.9 + - - +
315C SER* 3.2 6.1 + - - -
316C THR* 2.8 35.3 + - + +
319C LEU* 3.8 20.0 - - + -
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Residues in contact with VAL 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ARG* 2.7 38.0 + - - -
128C VAL* 3.7 35.0 - - + -
129C PRO* 6.2 0.7 - - + -
296C LEU* 3.5 23.3 - - + -
309C HIS 2.9 20.5 + - - +
310C LEU* 4.0 1.1 - - - +
312C VAL* 1.3 74.6 - - - +
314C SER* 1.3 59.5 + - - +
315C SER 3.2 0.7 + - - -
316C THR 3.3 3.5 + - - +
319C LEU* 3.6 35.7 - - + +
321C ARG 5.5 1.1 - - - +
323C ILE* 4.1 17.7 - - + -
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Residues in contact with SER 314 (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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117C THR* 3.7 7.9 - - - +
123C ALA* 3.5 14.5 - - - +
124C VAL* 2.7 37.8 + - - +
125C ARG* 2.7 27.1 + - - -
126C ASP* 4.5 0.3 - - - -
128C VAL* 4.8 0.6 - - - +
310C LEU 2.9 19.1 + - - -
311C ALA 3.7 4.9 - - - -
312C VAL 3.2 0.2 - - - -
313C VAL* 1.3 78.2 - - - +
315C SER* 1.3 50.9 + - - +
347C VAL* 3.5 27.4 - - - +
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Residues in contact with SER 315 (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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117C THR* 3.9 9.9 - - - -
120C LEU* 3.5 23.4 - - - +
121C GLY* 5.3 1.9 - - - -
122C GLY 3.0 27.1 - - - +
124C VAL* 4.2 5.6 - - - +
281C LYS* 3.0 22.9 + - - -
311C ALA 3.1 15.0 + - - -
312C VAL 3.2 4.5 + - - -
313C VAL 3.2 0.4 - - - -
314C SER* 1.3 77.3 - - - +
316C THR* 1.3 57.4 + - - +
317C PRO* 3.5 9.4 - - - +
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Residues in contact with THR 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C VAL* 4.2 0.2 - - - -
125C ARG* 2.8 20.3 + - - -
281C LYS* 2.8 27.7 + - - +
284C ALA* 3.4 32.3 - - + -
288C GLU* 6.5 0.2 - - - -
312C VAL* 2.8 24.3 + - + +
313C VAL 3.3 2.5 + - - +
314C SER 3.6 0.8 + - - -
315C SER* 1.3 75.7 - - - +
317C PRO* 1.3 65.5 - - + +
318C VAL* 3.8 13.5 - - + +
319C LEU* 3.0 25.6 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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