Contacts of the helix formed by residues 299 - 313 (chain A) in PDB entry 2VZ9
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 VAL 299 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A PHE* 3.6 44.2 - - + -
264A PRO* 4.4 7.4 - - + -
297A THR* 3.0 9.5 - - + +
298A LYS* 1.3 83.7 - - + +
300A GLY* 1.3 69.1 + - - +
301A ASP 3.3 1.3 - - - -
302A PRO* 3.1 12.1 - - - +
303A GLN* 3.4 15.9 + - + +
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Residues in contact with GLY 300 (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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264A PRO* 3.8 25.8 - - - +
295A THR* 4.8 5.2 - - - -
297A THR* 3.1 21.0 - - - +
299A VAL* 1.3 80.2 - - - +
301A ASP* 1.3 63.0 + - - +
303A GLN* 3.5 2.1 + - - +
304A GLU* 3.2 25.0 + - - +
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Residues in contact with ASP 301 (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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213A ARG 3.8 1.0 - - - +
214A SER* 3.7 0.3 - - - -
215A PHE* 2.7 40.4 + - + +
216A ASP 4.9 1.2 - - - +
294A GLY* 3.8 8.1 + - - -
295A THR* 3.4 13.7 + - - -
296A GLY* 3.1 36.2 + - - -
297A THR* 3.3 9.4 + - - +
300A GLY* 1.3 75.0 - - - +
302A PRO* 1.3 73.4 - - + +
304A GLU* 3.8 6.1 - - - +
305A LEU* 3.0 28.1 + - + +
363A ASN* 4.6 9.2 - - - +
366A ILE* 5.3 1.8 - - + -
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Residues in contact with PRO 302 (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 THR 4.0 1.1 - - - +
298A LYS 3.6 17.5 - - - +
299A VAL* 3.1 15.9 - - - +
301A ASP* 1.3 94.0 - - + +
303A GLN* 1.3 64.9 + - + +
304A GLU 2.8 2.4 + - - -
306A ASN* 2.8 31.3 + - - +
363A ASN* 3.6 19.0 - - - +
365A GLU* 4.1 21.5 - - + +
366A ILE* 3.3 27.6 - - + -
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Residues in contact with GLN 303 (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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259A GLN* 5.3 1.8 + - - -
263A PHE* 3.0 34.4 - - + -
264A PRO* 3.3 24.7 + - + +
265A SER* 4.7 2.4 - - - +
266A GLY* 3.0 42.7 + - - +
267A ASP* 4.2 8.7 + - - +
269A GLN* 4.4 0.4 - - - -
299A VAL* 3.4 19.3 + - + +
300A GLY 3.8 3.6 - - - +
302A PRO* 1.3 79.2 - - + +
304A GLU* 1.3 61.8 + - - +
306A ASN* 4.1 6.2 - - - +
307A GLY 3.5 8.5 + - - -
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Residues in contact with GLU 304 (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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264A PRO* 6.2 0.4 - - + -
269A GLN* 3.4 14.9 - - - +
292A ALA* 3.4 10.6 - - - +
293A HIS* 2.8 40.0 + - - +
294A GLY* 3.5 9.9 + - - -
295A THR* 5.1 1.4 + - - -
300A GLY 3.2 16.2 + - - +
301A ASP* 3.8 6.6 - - - +
302A PRO 2.8 4.8 + - - -
303A GLN* 1.3 71.3 - - - +
305A LEU* 1.3 70.0 + - - +
306A ASN 3.0 1.8 + - - -
307A GLY* 3.0 4.9 + - - -
308A ILE* 2.9 26.9 + - + +
391A ASN* 3.2 19.5 + - - +
393A PHE* 3.4 27.3 - - + -
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Residues in contact with LEU 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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215A PHE* 3.1 39.3 - - + -
292A ALA* 4.3 5.4 - - + -
301A ASP* 3.0 17.1 + - + +
302A PRO 4.0 0.2 - - - +
304A GLU* 1.3 82.0 - - + +
306A ASN* 1.3 62.2 + - - +
308A ILE* 3.3 19.2 + - + +
309A VAL* 3.1 29.3 + - - +
322A ILE* 3.2 32.1 - - + -
366A ILE* 3.7 29.8 - - + -
369A LEU* 4.4 10.8 - - + -
374A LEU* 4.7 6.7 - - + -
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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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302A PRO* 2.8 26.3 + - - +
303A GLN* 4.1 5.8 + - - +
305A LEU* 1.3 69.8 - - - +
307A GLY* 1.3 67.3 + - - +
308A ILE 3.1 0.5 + - - -
309A VAL* 3.2 7.2 + - - +
310A ASN* 2.9 36.3 + - - +
365A GLU 4.3 6.1 - - - +
366A ILE* 3.5 33.6 - - - +
367A PRO* 4.1 10.1 - - - +
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Residues in contact with GLY 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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266A GLY* 4.6 8.5 - - - -
269A GLN* 5.8 1.8 - - - -
270A GLU* 3.0 45.2 - - - +
273A ILE* 5.5 1.1 - - - +
303A GLN 3.5 8.8 + - - -
304A GLU 3.0 6.5 + - - -
306A ASN* 1.3 78.7 - - - +
308A ILE* 1.3 63.2 + - - +
310A ASN* 3.9 1.1 - - - +
311A ALA* 3.4 10.4 + - - +
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Residues in contact with ILE 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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273A ILE* 4.3 11.2 - - + -
290A ILE* 3.5 36.1 - - + -
292A ALA* 4.7 2.7 - - + -
304A GLU* 2.9 23.2 + - + +
305A LEU* 3.3 36.1 - - + +
306A ASN 3.1 0.2 - - - -
307A GLY* 1.3 75.4 - - - +
309A VAL* 1.3 68.2 + - + +
311A ALA* 3.0 5.0 + - - +
312A LEU* 3.0 26.3 + - + +
320A LEU* 3.9 20.9 - - + -
322A ILE* 4.3 5.6 - - + -
374A LEU* 4.8 1.8 - - + -
391A ASN* 3.8 19.1 - - - +
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Residues in contact with VAL 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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305A LEU 3.1 17.5 - - - +
306A ASN* 3.2 5.8 + - - +
308A ILE* 1.3 70.2 - - + +
310A ASN* 1.3 59.1 + - - +
311A ALA 2.9 11.8 + - - -
313A CYS* 3.3 50.6 + - + +
368A ALA* 4.3 5.8 - - + -
373A ARG* 3.3 46.6 + - + +
374A LEU* 3.3 33.0 - - + -
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Residues in contact with ASN 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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270A GLU* 2.8 29.2 + - - +
274A ARG* 2.8 31.1 + - - -
306A ASN* 2.9 36.1 + - - +
307A GLY 3.7 2.4 - - - +
308A ILE 3.2 0.4 - - - -
309A VAL* 1.3 75.8 - - - +
311A ALA* 1.3 49.9 + - - +
373A ARG* 4.9 8.8 + - - -
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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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270A GLU* 4.2 13.5 - - + +
273A ILE* 4.2 16.3 - - + +
274A ARG* 3.4 34.9 + - + +
277A TYR* 5.9 0.9 - - - +
284A PRO* 4.7 7.4 - - - +
307A GLY 3.4 12.8 + - - +
308A ILE 3.0 3.9 + - - +
309A VAL 2.9 0.4 - - - -
310A ASN* 1.3 80.9 - - - +
312A LEU* 1.3 66.6 + - - +
313A CYS 3.6 1.8 - - - -
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Residues in contact with LEU 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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273A ILE* 3.7 28.9 - - + -
277A TYR* 3.8 19.5 - - + +
284A PRO* 3.8 25.5 - - + +
287A LEU* 3.5 33.4 - - + -
290A ILE* 4.0 27.1 - - + -
308A ILE* 3.0 20.9 + - + +
311A ALA* 1.3 84.1 - - - +
313A CYS* 1.3 64.7 + - - +
314A ALA 3.9 1.3 - - - -
315A THR* 3.5 13.5 - - - +
320A LEU* 4.3 18.4 - - + +
401A HIS* 5.6 0.4 - - - +
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Residues in contact with CYS 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 VAL* 3.3 46.5 + - + +
310A ASN 5.3 0.2 - - - -
311A ALA 3.6 2.0 - - - -
312A LEU* 1.3 85.4 - - - +
314A ALA* 1.3 58.4 + - - +
315A THR* 3.6 7.9 - - + +
319A PRO* 3.8 29.8 - - + -
320A LEU* 4.0 10.3 - - - -
373A ARG* 4.8 8.9 + - + +
374A LEU* 4.7 5.8 - - - -
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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