Contacts of the helix formed by residues 318 - 337 (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 SER 318 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C GLY* 1.3 76.2 - - - +
319C ASP* 1.3 65.7 + - - +
320C ASP* 3.6 7.0 + - - +
321C GLU* 3.1 36.0 + - - +
322C ARG* 3.0 22.7 + - - +
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Residues in contact with ASP 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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301C ARG* 3.1 30.4 + - + +
305C LEU* 3.5 26.5 - - + +
318C SER* 1.3 72.9 - - - +
320C ASP* 1.3 60.9 + - - +
322C ARG* 3.3 20.0 + - - +
323C ILE* 3.0 36.1 + - + +
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Residues in contact with ASP 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ARG* 3.1 32.3 + - - +
318C SER* 3.3 6.5 + - - +
319C ASP* 1.3 81.5 - - - +
321C GLU* 1.3 59.3 + - + +
323C ILE* 4.4 4.4 - - - +
324C ASP* 2.9 38.0 + - - +
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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
----------------------------------------------------------
316C GLU 5.2 1.8 - - - +
317C GLY* 3.6 10.4 - - - -
318C SER* 3.1 37.6 + - - +
320C ASP* 1.3 76.1 - - + +
322C ARG* 1.3 59.6 + - - +
324C ASP* 3.5 9.7 + - - +
325C ALA* 3.0 29.1 + - - +
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Residues in contact with ARG 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C LEU* 3.8 36.7 + - + +
308C ALA* 3.9 6.1 - - + +
309C GLU* 4.8 12.9 + - - +
314C ILE* 3.8 28.3 + - + +
315C THR* 3.4 33.0 + - - +
316C GLU 3.3 18.8 - - - +
317C GLY 3.5 9.8 + - - -
318C SER 3.0 19.5 + - - +
319C ASP* 3.7 21.3 + - - +
321C GLU* 1.3 75.2 - - - +
323C ILE* 1.3 58.8 + - - +
325C ALA* 3.4 2.3 + - - +
326C ALA* 3.0 29.3 + - - +
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Residues in contact with ILE 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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297C ARG* 3.6 41.5 - - + +
301C ARG* 4.2 35.0 - - + +
304C LEU* 4.0 31.9 - - + -
305C LEU* 3.9 13.0 - - + +
319C ASP* 3.0 25.7 + - + +
320C ASP* 4.8 3.8 - - - +
322C ARG* 1.3 72.5 - - - +
324C ASP* 1.3 65.5 + - - +
326C ALA* 3.2 6.2 + - - +
327C ILE* 3.0 37.0 + - + +
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Residues in contact with ASP 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ASN* 4.7 0.9 - - - +
297C ARG* 3.0 29.7 + - - -
320C ASP* 2.9 27.7 + - - +
321C GLU* 3.7 10.8 - - - +
323C ILE* 1.3 77.5 - - - +
325C ALA* 1.3 56.9 + - - +
327C ILE* 3.4 6.9 + - - +
328C ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C ILE* 3.6 22.7 - - + +
321C GLU 3.0 17.5 + - - +
322C ARG 3.8 4.3 - - - +
324C ASP* 1.3 76.6 - - - +
326C ALA* 1.3 57.0 + - - +
328C ALA* 3.5 6.8 + - - +
329C ALA* 2.9 29.8 + - - +
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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
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304C LEU* 4.5 4.7 - - + +
307C TYR* 4.1 17.5 - - + -
308C ALA* 3.6 28.3 - - + -
312C TRP* 4.3 2.8 + - + -
314C ILE* 3.6 8.5 - - + +
322C ARG 3.0 17.5 + - - +
323C ILE* 3.2 6.7 + - - +
325C ALA* 1.3 75.0 - - - +
327C ILE* 1.3 60.2 + - + +
329C ALA* 3.4 3.7 + - - +
330C THR* 2.7 34.6 + - - -
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Residues in contact with ILE 327 (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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290C PRO* 4.0 28.4 - - + +
293C TRP* 4.1 24.2 - - + -
294C ASN* 3.8 37.5 - - + +
297C ARG* 4.2 6.1 - - - +
304C LEU* 5.0 2.5 - - + -
323C ILE* 3.0 37.9 + - + +
324C ASP* 3.7 5.6 - - - +
326C ALA* 1.3 74.6 - - - +
328C ALA* 1.3 65.2 + - - +
330C THR* 3.2 7.2 + - - -
331C ARG* 2.9 30.1 + - - +
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Residues in contact with ALA 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C ASP 2.9 18.7 + - - +
325C ALA* 3.7 8.3 - - - +
327C ILE* 1.3 78.1 - - - +
329C ALA* 1.3 56.6 + - - +
331C ARG* 3.5 10.8 + - - +
332C ASN* 2.9 28.8 + - - +
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Residues in contact with ALA 329 (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 TRP* 3.7 41.3 - - + -
314C ILE* 4.8 3.6 - - + -
325C ALA 2.9 18.5 + - - +
326C ALA 3.9 2.9 - - - +
327C ILE 3.3 0.4 - - - -
328C ALA* 1.3 76.5 - - - +
330C THR* 1.3 57.2 + - - +
332C ASN* 3.5 7.5 + - - +
333C PHE* 2.9 27.9 + - - +
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Residues in contact with THR 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C PHE* 4.0 9.0 - - + -
289C LEU* 4.2 3.4 - - + -
290C PRO* 6.0 4.0 - - + -
293C TRP* 3.6 17.9 - - + -
307C TYR* 2.5 31.3 + - - +
312C TRP* 3.7 7.4 + - - -
326C ALA 2.7 18.5 + - - -
327C ILE* 3.2 8.3 + - - -
329C ALA* 1.3 73.4 - - - +
331C ARG* 1.3 65.1 - - - +
333C PHE* 3.2 4.7 + - - +
334C PHE* 3.1 49.7 + - + -
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Residues in contact with ARG 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C ILE 5.1 0.6 + - - -
290C PRO* 3.5 38.0 - - + +
291C ALA* 4.1 14.1 - - - +
327C ILE* 2.9 17.3 + - - +
328C ALA* 3.5 12.6 - - - +
330C THR* 1.3 75.7 - - - +
332C ASN* 1.3 63.3 - - - +
334C PHE* 3.3 5.4 + - - +
335C GLU* 2.8 34.5 + - + +
341C THR* 2.9 54.5 + - - +
342C HIS* 3.4 27.2 + - - -
385C ALA 4.6 8.9 + - - -
386C ALA* 5.4 0.8 - - - +
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Residues in contact with ASN 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 ALA 2.9 18.7 + - - +
329C ALA* 3.8 8.3 + - - +
331C ARG* 1.3 76.6 - - - +
333C PHE* 1.3 65.3 + - - +
335C GLU* 3.4 6.1 + - - +
336C GLN* 3.0 53.5 + - - +
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Residues in contact with PHE 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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192C VAL* 3.9 9.2 - - + -
196C PHE* 3.6 35.2 - + + -
224C LEU 3.5 21.3 - - - -
225C ILE* 3.7 27.1 - - + -
229C PRO* 4.0 21.3 - - + -
312C TRP* 4.0 13.7 - + + -
329C ALA 2.9 18.1 + - - +
330C THR 3.2 5.1 + - - +
332C ASN* 1.3 79.6 - - - +
334C PHE* 1.3 78.4 + + - +
336C GLN* 3.4 4.3 + - + +
337C LEU* 3.2 49.4 + - + +
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Residues in contact with PHE 334 (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 VAL* 3.9 21.5 - - + -
196C PHE* 3.9 29.8 - + + -
197C VAL* 4.2 9.0 - - + -
285C LEU 4.7 0.4 - - - -
286C ALA* 3.7 41.3 - - + -
289C LEU* 4.0 19.3 - - + -
290C PRO* 4.8 2.7 - - + -
330C THR* 3.1 33.3 + - + -
331C ARG* 3.7 5.2 - - - +
333C PHE* 1.3 92.7 - + - +
335C GLU* 1.3 63.6 + - - +
337C LEU* 3.0 19.0 + - - +
339C VAL* 3.1 31.1 + - + +
341C THR* 3.9 6.7 - - + -
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Residues in contact with GLU 335 (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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331C ARG* 2.8 36.0 + - - +
332C ASN* 3.8 7.2 - - - +
334C PHE* 1.3 75.5 - - - +
336C GLN* 1.3 68.2 + - - +
338C GLY* 3.0 19.2 + - - -
339C VAL 3.5 9.2 + - - -
340C PRO* 3.5 18.2 - - - +
341C THR* 2.6 32.7 + - + -
342C HIS* 4.2 10.7 + - - -
345C ASP* 4.5 3.5 - - - +
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Residues in contact with GLN 336 (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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229C PRO* 6.5 0.7 - - + -
232C LEU* 4.8 4.0 - - - +
332C ASN* 3.0 46.3 + - - +
333C PHE* 3.9 5.2 - - + +
335C GLU* 1.3 80.7 - - - +
337C LEU* 1.3 61.9 + - - +
338C GLY 3.1 5.7 + - - -
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Residues in contact with LEU 337 (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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189C ALA* 3.2 29.4 - - + +
192C VAL* 3.7 31.2 - - + -
193C VAL* 3.7 20.6 - - + -
228C GLY 4.1 4.0 - - - -
229C PRO* 3.9 32.5 - - + -
232C LEU* 3.5 29.7 - - + +
333C PHE* 3.2 31.0 + - + +
334C PHE* 3.0 10.4 + - - +
336C GLN* 1.3 76.4 - - - +
338C GLY* 1.3 56.7 + - - +
339C VAL* 4.4 2.7 - - + -
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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