Contacts of the helix formed by residues 302 - 316 (chain C) in PDB entry 6KQG
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 VAL 302 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C VAL* 4.4 10.8 - - + -
162C ILE* 3.8 20.6 - - + -
269C LEU* 5.0 7.0 - - + -
277C ALA* 5.4 4.9 - - + -
281C LEU* 4.2 3.2 - - + +
283C ILE* 4.6 4.9 - - + -
285C LEU* 3.9 30.3 - - + -
289C THR 4.1 0.7 - - - +
290C LEU* 3.0 38.3 + - + +
301C GLU* 1.3 78.7 - - - +
303C PHE* 1.3 69.4 + - - +
304C LEU 3.4 0.9 - - - -
305C PRO* 3.2 5.9 - - - +
306C THR* 3.1 32.5 + - - +
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Residues in contact with PHE 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C ILE* 4.9 7.6 - - + -
172C ILE* 4.3 7.4 - - + -
174C LEU* 4.9 8.1 - - + +
184C MET* 3.7 21.3 - - + -
193C LEU* 4.3 15.8 - - + +
196C LEU* 3.5 32.1 - - + -
197C LEU* 4.7 13.7 - - + -
200C LEU* 5.0 9.0 - - + -
261C ILE* 3.9 16.8 - - + -
290C LEU* 3.5 50.5 - - + -
291C ALA* 5.3 1.1 - - + -
300C ASP* 3.2 16.5 + - - +
302C VAL* 1.3 79.7 - - + +
304C LEU* 1.3 58.4 + - - +
306C THR* 3.1 7.2 + - - +
307C LEU* 2.9 29.6 + - - +
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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
----------------------------------------------------------
197C LEU* 5.2 5.4 - - + -
202C TYR* 3.3 47.8 - - + +
206C THR* 5.6 2.0 - - + -
207C LEU* 3.8 21.5 - - + -
210C GLU* 4.2 23.3 - - + +
211C LEU* 3.6 30.5 - - + -
300C ASP* 3.5 2.6 + - - -
303C PHE* 1.3 77.7 - - - +
305C PRO* 1.3 66.2 - - + +
307C LEU* 3.3 8.1 + - + +
308C ARG* 2.9 29.8 + - + +
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Residues in contact with PRO 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C LEU* 4.0 12.5 - - + +
283C ILE* 3.7 38.6 - - + -
300C ASP* 4.0 3.4 - - - +
301C GLU 3.7 16.4 - - - +
302C VAL 3.2 13.0 - - - +
304C LEU* 1.3 94.6 - - + +
306C THR* 1.3 55.9 + - - +
308C ARG* 3.3 13.3 + - + +
309C TYR* 2.9 30.3 + - - +
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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
----------------------------------------------------------
146C VAL* 3.8 16.4 - - + +
148C PHE* 3.8 1.8 - - + -
160C ALA* 4.0 17.0 - - + -
162C ILE* 4.2 10.3 - - + +
174C LEU* 3.7 22.2 - - + -
281C LEU* 3.2 26.1 - - - +
302C VAL* 3.1 21.9 + - - +
303C PHE* 3.1 11.9 + - - -
305C PRO* 1.3 76.0 - - - +
307C LEU* 1.3 58.4 + - - +
309C TYR* 3.3 3.5 + - - +
310C LEU* 2.9 26.3 + - - +
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Residues in contact with LEU 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C LEU* 4.6 4.0 - - + -
182C VAL* 3.9 17.9 - - + -
193C LEU* 3.6 23.1 - - + -
197C LEU* 4.2 7.4 - - + -
211C LEU* 3.6 16.2 - - + -
221C LEU* 3.5 32.1 - - + -
303C PHE 2.9 15.6 + - - +
304C LEU* 3.8 9.2 - - + +
306C THR* 1.3 75.3 - - - +
308C ARG* 1.3 60.8 + - - +
310C LEU* 4.3 11.7 - - + -
311C PHE* 2.9 55.0 + - + +
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Residues in contact with ARG 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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210C GLU* 4.9 9.4 - - + +
211C LEU* 4.6 17.6 - - + +
214C TYR* 3.1 32.3 + - + +
281C LEU* 3.7 21.0 + - - +
304C LEU* 2.9 18.4 + - + +
305C PRO* 3.5 12.0 + - + +
307C LEU* 1.3 77.9 - - - +
309C TYR* 1.3 94.8 + - - +
311C PHE* 3.4 4.5 + - - +
312C ALA* 3.0 25.2 + - - +
320C HIS* 2.9 36.4 + - - -
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Residues in contact with TYR 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C PHE* 3.5 33.7 - + + -
280C LYS* 3.1 57.6 + - - +
281C LEU* 3.8 8.3 - - + -
305C PRO 2.9 16.3 + - - +
306C THR 3.6 0.2 - - - +
308C ARG* 1.3 100.6 - - - +
310C LEU* 1.3 58.4 + - - +
312C ALA* 3.3 2.0 + - - +
313C LEU* 2.9 29.4 + - + +
319C GLY 4.0 3.9 + - - -
320C HIS* 3.5 34.6 - + + -
321C GLU* 3.3 23.6 + - - +
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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
----------------------------------------------------------
148C PHE* 3.8 21.7 - - + -
158C TYR* 3.7 38.1 - - + +
160C ALA* 4.3 5.4 - - + +
174C LEU* 3.8 35.7 - - + +
175C GLU 4.7 0.7 - - - +
176C VAL* 4.3 19.1 - - + -
182C VAL* 5.1 1.1 - - + -
306C THR 2.9 16.5 + - - +
307C LEU* 3.7 17.0 - - + +
308C ARG 3.2 0.4 - - - -
309C TYR* 1.3 76.8 - - - +
311C PHE* 1.3 65.1 + - + +
313C LEU* 3.2 3.9 + - + +
314C THR* 2.9 32.4 + - - +
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Residues in contact with PHE 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C VAL* 4.2 25.8 - - + -
182C VAL* 4.6 15.0 - - + -
211C LEU* 3.5 41.5 - - + -
214C TYR* 4.0 16.4 - + + -
217C LEU* 3.3 61.3 - - + +
218C VAL* 4.2 6.3 - - - -
221C LEU* 4.6 3.6 - - + -
307C LEU* 2.9 39.8 + - + +
308C ARG 3.8 3.4 - - - +
310C LEU* 1.3 77.3 - - + +
312C ALA* 1.3 58.0 + - - +
314C THR* 3.2 2.6 + - - -
315C ALA* 2.9 26.5 + - - +
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Residues in contact with ALA 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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214C TYR* 3.7 19.9 - - + +
308C ARG* 3.0 19.6 + - - +
309C TYR 3.7 4.0 - - - +
311C PHE* 1.3 76.5 - - - +
313C LEU* 1.3 62.5 + - - +
316C GLY 3.1 17.5 + - - -
317C VAL* 3.1 23.7 + - + +
320C HIS* 3.3 35.0 - - + +
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Residues in contact with LEU 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C PHE* 3.7 33.7 - - + -
158C TYR* 3.6 49.9 + - + +
309C TYR* 2.9 20.2 + - + +
310C LEU* 3.2 6.0 + - + +
312C ALA* 1.3 75.9 - - - +
314C THR* 1.3 63.6 + - - +
316C GLY* 3.5 10.2 + - - -
320C HIS* 3.5 35.8 - - + +
321C GLU* 4.0 14.4 - - - +
322C VAL* 4.3 5.2 - - + +
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Residues in contact with THR 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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156C GLY 3.9 19.2 - - - +
157C ARG* 4.0 23.1 - - - +
158C TYR* 4.1 18.3 + - - -
176C VAL* 5.0 8.4 - - + +
217C LEU* 4.3 22.2 - - + -
310C LEU* 2.9 24.2 + - - +
311C PHE* 3.2 8.8 + - - -
313C LEU* 1.3 79.7 - - - +
315C ALA* 1.3 61.6 + - - +
316C GLY* 3.3 1.0 + - - -
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Residues in contact with ALA 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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214C TYR* 4.5 11.0 - - + -
215C GLY 5.2 4.0 - - - +
217C LEU* 4.1 13.2 - - + +
311C PHE 2.9 15.4 + - - +
314C THR* 1.3 76.6 - - - +
316C GLY* 1.3 59.5 + - - +
317C VAL* 3.9 17.3 - - + -
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Residues in contact with GLY 316 (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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312C ALA 3.1 5.5 + - - -
313C LEU* 4.0 7.4 - - - -
314C THR 3.2 4.0 - - - -
315C ALA* 1.3 80.3 - - - +
317C VAL* 1.3 66.5 + - - +
318C PRO* 3.6 5.2 - - - +
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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