Contacts of the helix formed by residues 302 - 319 (chain C) in PDB entry 4OGB
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 ASN 302 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291C LYS* 5.2 1.4 - - - +
301C ASP* 1.3 90.6 + - + +
303C TYR* 1.3 63.8 + - - +
304C SER* 3.4 14.0 - - - +
305C ASP* 2.7 58.8 + - - +
306C ARG* 3.0 22.0 + - - +
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Residues in contact with TYR 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C GLU* 5.9 2.7 - - - -
259C SER* 6.1 0.2 - - - -
262C LYS* 3.5 30.1 - - + +
263C MET* 3.9 25.7 - - + +
266C ASP* 2.6 27.6 + - - -
302C ASN* 1.3 69.9 - - - +
304C SER* 1.3 70.2 + - - +
305C ASP 3.0 0.2 + - - -
306C ARG* 4.3 10.5 - - + +
307C ILE* 3.0 62.1 + - + +
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Residues in contact with SER 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C ASN* 3.2 13.6 + - - +
303C TYR* 1.3 85.2 - - - +
305C ASP* 1.3 58.6 + - - +
307C ILE* 3.9 7.2 - - - +
308C GLN* 3.0 32.9 + - - +
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Residues in contact with ASP 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C MET* 3.2 24.5 - - + +
291C LYS* 4.4 10.6 + - - -
299C LEU 5.3 0.7 - - - +
300C LEU* 4.3 18.8 - - + +
301C ASP* 4.1 7.3 - - - +
302C ASN* 2.7 41.2 + - - +
303C TYR 3.1 0.2 - - - -
304C SER* 1.3 77.6 + - - +
306C ARG* 1.3 64.9 + - - +
308C GLN* 3.4 8.7 + - - +
309C VAL* 3.1 29.2 + - - +
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Residues in contact with ARG 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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184C VAL* 2.6 31.1 + - - +
185C PHE* 3.6 20.0 - - + +
186C THR* 3.9 13.7 - - - +
189C GLU* 2.6 45.6 + - - +
300C LEU* 3.8 33.9 + - + +
301C ASP 4.0 7.0 - - - -
302C ASN 3.0 19.5 - - - +
303C TYR* 3.2 8.9 + - + +
305C ASP* 1.3 75.6 - - - +
307C ILE* 1.3 57.2 + - - +
309C VAL* 3.2 5.0 + - - +
310C LEU* 3.0 31.9 + - + +
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Residues in contact with ILE 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C MET* 3.8 36.8 - - + +
266C ASP* 3.8 15.7 - - + +
267C ILE* 4.0 14.1 - - + -
303C TYR* 3.0 62.9 + - + +
304C SER* 3.9 7.4 - - - +
306C ARG* 1.3 74.2 - - - +
308C GLN* 1.3 61.0 + - - +
310C LEU* 3.1 11.2 + - + -
311C GLN* 2.6 50.5 + - + +
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Residues in contact with GLN 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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279C LEU* 5.5 2.2 - - + -
282C ASP* 2.7 55.4 + - + +
283C LEU* 3.7 3.6 - - + +
286C MET* 3.2 25.7 - - + +
304C SER* 3.0 23.7 + - - +
305C ASP* 3.4 10.2 - - - +
307C ILE* 1.3 82.7 - - + +
309C VAL* 1.3 56.8 + - - +
311C GLN* 3.6 14.2 - - - +
312C ASN* 2.8 45.5 + - - +
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Residues in contact with VAL 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C LEU* 4.5 10.1 - - + -
185C PHE* 3.8 22.4 - - + -
283C LEU* 5.4 2.0 - - + -
286C MET* 3.5 24.7 - - - -
298C LEU* 5.3 1.1 - - + -
300C LEU* 3.9 17.3 - - + -
305C ASP 3.1 15.7 + - - +
306C ARG 3.5 7.2 - - - +
307C ILE 3.1 0.2 - - - -
308C GLN* 1.3 73.0 - - - +
310C LEU* 1.3 61.8 + - - +
312C ASN* 3.7 3.7 - - - -
313C MET* 2.8 32.5 + - + +
384C TRP* 3.9 24.5 - - + -
387C LEU* 4.6 9.6 - - + -
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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
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176C LEU* 4.1 19.5 - - + -
185C PHE* 3.8 30.5 - - + -
189C GLU* 4.1 35.9 - - + +
193C ALA* 4.2 10.3 - - + -
263C MET* 4.9 3.8 - - - -
267C ILE* 4.0 21.9 - - + +
306C ARG* 3.0 20.3 + - + +
307C ILE* 3.7 20.6 - - + +
309C VAL* 1.3 74.1 - - - +
311C GLN* 1.3 64.9 + - - +
313C MET* 3.5 7.2 - - + +
314C VAL* 3.0 29.6 + - - +
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Residues in contact with GLN 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C ASP* 2.9 37.6 + - - +
267C ILE* 4.0 14.1 - - - +
270C ALA* 3.8 21.3 - - + +
271C THR* 6.0 0.3 - - - +
279C LEU* 4.1 17.1 - - + +
307C ILE* 2.6 36.9 + - + +
308C GLN* 3.6 16.3 + - - +
310C LEU* 1.3 73.7 - - - +
312C ASN* 1.3 55.9 + - - +
314C VAL* 3.6 1.9 + - - +
315C HIS* 3.0 29.8 + - - +
508C EDO 3.4 20.0 + - - -
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Residues in contact with ASN 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C LEU* 3.7 47.1 + - - +
283C LEU* 3.7 42.5 - - + +
308C GLN* 2.8 35.7 + - - +
309C VAL 4.0 2.9 - - - +
311C GLN* 1.3 74.6 - - - +
313C MET* 1.3 56.7 + - - +
315C HIS* 3.5 5.1 - - - +
316C CYS* 2.7 41.8 + - - -
380C LEU* 4.2 10.2 - - - +
384C TRP* 4.5 5.2 - - + -
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Residues in contact with MET 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C THR* 4.1 12.6 - - + +
175C LEU* 3.6 27.2 - - + +
176C LEU* 3.5 47.1 - - + -
181C LEU* 3.7 29.8 - - + -
185C PHE* 4.1 11.2 - - + -
193C ALA* 5.3 0.7 - - - -
309C VAL* 2.8 25.7 + - + +
310C LEU* 3.5 13.7 - - + +
312C ASN* 1.3 73.1 - - - +
314C VAL* 1.3 52.2 + - + +
316C CYS* 3.0 7.7 + - - +
317C ALA* 2.8 30.5 + - - +
384C TRP* 3.8 19.9 - - + -
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Residues in contact with VAL 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C VAL* 4.5 8.7 - - + -
172C THR* 3.8 18.4 - - + +
193C ALA* 3.9 15.5 - - + +
196C ALA 5.4 0.7 - - - -
197C SER* 3.8 22.7 - - - +
200C HIS* 5.5 2.5 - - + -
267C ILE* 3.6 30.3 - - + +
271C THR* 4.2 17.3 - - + -
310C LEU 3.0 16.5 + - - +
311C GLN 4.1 1.1 - - - +
313C MET* 1.3 72.8 - - + +
315C HIS* 1.3 61.5 + - - +
317C ALA* 3.2 8.1 + - - +
318C ASP* 2.8 28.4 + - - +
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Residues in contact with HIS 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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270C ALA 4.3 13.6 + - - +
271C THR* 4.8 11.7 + - - +
273C MET* 3.7 16.6 - - - -
276C HIS* 2.9 35.7 + - + +
279C LEU* 3.7 27.6 - - + -
311C GLN 3.0 20.0 + - - +
312C ASN* 3.5 4.7 - - - +
313C MET 3.2 0.2 - - - -
314C VAL* 1.3 76.6 - - - +
316C CYS* 1.3 56.8 + - - +
318C ASP* 3.3 7.8 + - - +
319C LEU* 3.0 52.2 + - + +
380C LEU* 3.6 23.6 - - + -
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Residues in contact with CYS 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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175C LEU* 4.2 4.3 - - + -
283C LEU* 5.6 0.2 - - - -
312C ASN* 2.7 26.2 + - - -
313C MET* 3.2 8.7 - - - +
315C HIS* 1.3 70.7 - - - +
317C ALA* 1.3 66.5 + - - +
319C LEU 3.0 12.8 + - - -
320C SER* 3.0 14.0 + - - -
380C LEU* 3.7 33.7 - - - -
381C TRP* 3.5 26.5 - - + -
384C TRP* 4.0 31.0 - - + -
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Residues in contact with ALA 317 (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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167C ASP* 5.3 0.9 - - - +
168C VAL* 3.8 26.7 - - + +
171C SER* 4.0 7.3 - - - -
172C THR* 3.3 36.3 - - - +
175C LEU* 4.1 5.0 - - + +
313C MET 2.8 14.0 + - - +
314C VAL 3.2 7.8 + - - +
316C CYS* 1.3 71.7 - - - +
318C ASP* 1.3 58.6 + - - +
320C SER* 2.8 26.5 + - - -
321C ASN* 5.4 0.7 + - - -
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Residues in contact with ASP 318 (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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159C TYR* 4.2 13.9 + - - -
164C HIS* 3.2 9.9 + - - -
168C VAL* 3.9 9.4 - - + +
200C HIS* 3.1 10.5 + - + +
271C THR* 4.1 24.8 - - + +
273C MET* 5.7 0.2 - - - +
314C VAL* 2.8 19.2 + - + +
315C HIS* 3.4 12.1 + - - +
316C CYS 3.1 0.2 - - - -
317C ALA* 1.3 73.0 - - - +
319C LEU* 1.3 68.1 + - + +
320C SER 3.4 2.3 + - - -
321C ASN* 4.8 4.0 + - - -
502C 2SR 4.2 15.1 - - - +
510C ZN 2.3 35.2 - - - -
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Residues in contact with LEU 319 (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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273C MET* 4.0 5.6 - - + -
315C HIS* 3.0 44.8 + - + +
316C CYS 3.0 6.5 + - - +
318C ASP* 1.3 83.0 - - - +
320C SER* 1.3 56.8 + - - +
321C ASN* 3.5 1.6 - - - -
322C PRO* 4.2 4.3 - - - -
372C PHE* 4.1 11.0 - - + -
376C ILE* 3.9 24.0 - - + -
377C VAL* 3.7 20.5 - - + +
380C LEU* 3.9 15.9 - - + -
381C TRP* 3.1 15.1 + - - -
502C 2SR 3.6 38.1 - - + -
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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