Contacts of the helix formed by residues 316 - 335 (chain A) in PDB entry 3VPM
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 316 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A VAL* 4.4 1.7 - - - +
314A GLY 4.3 0.2 + - - -
315A MET* 1.3 72.4 - - - +
317A CYS* 1.3 65.9 + - - +
318A THR* 3.2 16.3 + - - +
319A LEU* 2.8 48.4 + - + +
320A MET* 3.2 21.7 + - - +
347A PHE* 5.0 4.4 - - + -
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Residues in contact with CYS 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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304A LEU 4.1 9.4 - - - -
305A THR* 3.7 29.5 - - + +
309A PRO* 4.5 2.5 - - - -
310A VAL* 3.9 23.8 - - - -
311A LYS* 4.0 28.0 - - - -
315A MET 3.6 1.0 + - - -
316A ASN* 1.3 75.9 - - - +
318A THR* 1.3 61.8 + - - +
320A MET* 3.8 0.6 - - - +
321A LYS* 3.2 30.9 + - - +
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Residues in contact with THR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ASN* 3.2 17.9 + - - +
317A CYS* 1.3 79.4 - - - +
319A LEU* 1.3 66.5 + - + +
320A MET 3.4 0.2 + - - -
321A LYS* 3.4 22.9 + - - +
322A GLN* 3.4 21.0 + - - +
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ASN* 2.8 33.1 + - + +
318A THR* 1.3 77.1 - - + +
320A MET* 1.3 59.7 + - - +
322A GLN* 3.5 15.2 + - - +
323A TYR 3.1 19.1 + - - -
346A PRO* 3.2 36.6 - - + +
347A PHE* 3.6 24.8 - - + -
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Residues in contact with MET 320 (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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238A GLY* 4.0 16.6 - - - +
241A ALA* 3.9 13.2 - - + -
304A LEU* 3.5 39.5 - - + -
305A THR* 5.3 0.9 - - + -
310A VAL* 4.2 18.6 - - + -
315A MET* 3.5 42.4 - - + -
316A ASN 3.2 14.7 + - - +
317A CYS 3.8 4.7 - - - +
318A THR 3.2 0.2 - - - -
319A LEU* 1.3 72.7 - - - +
321A LYS* 1.3 67.7 + - - +
322A GLN 3.0 1.1 - - - -
323A TYR* 2.9 17.8 + - - +
324A ILE* 3.1 17.5 + - - +
347A PHE* 3.8 19.5 - - + -
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Residues in contact with LYS 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A GLN* 2.7 51.9 + - + +
305A THR* 4.0 26.5 - - + +
317A CYS* 3.2 17.4 + - - +
318A THR* 3.4 27.5 + - - +
320A MET* 1.3 79.3 - - - +
322A GLN* 1.3 61.4 + - - +
324A ILE* 3.6 1.7 + - - +
325A GLU* 3.4 13.8 + - - +
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Residues in contact with GLN 322 (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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318A THR* 3.4 10.9 + - - +
319A LEU* 3.5 22.6 - - - +
320A MET 3.0 0.6 - - - -
321A LYS* 1.3 78.3 - - - +
323A TYR* 1.3 60.6 + - - +
325A GLU* 3.2 11.9 + - - +
326A PHE* 3.0 24.6 + - - +
343A VAL* 3.7 25.3 - - + +
344A GLU* 2.8 31.5 + - - +
346A PRO* 3.6 18.9 - - + +
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Residues in contact with TYR 323 (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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237A SER* 3.7 24.3 + - - -
241A ALA* 4.1 9.6 - - + -
319A LEU 3.1 6.3 + - - +
320A MET* 2.9 8.1 + - - +
322A GLN* 1.3 74.7 - - - +
324A ILE* 1.3 76.8 + - + +
326A PHE* 3.1 13.4 + + - +
327A VAL* 3.0 49.1 + - + +
330A ARG* 4.5 7.2 + - - -
345A ASN* 3.3 26.9 - - - -
346A PRO* 3.9 8.3 - - + -
347A PHE* 3.4 35.0 - + + -
350A MET* 3.2 42.3 - - + +
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Residues in contact with ILE 324 (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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234A ILE* 4.0 13.8 - - + +
237A SER* 3.4 21.3 - - - +
238A GLY* 3.7 9.6 - - - +
297A VAL* 3.8 23.1 - - + +
300A GLU* 3.7 24.9 - - + -
301A GLN* 4.2 8.3 - - + -
304A LEU* 3.6 31.4 - - + -
320A MET* 3.1 13.2 + - - +
321A LYS 3.8 7.0 - - - +
323A TYR* 1.3 83.0 - - + +
325A GLU* 1.3 62.6 + - - +
327A VAL* 3.2 7.9 + - - +
328A ALA* 3.0 22.7 + - - +
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Residues in contact with GLU 325 (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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297A VAL* 4.0 1.8 - - + -
298A ARG* 3.2 19.8 + - - -
301A GLN* 3.3 20.2 + - - +
321A LYS* 3.4 5.7 + - - +
322A GLN* 3.2 13.8 + - - +
324A ILE* 1.3 78.9 - - - +
326A PHE* 1.3 56.6 + - - +
328A ALA* 3.5 0.4 + - - -
329A ASP* 3.1 25.3 + - - -
341A PHE* 3.4 59.4 - - + +
343A VAL* 3.6 22.9 - - + +
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Residues in contact with PHE 326 (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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322A GLN 3.0 13.1 + - - +
323A TYR* 3.1 18.3 + + - +
325A GLU* 1.3 74.5 - - - +
327A VAL* 1.3 67.9 + - - +
329A ASP* 3.4 7.3 + - + +
330A ARG* 3.1 57.9 + - + +
339A LYS* 5.8 6.7 - - - -
343A VAL* 3.8 20.8 - - - +
344A GLU* 4.1 8.7 - - - +
345A ASN* 3.6 53.4 - - + -
350A MET* 5.8 0.7 - - + -
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Residues in contact with VAL 327 (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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233A GLY* 3.4 30.3 - - - +
234A ILE* 4.3 7.4 - - + -
237A SER* 3.9 11.9 - - - +
323A TYR* 3.0 51.2 + - + +
324A ILE 3.2 7.8 + - - +
326A PHE* 1.3 77.7 - - + +
328A ALA* 1.3 57.8 + - - +
330A ARG* 3.3 25.8 + - - +
331A LEU* 3.0 28.1 + - + +
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Residues in contact with ALA 328 (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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234A ILE* 3.9 12.3 - - + -
293A ILE* 3.7 15.7 - - + +
297A VAL* 3.5 31.6 - - + -
324A ILE 3.0 10.4 + - - +
325A GLU 3.8 4.7 - - - +
326A PHE 3.3 0.2 - - - -
327A VAL* 1.3 75.7 - - - +
329A ASP* 1.3 59.2 - - - +
331A LEU* 3.2 4.2 + - - +
332A MET* 2.8 35.4 + - - +
340A VAL* 6.3 0.2 - - + -
341A PHE* 4.1 6.3 - - + -
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Residues in contact with ASP 329 (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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325A GLU 3.1 15.4 + - - +
326A PHE* 3.7 11.2 - - + +
327A VAL 3.4 0.2 - - - -
328A ALA* 1.3 75.4 - - - +
330A ARG* 1.3 57.8 + - - +
332A MET* 3.3 7.0 + - - +
333A LEU* 3.0 34.1 + - - +
339A LYS* 3.8 22.4 + - + +
340A VAL* 2.8 29.9 + - - +
341A PHE* 2.9 18.3 + - - +
342A ARG* 2.8 29.7 + - - -
343A VAL 3.8 7.7 + - - +
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Residues in contact with ARG 330 (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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323A TYR* 4.5 7.7 + - - -
326A PHE* 3.1 43.2 + - + +
327A VAL* 3.5 32.0 + - - +
328A ALA 3.1 0.4 - - - -
329A ASP* 1.3 74.0 - - - +
331A LEU* 1.3 64.6 + - - +
333A LEU* 3.4 12.3 + - + +
334A GLU* 3.0 28.4 + - - +
350A MET 4.6 12.5 + - - -
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Residues in contact with LEU 331 (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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229A ALA* 3.9 37.7 - - + +
233A GLY* 5.3 2.5 - - - -
234A ILE* 4.1 14.8 - - + -
270A CYS* 5.0 9.6 - - + -
274A CYS* 3.8 23.8 - - - -
293A ILE* 3.9 27.6 - - + -
327A VAL* 3.0 15.5 + - + +
328A ALA* 3.6 8.5 - - - +
330A ARG* 1.3 77.1 - - - +
332A MET* 1.3 56.8 + - - +
334A GLU* 3.0 11.6 + - - +
335A LEU* 2.9 37.2 + - + +
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Residues in contact with MET 332 (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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286A GLU* 4.6 2.7 - - - +
289A VAL* 3.6 19.3 - - + +
290A ARG* 3.7 30.7 - - + +
293A ILE* 3.6 39.0 - - + -
328A ALA 2.8 25.3 + - - +
329A ASP* 3.6 6.1 - - - +
330A ARG 3.3 0.2 - - - -
331A LEU* 1.3 73.6 - - - +
333A LEU* 1.3 62.3 + - - +
335A LEU* 3.1 11.4 + - - -
336A GLY 3.4 0.2 + - - -
337A PHE* 3.0 44.4 + - + +
338A SER 3.6 22.7 - - - +
339A LYS* 5.0 0.2 - - - -
340A VAL* 4.1 12.8 - - + -
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Residues in contact with LEU 333 (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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329A ASP 3.0 16.3 + - - +
330A ARG* 3.6 15.0 - - + +
332A MET* 1.3 76.0 - - - +
334A GLU* 1.3 60.5 + - - +
336A GLY* 3.2 14.0 + - - -
337A PHE 3.5 19.3 + - - +
338A SER* 4.4 1.3 - - - -
339A LYS* 3.9 41.5 - - + +
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Residues in contact with GLU 334 (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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270A CYS* 5.4 1.9 - - - +
271A ASP* 2.7 38.7 + - - +
274A CYS* 3.6 32.6 - - + +
278A LYS* 6.1 0.7 - - - +
330A ARG* 3.0 18.7 + - - +
331A LEU* 3.0 17.1 + - - +
333A LEU* 1.3 73.4 - - - +
335A LEU* 1.3 60.6 + - - +
336A GLY 3.1 6.5 + - - -
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Residues in contact with LEU 335 (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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225A VAL 6.3 0.2 - - - -
226A VAL* 4.1 21.8 - - + -
229A ALA* 5.8 3.8 - - + -
273A ALA* 5.0 1.1 - - + +
274A CYS* 3.9 23.1 - - - +
277A PHE* 3.6 55.5 - - + -
278A LYS* 6.0 1.5 - - - +
283A LYS* 5.2 3.8 - - - +
289A VAL* 4.0 23.8 - - + -
293A ILE* 5.0 0.9 - - + -
331A LEU* 2.9 32.1 + - + +
332A MET* 3.1 11.8 + - - +
334A GLU* 1.3 75.8 - - - +
336A GLY* 1.3 59.4 + - - +
337A PHE* 3.5 14.7 - - + -
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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
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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