Contacts of the helix formed by residues 315 - 334 (chain C) in PDB entry 3OX4
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 GLY 315 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C ASN 4.0 0.4 + - - -
314C LEU* 1.3 73.7 - - - +
316C ASP* 1.3 55.1 + - - -
317C LYS 3.3 3.1 - - - -
318C GLU* 2.6 25.8 + - - +
319C GLY* 2.7 31.7 + - - -
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Residues in contact with ASP 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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297C ALA* 3.9 8.5 - - + +
298C GLY* 3.5 30.1 + - - +
301C LYS* 2.9 32.5 + - - +
314C LEU 3.5 0.4 + - - -
315C GLY* 1.3 70.3 - - - -
317C LYS* 1.3 58.6 + - - +
319C GLY* 3.1 1.1 + - - +
320C ALA* 2.9 31.5 + - - +
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Residues in contact with LYS 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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293C ALA 5.7 4.3 - - - -
294C SER* 6.0 4.9 - - - +
297C ALA* 4.3 12.0 - - + +
315C GLY 3.3 1.0 - - - -
316C ASP* 1.3 78.6 - - - +
318C GLU* 1.3 60.4 + - - +
320C ALA* 3.6 3.3 + - - +
321C GLU* 3.4 30.2 + - + +
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Residues in contact with GLU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C LEU* 3.5 33.3 - - + +
315C GLY* 2.6 41.8 + - - +
317C LYS* 1.3 76.1 - - - +
319C GLY* 1.3 65.0 - - - +
320C ALA 3.2 0.7 - - - -
321C GLU* 3.3 7.8 + - - +
322C ALA* 3.0 24.6 + - - +
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Residues in contact with GLY 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C LYS* 3.7 22.2 - - - -
311C ILE* 3.1 21.8 - - - +
314C LEU* 4.4 2.5 - - - -
315C GLY 2.7 17.8 + - - -
316C ASP 3.6 2.0 - - - -
318C GLU* 1.3 80.2 - - - +
320C ALA* 1.3 58.6 + - - +
322C ALA* 3.4 0.4 + - - -
323C THR* 2.9 25.5 + - - -
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Residues in contact with ALA 320 (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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293C ALA* 4.4 9.0 - - + -
297C ALA* 3.7 30.3 - - + +
300C LEU* 4.0 21.8 - - + -
301C LYS* 4.3 1.2 - - - +
316C ASP 2.9 15.9 + - - +
317C LYS 3.8 5.2 - - - +
319C GLY* 1.3 74.7 - - - +
321C GLU* 1.3 62.7 + - - +
323C THR* 3.2 4.1 + - - -
324C ILE* 2.8 35.5 + - - +
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Residues in contact with GLU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C ALA* 5.2 4.7 - - - +
293C ALA* 4.5 11.1 - - - +
317C LYS* 3.4 20.9 + - + +
318C GLU* 3.3 10.4 + - - +
320C ALA* 1.3 77.9 - - - +
322C ALA* 1.3 64.2 - - - +
324C ILE* 3.3 20.0 + - - +
325C GLN* 2.9 25.9 + - - +
328C ARG* 4.9 10.4 + - - -
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Residues in contact with ALA 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C LEU* 3.5 12.6 - - + +
311C ILE* 3.7 25.8 - - + -
314C LEU* 4.9 3.1 - - + -
318C GLU 3.0 17.4 + - - +
319C GLY 3.6 5.2 - - - +
321C GLU* 1.3 75.3 - - - +
323C THR* 1.3 63.9 + - - +
325C GLN* 3.3 7.7 + - - +
326C ALA* 3.1 17.8 + - - +
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Residues in contact with THR 323 (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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200C PHE* 3.6 26.9 - - + -
300C LEU* 3.4 21.8 + - + +
301C LYS* 3.7 0.2 - - - -
304C GLY* 3.0 34.3 - - - +
307C MET* 4.5 3.3 - - - +
309C LEU* 3.8 9.4 - - - -
311C ILE* 3.2 5.2 - - - +
319C GLY 2.9 12.8 + - - -
320C ALA* 3.4 9.6 - - - -
322C ALA* 1.3 78.0 - - - +
324C ILE* 1.3 64.6 + - + +
326C ALA* 3.1 14.9 + - - +
327C VAL* 3.2 11.8 + - - +
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Residues in contact with ILE 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C PRO* 3.8 16.6 - - + +
289C LEU* 3.7 19.5 - - + +
290C ALA* 3.3 38.8 - - + +
293C ALA* 4.6 1.6 - - + -
300C LEU* 4.5 9.2 - - + -
320C ALA 2.8 25.3 + - - +
321C GLU* 3.7 19.5 - - - +
323C THR* 1.3 75.0 - - + +
325C GLN* 1.3 64.1 + - - +
327C VAL* 2.9 21.3 + - - +
328C ARG* 2.9 42.3 + - + +
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Residues in contact with GLN 325 (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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321C GLU 2.9 17.2 + - - +
322C ALA* 3.5 7.9 - - - +
324C ILE* 1.3 75.7 - - - +
326C ALA* 1.3 57.8 + - - +
328C ARG* 3.0 37.3 + - - +
329C ASP* 2.8 62.4 + - - +
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Residues in contact with ALA 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C MET* 5.3 10.0 - - + +
309C LEU* 3.8 26.9 - - + -
322C ALA 3.1 12.5 + - - +
323C THR* 3.1 11.0 + - - +
325C GLN* 1.3 77.2 - - - +
327C VAL* 1.3 57.7 + - + +
329C ASP* 3.4 9.1 + - - +
330C LEU* 2.9 30.0 + - - +
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Residues in contact with VAL 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C MET* 4.3 10.7 - - + +
196C LEU* 4.8 2.9 - - + -
200C PHE* 3.8 31.6 - - + -
285C LEU* 3.7 31.6 - - + -
286C PRO* 4.3 14.1 - - + -
289C LEU* 4.1 9.6 - - + -
307C MET* 4.7 8.7 - - + -
323C THR 3.4 13.9 - - - +
324C ILE* 2.9 9.9 + - - +
326C ALA* 1.3 76.2 - - - +
328C ARG* 1.3 65.0 + - - +
330C LEU* 3.8 6.7 - - - +
331C ALA* 3.0 24.3 + - - +
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Residues in contact with ARG 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C PRO* 3.9 29.1 + - + +
287C HIS* 5.4 10.8 + - - -
290C ALA* 4.6 10.1 - - - +
321C GLU* 4.9 10.1 + - - -
324C ILE* 2.9 38.3 + - - +
325C GLN* 3.1 44.3 + - - +
327C VAL* 1.3 77.6 - - - +
329C ASP* 1.3 61.9 + - - +
331C ALA* 3.7 4.4 + - - +
332C ALA* 3.2 24.1 + - - +
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Residues in contact with ASP 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C GLN* 2.8 46.3 + - - +
326C ALA* 3.8 8.7 - - - +
328C ARG* 1.3 75.9 - - - +
330C LEU* 1.3 59.6 + - - +
332C ALA* 3.3 5.9 + - - +
333C SER* 2.9 30.0 + - - -
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Residues in contact with LEU 330 (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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193C MET* 4.2 4.3 - - - -
196C LEU* 4.0 27.4 - - + -
223C ILE* 4.6 9.2 - - + +
224C ALA* 5.2 6.7 - - - +
227C LEU* 4.1 31.2 - - + -
228C LYS* 3.8 27.4 - - + +
307C MET* 4.5 12.8 - - + -
326C ALA 2.9 18.4 + - - +
327C VAL* 3.8 4.3 - - - +
329C ASP* 1.3 78.3 - - - +
331C ALA* 1.3 62.1 + - - +
333C SER* 2.8 19.9 + - - +
334C ILE* 3.2 14.4 - - + +
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Residues in contact with ALA 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C MET* 3.6 23.1 - - + +
282C ALA 5.0 2.9 - - - +
283C VAL* 6.2 0.4 - - - -
286C PRO* 5.9 4.3 - - + -
327C VAL* 3.0 17.1 + - + +
328C ARG* 4.1 5.2 - - - +
330C LEU* 1.3 77.3 - - - +
332C ALA* 1.3 59.6 + - - +
334C ILE* 3.6 3.9 - - - +
336C ILE* 2.9 54.6 + - + +
337C PRO 5.9 0.2 - - - +
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Residues in contact with ALA 332 (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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328C ARG 3.2 18.8 + - - +
329C ASP* 3.7 7.4 - - - +
330C LEU 3.1 0.6 - - - -
331C ALA* 1.3 78.4 - - - +
333C SER* 1.3 60.2 + - - +
334C ILE 3.3 1.4 + - - -
335C GLY* 3.7 7.9 + - - +
336C ILE 4.9 5.4 - - - +
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Residues in contact with SER 333 (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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185C LYS* 4.7 4.2 + - - -
228C LYS* 3.1 50.0 + - - +
232C ASP* 5.0 1.6 - - - +
329C ASP 2.9 14.3 + - - -
330C LEU* 2.8 23.0 + - - +
332C ALA* 1.3 77.9 - - - +
334C ILE* 1.3 56.3 + - - +
335C GLY 3.6 0.2 - - - -
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Residues in contact with ILE 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LYS* 3.1 27.2 + - - +
186C GLY* 5.8 0.9 - - - -
189C ALA* 3.5 32.9 - - + +
193C MET* 3.6 30.1 - - + -
227C LEU* 3.9 16.8 - - + -
228C LYS* 4.2 17.9 - - + -
231C CYS* 3.6 24.2 - - + -
330C LEU* 3.2 19.1 - - + +
331C ALA 3.6 9.9 - - - +
333C SER* 1.3 85.6 - - - +
335C GLY* 1.3 60.1 + - - +
336C ILE* 3.6 6.7 - - + -
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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