Contacts of the helix formed by residues 319 - 337 (chain A) in PDB entry 2VZC
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 319 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A PRO 3.4 1.8 + - - -
318A ASP* 1.3 92.0 + - - +
320A PHE* 1.3 64.4 + - - +
321A GLU* 3.5 17.4 + - - +
322A GLN* 3.1 23.2 + - - +
323A LYS* 3.1 30.7 + - - +
321B GLU* 5.1 2.1 + - - +
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Residues in contact with PHE 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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319A SER* 1.3 71.4 - - - +
321A GLU* 1.3 83.1 + - - +
323A LYS* 3.1 12.8 + - - +
324A VAL* 2.9 49.2 + - + +
347A GLU* 4.0 17.3 - - + -
350A VAL* 3.6 21.3 - - + -
351A ASN* 4.0 20.0 - - - -
314B PHE* 4.9 5.6 - + - -
325B LEU* 6.0 0.2 - - + -
1373B MRD 4.0 25.6 - - + -
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Residues in contact with GLU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A SER* 3.2 18.0 - - - +
320A PHE* 1.3 91.5 + - + +
322A GLN* 1.3 58.9 + - - +
324A VAL* 3.3 1.6 + - - +
325A LEU* 3.0 33.5 + - - +
314B PHE* 4.3 9.2 - - + -
319B SER* 5.2 1.3 - - - +
321B GLU* 3.9 17.0 - - + -
322B GLN* 3.0 42.2 + - + -
325B LEU* 3.7 22.7 - - + +
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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
----------------------------------------------------------
314A PHE* 3.3 45.3 - - + +
316A THR 4.0 2.4 - - - +
317A PRO* 3.3 20.3 - - + +
318A ASP* 2.9 41.4 + - - +
319A SER* 3.1 18.4 + - - +
321A GLU* 1.3 75.7 - - - +
323A LYS* 1.3 58.6 + - - +
325A LEU* 3.3 3.0 + - - +
326A ASN* 2.9 31.4 + - - -
321B GLU* 2.8 30.2 + - + +
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Residues in contact with LYS 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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291A ALA* 4.4 1.3 - - + +
292A ASP* 3.7 42.2 - - + +
317A PRO* 3.8 22.9 - - + -
319A SER* 3.1 21.8 + - - +
320A PHE* 3.1 9.0 + - - +
322A GLN* 1.3 73.2 - - - +
324A VAL* 1.3 66.1 + - - +
326A ASN* 3.2 3.1 + - - +
327A VAL* 3.0 26.5 + - - +
350A VAL* 3.7 27.8 - - + -
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Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PHE* 2.9 55.3 + - + +
321A GLU* 3.8 4.9 - - - +
323A LYS* 1.3 74.8 - - - +
325A LEU* 1.3 58.2 + - - +
327A VAL* 3.3 3.4 + - - +
328A SER* 2.8 32.6 + - - +
346A PRO* 4.0 24.5 - - + -
347A GLU* 4.2 7.4 - - + +
350A VAL* 3.8 14.4 - - + -
325B LEU* 3.6 22.7 - - + -
1373B MRD 3.9 13.5 - - - +
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Residues in contact with LEU 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PHE* 3.7 27.8 - - + -
321A GLU 3.0 21.8 + - - +
322A GLN 3.6 4.5 - - - +
323A LYS 3.3 0.2 - - - -
324A VAL* 1.3 76.6 - - - +
326A ASN* 1.3 61.9 + - - +
328A SER* 3.4 8.7 + - - -
329A PHE* 2.9 23.9 + - - +
320B PHE* 6.1 0.7 - - + -
321B GLU* 3.8 32.8 - - + +
324B VAL* 3.6 30.3 - - + -
325B LEU* 3.5 23.1 - - + +
328B SER* 4.6 6.1 - - - +
1374B MPD 3.8 20.1 + - - +
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Residues in contact with ASN 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ASP 3.0 23.5 + - - +
293A GLY* 3.7 10.1 - - - +
294A VAL* 3.7 8.5 - - - +
297A VAL* 3.2 14.7 - - + +
313A PHE* 3.4 12.8 - - - +
314A PHE* 2.9 55.2 + - - +
317A PRO* 3.9 3.6 - - - +
322A GLN 2.9 16.2 + - - -
323A LYS 3.2 7.4 + - - +
325A LEU* 1.3 77.1 - - - +
327A VAL* 1.3 63.9 + - - +
329A PHE* 3.1 4.6 + - - +
330A ALA 3.0 18.0 + - - -
1374B MPD 4.2 0.6 - - - +
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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
----------------------------------------------------------
293A GLY* 3.7 20.0 - - - +
296A LEU* 4.3 4.9 - - + -
323A LYS 3.0 20.2 + - - +
324A VAL 3.3 3.6 + - - +
326A ASN* 1.3 74.4 - - - +
328A SER* 1.3 58.1 + - - +
330A ALA* 3.1 8.5 + - - +
331A PHE* 2.9 51.4 + - + -
346A PRO* 3.6 27.6 - - + +
349A ILE* 3.9 22.0 - - + -
350A VAL* 3.7 17.9 - - + -
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Residues in contact with SER 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A VAL* 2.8 23.6 + - - +
325A LEU* 3.6 12.1 - - - -
327A VAL* 1.3 76.0 - - - +
329A PHE* 1.3 57.2 + - - +
331A PHE* 3.2 9.1 + - - +
332A GLU* 2.9 28.6 + - - +
346A PRO* 3.5 22.6 - - - +
325B LEU* 4.6 5.2 - - - +
328B SER* 5.6 8.9 - - - -
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Residues in contact with PHE 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A VAL* 3.9 31.9 - - + -
308A VAL* 4.2 5.4 - - + -
312A SER* 4.2 23.6 - - - -
313A PHE* 4.1 13.5 - - + -
325A LEU 2.9 13.4 + - - +
326A ASN* 3.4 7.6 - - - +
328A SER* 1.3 73.5 - - - +
330A ALA* 1.3 65.3 + - - +
332A GLU* 3.1 29.7 + - - +
333A LEU* 2.9 47.4 + - + +
345B ARG* 4.2 10.5 - - - +
1374B MPD 3.8 25.1 - - + +
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Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU* 3.6 49.1 - - + +
297A VAL* 3.9 7.2 - - + +
300A MET* 3.8 5.6 - - + +
326A ASN 3.0 12.4 + - - +
327A VAL 3.1 7.4 + - - +
329A PHE* 1.3 76.4 - - - +
331A PHE* 1.3 56.3 + - - +
333A LEU* 3.2 8.6 + - - +
334A MET* 3.0 34.7 + - + +
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Residues in contact with PHE 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU* 4.2 10.3 - - + -
327A VAL* 2.9 35.4 + - + -
328A SER* 3.2 10.3 + - - +
330A ALA* 1.3 75.9 - - - +
332A GLU* 1.3 62.0 + - - +
334A MET* 3.2 20.0 + - + +
335A GLN* 3.0 40.1 + - - +
341A LYS* 5.7 2.5 - - + -
342A PRO* 3.8 26.9 - - + +
344A PRO 3.4 24.7 - - - -
345A ARG 4.5 0.4 - - - -
346A PRO* 3.9 24.5 - - + -
349A ILE* 4.0 14.6 - - + -
360A VAL* 4.1 20.6 - - + -
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Residues in contact with GLU 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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328A SER 2.9 13.3 + - - +
329A PHE* 3.1 23.2 + - + +
331A PHE* 1.3 76.8 - - - +
333A LEU* 1.3 57.4 + - - +
335A GLN* 3.2 10.2 + - - +
336A ASP* 2.8 37.8 + - - +
341B LYS* 2.7 40.2 + - - +
345B ARG* 2.9 42.7 + - - -
346B PRO* 5.9 0.6 - - - +
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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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297A VAL* 4.4 9.6 - - + +
300A MET* 3.9 32.7 - - + +
301A GLY* 4.8 2.2 - - - +
304A GLU* 5.5 4.5 - - + +
306A TYR* 6.6 0.7 - - + -
308A VAL* 4.5 11.4 - - + -
329A PHE* 2.9 54.4 + - + +
330A ALA* 3.5 9.4 - - - +
332A GLU* 1.3 76.1 - - + +
334A MET* 1.3 63.1 + - - +
336A ASP* 3.3 17.5 + - + +
337A GLY* 3.1 18.2 + - - -
368A TYR* 5.3 0.5 + - - -
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Residues in contact with MET 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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296A LEU* 4.0 22.4 - - + -
300A MET* 3.6 30.7 - - + -
330A ALA 3.0 21.4 + - - +
331A PHE* 3.4 19.7 - - + +
332A GLU 3.2 0.2 - - - -
333A LEU* 1.3 76.1 - - - +
335A GLN* 1.3 63.4 + - + +
337A GLY* 3.2 10.2 + - - -
338A GLY 3.3 0.3 + - - -
339A LEU* 3.1 38.7 + - + +
342A PRO* 4.0 25.8 - - + -
360A VAL* 3.8 27.8 - - + +
364A LEU* 4.1 13.2 - - + -
367A LYS* 5.0 0.5 + - - -
368A TYR* 5.1 1.0 + - - -
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Residues in contact with GLN 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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331A PHE* 3.0 31.4 + - - +
332A GLU* 3.8 8.5 - - - +
334A MET* 1.3 71.0 - - - +
336A ASP* 1.3 66.9 + - - +
337A GLY 3.1 1.3 - - - -
338A GLY* 2.9 14.9 + - - -
339A LEU 3.4 19.7 - - - +
340A GLU 4.1 1.8 - - - +
341A LYS* 3.4 46.7 + - - +
342A PRO* 4.0 6.1 - - + +
335B GLN* 4.6 13.0 - - - +
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Residues in contact with ASP 336 (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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332A GLU* 2.8 31.7 + - - +
333A LEU* 3.6 18.7 - - + +
335A GLN* 1.3 74.0 - - - +
337A GLY* 1.3 58.8 + - - +
338A GLY* 3.2 0.7 + - - -
341B LYS* 2.8 38.7 + - - +
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Residues in contact with GLY 337 (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 GLU* 4.1 22.2 - - - +
333A LEU 3.1 12.0 + - - -
334A MET 3.6 4.3 - - - -
335A GLN 3.1 0.8 - - - -
336A ASP* 1.3 76.4 - - - +
338A GLY* 1.3 57.4 + - - +
339A LEU 3.6 0.9 - - - -
367A LYS* 2.8 21.7 + - - -
368A TYR* 4.8 0.9 - - - -
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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