Contacts of the helix formed by residues 304 - 317 (chain C) in PDB entry 1XV9
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 304 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300C LEU 4.2 3.9 + - - -
301C LEU 2.9 4.4 + - - -
302C ARG 2.8 8.5 + - - -
303C ALA* 1.3 77.3 - - - +
305C TRP* 1.3 61.4 + - - +
306C ASN* 2.8 11.8 + - - -
307C GLU* 3.0 14.3 + - - +
308C LEU* 2.9 26.7 + - - +
374C VAL* 4.5 11.7 - - - +
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Residues in contact with TRP 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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272C ALA* 5.4 1.6 - - + -
276C LEU* 3.6 29.2 - - + -
279C LEU* 3.9 17.0 - - + -
301C LEU* 3.0 15.1 + - + +
302C ARG 2.9 29.8 + - - -
304C GLY* 1.3 75.2 - - - +
306C ASN* 1.3 85.9 + - + +
308C LEU* 3.2 13.0 - - - +
309C LEU* 2.8 47.4 + - + +
433C LEU* 4.2 16.2 - - + -
436C LEU* 4.0 24.9 - - + -
451C LEU* 4.8 17.7 - - + -
454C MET* 3.4 52.0 + - + +
455C LEU* 5.2 3.6 - - + -
1002C F15 5.4 7.4 - - + -
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Residues in contact with ASN 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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302C ARG 6.0 0.2 - - - +
304C GLY* 2.8 3.3 + - - -
305C TRP* 1.3 99.4 - - + +
307C GLU* 1.3 65.0 + - + +
308C LEU 2.9 4.8 + - - -
309C LEU* 3.0 4.4 + - - +
310C ILE* 2.9 35.8 + - - +
429C GLY* 2.6 47.9 + - - -
433C LEU* 3.8 19.7 - - + +
436C LEU* 3.7 21.0 - - - +
1002C F15 4.0 7.8 - - - +
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Residues in contact with GLU 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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304C GLY* 3.0 13.4 + - - +
306C ASN* 1.3 81.0 - - + +
308C LEU* 1.3 57.2 + - - +
310C ILE* 4.1 3.4 - - - -
311C ALA* 3.0 24.8 + - - +
374C VAL* 5.1 12.2 - - + +
422C LEU* 3.9 3.5 - - - +
425C LEU* 3.1 49.9 - - + +
426C ARG* 2.8 62.0 + - - +
429C GLY* 4.0 10.1 - - - -
430C LEU* 5.6 0.7 + - - +
317D ALA* 5.8 0.2 - - - +
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Residues in contact with LEU 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C LEU* 3.4 31.9 - - + -
282C TRP* 4.2 11.7 - - + -
301C LEU* 5.8 2.7 - - + +
304C GLY 2.9 16.3 + - - +
305C TRP* 3.2 14.1 - - - +
306C ASN 2.9 0.8 + - - -
307C GLU* 1.3 76.3 - - - +
309C LEU* 1.3 58.7 + - - +
311C ALA* 2.6 32.7 + - + +
312C SER 2.9 4.7 + - - -
371C ARG* 3.0 42.4 + - - +
374C VAL* 3.4 30.3 - - + -
375C LEU* 4.5 12.1 - - + +
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Residues in contact with LEU 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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272C ALA* 3.8 14.4 - - - +
275C GLN* 3.4 29.6 - - + +
276C LEU* 3.2 31.0 - - + -
279C LEU* 3.9 22.0 - - + -
305C TRP* 2.8 30.0 + - + +
306C ASN* 3.7 3.1 - - - +
308C LEU* 1.3 73.6 - - - +
310C ILE* 1.3 58.3 + - - +
312C SER* 3.0 23.1 + - - +
313C PHE* 3.2 21.5 + - - -
371C ARG* 4.5 2.0 - - - +
1002C F15 3.4 29.5 - - + +
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Residues in contact with ILE 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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306C ASN* 2.9 33.5 + - - +
307C GLU* 3.7 6.7 - - - +
309C LEU* 1.3 74.8 - - - +
311C ALA* 1.3 57.1 + - - +
313C PHE* 3.6 20.7 - - + -
314C SER* 2.9 27.8 + - - +
349C VAL* 4.9 3.4 - - + -
353C LEU* 3.7 25.0 - - + +
425C LEU* 3.9 7.2 - - + -
428C ILE* 4.2 6.1 - - + -
429C GLY* 3.5 31.9 - - - -
432C CYS* 3.7 18.4 - - + -
1002C F15 4.1 15.9 - - + -
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Residues in contact with ALA 311 (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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307C GLU 3.0 12.3 + - - +
308C LEU* 2.6 21.9 + - + +
310C ILE* 1.3 72.5 - - - +
312C SER* 1.3 64.2 + - - +
314C SER* 3.5 3.5 + - - -
315C HIS* 3.3 20.8 + - - +
353C LEU* 6.0 0.4 - - - -
357C MET* 3.8 9.6 - - + +
367C LEU* 4.1 6.3 - - + +
371C ARG* 3.7 23.1 - - + -
425C LEU* 4.9 8.3 - - + -
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Residues in contact with SER 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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275C GLN* 5.6 2.0 - - - -
308C LEU 2.9 6.0 + - - -
309C LEU* 3.0 15.5 + - - +
311C ALA* 1.3 80.9 - - - +
313C PHE* 1.3 63.1 + - - -
314C SER 3.0 0.3 + - - -
315C HIS* 3.0 11.0 + - - +
316C ARG* 3.1 22.5 + - - +
367C LEU* 5.4 5.7 - - - +
371C ARG* 3.0 35.5 + - - +
1002C F15 3.9 8.3 - - - -
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Residues in contact with PHE 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 LEU 3.2 8.2 + - - -
310C ILE* 3.6 34.1 - - + -
312C SER* 1.3 76.0 - - - +
314C SER* 1.3 65.9 + - - +
316C ARG* 3.6 19.6 - - - +
317C SER* 2.5 34.0 + - - -
324C ILE* 3.9 23.6 - - + -
325C LEU 3.9 6.3 - - - +
326C LEU* 5.1 4.0 - - + -
349C VAL* 3.8 28.7 - - + -
432C CYS* 6.0 0.7 - - - -
1002C F15 3.1 81.4 + - + +
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Residues in contact with SER 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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310C ILE 2.9 23.3 + - - -
311C ALA* 3.5 5.8 + - - -
312C SER 3.0 1.2 + - - -
313C PHE* 1.3 87.6 - - - +
315C HIS* 1.3 64.6 + - - +
317C SER* 3.2 5.4 + - - -
318C ILE* 3.7 3.8 + - - +
349C VAL* 3.4 14.6 - - - +
353C LEU* 3.2 26.0 - - - +
354C VAL* 3.2 24.0 + - - +
357C MET* 3.8 16.6 - - - -
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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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311C ALA 3.3 4.4 + - - +
312C SER 3.0 8.6 + - - +
314C SER* 1.3 77.0 - - - +
316C ARG* 1.3 68.3 + - - +
318C ILE* 2.8 52.6 + - + +
357C MET* 3.5 19.0 - - + -
362C MET* 2.7 44.1 + - + +
363C ASP* 3.9 17.9 - - - -
364C LYS* 4.0 20.5 - - + +
367C LEU* 3.7 20.5 - - + +
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Residues in contact with ARG 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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247C GLU* 5.2 10.6 + - - +
249C TYR* 3.9 15.3 - - - +
275C GLN* 3.6 20.6 + - - -
312C SER* 3.1 17.8 + - - +
313C PHE* 3.6 15.3 - - - +
315C HIS* 1.3 80.2 + - - +
317C SER* 1.3 56.9 + - - +
318C ILE 3.1 4.5 + - - -
319C ALA* 3.6 8.8 + - - +
325C LEU* 2.9 50.9 + - + +
326C LEU 3.4 0.6 - - - -
327C ALA* 3.0 20.0 - - - +
1002C F15 2.8 35.1 + - - -
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Residues in contact with SER 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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313C PHE 2.5 23.7 + - - -
314C SER 3.5 7.6 - - - -
315C HIS 3.0 0.8 - - - -
316C ARG* 1.3 72.2 - - - +
318C ILE* 1.3 61.0 + - - +
319C ALA 3.1 2.0 - - - -
320C VAL* 3.3 19.9 - - - +
323C GLY 3.9 5.5 - - - +
324C ILE* 3.4 16.0 - - - +
325C LEU* 2.7 39.3 + - - -
354C VAL* 3.6 18.0 - - - +
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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