Contacts of the helix formed by residues 300 - 313 (chain C) in PDB entry 1OJ7
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 LYS 300 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204C VAL* 2.8 27.8 + - + +
205C THR 3.8 10.5 - - - +
263C ASP* 2.7 29.3 + - - -
292C LEU* 3.7 17.7 - - - -
293C TRP* 3.8 22.1 - - + +
296C LYS* 3.0 28.4 + - + +
297C ARG 3.8 1.6 - - - -
299C THR* 1.3 79.4 - - - +
301C ARG* 1.3 64.7 + - - +
302C ALA 3.3 2.5 + - - -
303C LYS* 3.4 3.5 + - - -
304C LEU* 2.9 36.3 + - + +
370C GLU* 2.8 35.2 + - - +
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Residues in contact with ARG 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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297C ARG 3.1 20.0 + - - +
298C ASP* 3.5 11.9 - - - +
299C THR 3.3 3.2 + - - -
300C LYS* 1.3 76.1 - - - +
302C ALA* 1.3 80.3 + - - +
304C LEU* 3.3 2.1 + - - +
305C LEU* 3.0 49.5 + - + +
319C ASP* 3.1 29.9 + - + +
323C ILE* 4.2 14.6 - - + -
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Residues in contact with ALA 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C PRO* 3.9 30.5 - - + +
299C THR 5.3 0.6 + - - -
300C LYS 3.4 0.6 - - - -
301C ARG* 1.3 94.5 - - - +
303C LYS* 1.3 59.7 + - + +
305C LEU* 3.3 9.8 + - - +
306C GLN* 3.0 27.0 + - - +
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Residues in contact with LYS 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2C LYS* 5.2 2.9 - - - +
203C TYR* 2.8 51.7 + - - +
204C VAL* 3.9 6.1 - - - +
205C THR* 3.8 30.7 + - - +
206C LYS 3.9 16.5 + - - +
207C PRO* 4.0 17.5 - - + +
208C VAL 5.1 4.2 + - - +
214C ASP* 2.8 36.0 + - - -
300C LYS 3.4 3.6 + - - +
302C ALA* 1.3 76.3 - - + +
304C LEU* 1.3 60.4 + - - +
306C GLN* 3.8 17.5 - - - +
307C TYR* 2.9 30.3 + - - +
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Residues in contact with LEU 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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204C VAL* 3.7 22.2 - - + +
293C TRP* 3.7 43.3 - - + +
297C ARG* 3.9 21.3 - - + -
300C LYS* 2.9 33.6 + - + +
301C ARG 3.7 3.6 - - - +
303C LYS* 1.3 77.3 - - - +
305C LEU* 1.3 58.8 + - - +
307C TYR* 3.6 12.7 + - + +
308C ALA* 3.0 27.5 + - - +
323C ILE* 4.0 30.5 - - + +
326C ALA* 4.5 4.5 - - + +
327C ILE* 5.0 2.7 - - + -
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Residues in contact with LEU 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 ARG* 3.0 52.5 + - + +
302C ALA* 3.6 7.2 - - - +
303C LYS 3.2 0.2 - - - -
304C LEU* 1.3 75.6 - - - +
306C GLN* 1.3 63.6 + - - +
308C ALA* 3.3 4.7 + - - +
309C GLU* 3.1 23.0 + - - +
314C ILE 4.8 0.2 - - - +
319C ASP* 3.5 43.1 - - + +
322C ARG* 3.8 41.1 + - + +
323C ILE* 3.9 9.9 - - + -
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Residues in contact with GLN 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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-2C LYS* 4.0 14.9 + - - +
203C TYR* 3.8 2.6 + - - +
214C ASP* 3.2 29.0 + - - +
218C GLU* 2.7 26.3 + - - +
302C ALA 3.0 16.4 + - - +
303C LYS* 3.4 17.1 + - - +
305C LEU* 1.3 73.2 - - - +
307C TYR* 1.3 56.6 + - - +
309C GLU* 3.3 6.4 + - - +
310C ARG* 2.8 67.8 + - + +
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Residues in contact with TYR 307 (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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196C PHE* 3.3 20.3 - + - -
200C VAL* 4.4 1.3 - - + -
203C TYR* 3.6 20.7 + + + -
204C VAL* 4.3 8.7 - - + -
221C LEU* 3.9 22.4 - - + -
293C TRP* 3.6 25.4 - + - -
303C LYS 2.9 18.9 + - - +
304C LEU* 3.6 13.5 - - + +
306C GLN* 1.3 76.7 - - - +
308C ALA* 1.3 59.0 + - - +
311C VAL* 2.8 61.3 + - + +
312C TRP* 3.0 22.3 + + - -
326C ALA* 4.1 13.2 - - + -
330C THR* 2.5 31.0 + - - +
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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
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304C LEU 3.0 18.7 + - - +
305C LEU* 3.5 9.9 - - - +
306C GLN 3.3 0.4 - - - -
307C TYR* 1.3 77.0 - - - +
309C GLU* 1.3 56.6 + - - +
312C TRP* 3.2 11.5 + - - +
313C ASN 3.1 9.9 + - - -
314C ILE* 2.9 33.8 + - + +
322C ARG* 3.9 15.5 - - + +
326C ALA* 3.6 25.4 - - + -
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Residues in contact with GLU 309 (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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305C LEU 3.1 16.0 + - - +
306C GLN* 3.8 6.8 - - - +
308C ALA* 1.3 76.2 - - - +
310C ARG* 1.3 73.2 + - + +
313C ASN* 3.1 26.3 + - - +
314C ILE 3.4 15.6 + - - +
315C THR* 3.6 24.4 - - + +
322C ARG* 4.8 10.8 + - - +
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Residues in contact with ARG 310 (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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203C TYR* 4.5 0.2 - - - +
214C ASP* 4.7 3.0 - - - +
215C ARG* 3.5 46.7 - - - +
218C GLU* 3.0 51.9 + - + +
222C LEU* 3.8 20.7 - - - +
306C GLN* 2.8 46.2 + - + +
309C GLU* 1.3 87.3 + - + +
311C VAL* 1.3 59.4 + - - +
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Residues in contact with VAL 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C TYR* 4.7 0.2 - - - +
218C GLU* 4.2 21.3 - - + +
221C LEU* 4.0 25.1 - - + -
222C LEU* 3.4 21.8 - - + +
225C ILE* 3.4 31.0 - - + +
307C TYR* 2.8 44.4 + - + +
310C ARG* 1.3 82.4 - - - +
312C TRP* 1.3 73.2 + - + +
313C ASN 3.7 1.1 - - - -
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Residues in contact with TRP 312 (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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196C PHE* 4.9 2.0 - + - -
225C ILE* 3.4 44.2 - - + -
307C TYR* 3.0 46.8 + + - -
308C ALA 3.2 11.2 + - - +
311C VAL* 1.3 87.5 - - + +
313C ASN* 1.3 72.1 + - - +
314C ILE* 3.2 21.4 + - + +
326C ALA* 4.3 8.9 + - + -
329C ALA* 3.7 44.4 - - + -
330C THR* 3.7 5.9 + - - -
333C PHE* 4.0 15.9 - + + -
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Residues in contact with ASN 313 (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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309C GLU* 3.1 19.9 + - - +
310C ARG 4.7 0.2 - - - -
311C VAL 3.7 1.0 - - - -
312C TRP* 1.3 79.0 - - - +
314C ILE* 1.3 60.1 + - - +
315C THR* 3.7 15.0 + - - +
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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