Contacts of the helix formed by residues 304 - 317 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A LEU 3.8 7.4 - - - -
301A LEU 2.9 4.8 + - - -
302A ARG 3.5 2.0 + - - -
303A ALA* 1.3 74.6 - - - +
305A TRP* 1.3 70.3 + - - +
306A ASN* 2.8 6.9 + - - +
307A GLU* 3.1 12.5 + - - +
308A LEU* 2.9 30.2 + - - +
374A VAL* 4.5 13.9 - - - -
375A LEU* 6.2 0.2 - - - -
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Residues in contact with TRP 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ALA* 5.3 0.7 - - + -
276A LEU* 3.7 30.3 - - + -
279A LEU* 3.5 16.4 - - + -
301A LEU* 2.9 11.0 + - + +
302A ARG 2.9 29.7 + - - -
304A GLY* 1.3 76.7 - - - +
306A ASN* 1.3 96.9 + - + +
308A LEU* 3.3 3.6 - - - +
309A LEU* 3.0 32.8 + - + +
433A LEU* 4.2 15.5 - - + +
436A LEU* 3.6 27.4 - - + -
451A LEU* 4.0 23.3 - - + -
454A MET* 3.2 50.7 + - + +
455A LEU* 4.8 4.3 - - + -
1003A F15 4.8 11.0 - - + -
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Residues in contact with ASN 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A GLY* 2.8 4.1 + - - +
305A TRP* 1.3 121.0 - - + +
307A GLU* 1.3 62.5 + - + +
308A LEU 2.8 3.6 + - - -
309A LEU* 3.8 1.9 - - - +
310A ILE* 3.0 27.5 + - - +
429A GLY* 2.7 47.5 + - - +
432A CYS* 4.4 5.4 - - - +
433A LEU* 4.2 13.7 - - + +
436A LEU* 4.1 10.4 - - - +
1003A F15 4.8 4.8 - - - +
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ALA 5.7 0.5 - - - +
304A GLY* 3.1 11.4 + - - +
306A ASN* 1.3 82.3 - - + +
308A LEU* 1.3 65.3 + - - +
310A ILE* 4.0 9.4 - - - -
311A ALA* 3.3 15.1 + - - +
374A VAL* 4.2 18.1 - - + +
422A LEU 4.9 0.9 - - - +
425A LEU* 3.5 42.8 - - + +
426A ARG* 3.3 52.4 + - - +
429A GLY* 4.2 10.8 - - - -
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A LEU* 3.3 42.2 - - + -
282A TRP* 4.4 5.6 - - + -
301A LEU* 4.2 17.3 - - + -
304A GLY 2.9 20.7 + - - +
305A TRP* 3.3 12.3 - - - +
306A ASN 2.8 1.2 + - - -
307A GLU* 1.3 79.9 - - - +
309A LEU* 1.3 66.1 + - - +
310A ILE 2.9 2.1 + - - -
311A ALA 3.1 7.1 + - - -
312A SER 3.2 8.7 + - - -
371A ARG* 3.4 42.1 + - - +
374A VAL* 3.3 27.6 - - + -
375A LEU* 4.3 12.3 - - + +
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ALA* 3.7 27.4 - - + +
275A GLN* 3.1 38.6 - - + +
276A LEU* 3.7 23.1 - - + -
279A LEU* 3.9 14.4 - - + -
305A TRP* 3.0 22.7 + - + +
306A ASN 3.9 1.8 - - - +
308A LEU* 1.3 77.0 - - - +
310A ILE* 1.3 61.1 + - - +
312A SER* 3.3 16.7 - - - +
313A PHE* 3.1 17.7 + - - -
371A ARG* 4.1 11.0 - - - +
1003A F15 3.7 19.5 - - + +
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Residues in contact with ILE 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ASN* 3.0 25.1 + - - +
307A GLU* 3.9 6.7 - - - +
308A LEU 2.9 1.6 + - - -
309A LEU* 1.3 77.9 - - - +
311A ALA* 1.3 63.3 + - - +
312A SER 3.1 0.5 + - - -
313A PHE* 3.2 26.8 + - + -
314A SER* 2.8 25.1 + - - +
349A VAL* 5.6 0.4 - - + -
353A LEU* 3.5 26.5 - - + -
425A LEU* 3.5 7.9 - - + -
428A ILE* 4.0 5.6 - - + -
429A GLY* 3.7 26.9 - - - +
432A CYS* 3.6 33.0 - - + -
1003A F15 4.6 9.9 - - + -
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A GLU 3.3 13.4 + - - +
308A LEU 3.1 3.8 + - - +
310A ILE* 1.3 78.1 - - - +
312A SER* 1.3 67.6 + - - +
314A SER* 3.6 10.2 - - - -
315A HIS* 3.2 22.0 + - - +
353A LEU* 4.6 1.8 - - + -
357A MET* 3.9 10.2 - - + +
367A LEU* 3.6 8.4 - - + +
370A LEU* 6.4 2.2 - - + -
371A ARG* 4.7 12.6 - - + +
425A LEU* 4.2 15.7 - - + -
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Residues in contact with SER 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A VAL* 5.9 1.6 - - - +
275A GLN* 4.9 3.8 + - - -
308A LEU 3.2 10.9 + - - -
309A LEU* 3.3 15.8 - - - +
311A ALA* 1.3 79.9 - - - +
313A PHE* 1.3 58.1 + - - +
315A HIS* 3.6 4.2 + - - +
316A ARG* 3.0 45.2 + - - +
367A LEU* 4.8 9.4 - - - +
371A ARG* 3.8 29.9 + - - +
1003A F15 4.6 0.7 - - - -
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Residues in contact with PHE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A LEU 3.1 16.1 + - - -
310A ILE* 3.2 35.9 + - + -
312A SER* 1.3 78.0 + - - +
314A SER* 1.3 74.6 + - - +
316A ARG* 3.8 15.5 - - - +
317A SER* 2.8 30.3 + - - -
324A ILE* 3.6 28.5 - - + -
325A LEU 4.2 7.2 - - - +
326A LEU* 5.5 1.8 - - + -
349A VAL* 3.9 17.7 - - + -
1003A F15 3.3 67.3 - - + +
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Residues in contact with SER 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ILE 2.8 21.0 + - - -
311A ALA* 3.6 2.0 - - - -
312A SER 3.2 0.2 - - - -
313A PHE* 1.3 92.6 - - - +
315A HIS* 1.3 64.8 + - - +
317A SER* 3.1 7.8 + - - -
318A ILE* 3.6 4.5 + - - +
349A VAL* 4.0 1.6 - - - +
353A LEU* 3.0 34.0 - - - +
354A VAL* 3.2 25.6 - - - +
357A MET* 3.6 21.3 - - - -
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Residues in contact with HIS 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311A ALA 3.2 3.9 + - - +
312A SER 3.6 2.6 + - - +
314A SER* 1.3 75.4 - - - +
316A ARG* 1.3 67.9 + - - +
318A ILE* 2.7 48.8 + - + +
357A MET* 3.3 12.7 - - - -
362A MET* 3.3 35.0 + - + -
363A ASP* 4.0 1.0 - - - -
364A LYS* 3.4 44.5 + - + -
367A LEU* 3.3 37.8 - - + +
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Residues in contact with ARG 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A PRO* 6.2 3.7 - - - +
247A GLU* 5.2 7.6 - - - +
249A TYR* 3.9 20.6 - - - +
275A GLN* 4.1 13.3 + - - -
312A SER* 3.0 34.9 + - - +
313A PHE* 3.7 10.3 - - - +
315A HIS* 1.3 81.5 + - - +
317A SER* 1.3 56.4 + - - +
318A ILE 3.0 5.7 + - - -
319A ALA* 3.7 9.4 + - - +
325A LEU* 3.4 28.8 + - + +
326A LEU 3.4 2.0 - - - -
327A ALA* 3.1 23.7 - - - +
1003A F15 2.7 43.7 + - - -
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Residues in contact with SER 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A PHE 2.8 19.3 + - - -
314A SER 3.1 6.4 + - - -
316A ARG* 1.3 70.7 - - - +
318A ILE* 1.3 61.8 + - - +
319A ALA 3.1 2.7 - - - -
320A VAL* 3.2 20.3 - - - +
323A GLY 3.8 8.6 - - - +
324A ILE* 3.4 18.0 - - - +
325A LEU* 2.8 43.7 + - - -
354A VAL* 3.8 10.5 - - - +
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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