Contacts of the helix formed by residues 285 - 306 (chain A) in PDB entry 3VPN
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 285 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A LYS 3.9 0.4 + - - -
284A PRO* 1.3 76.9 - - - +
286A GLU* 1.3 67.0 + - - +
287A GLU* 3.1 14.6 - - - +
288A ARG* 2.9 32.4 + - - +
289A VAL* 3.0 13.9 + - - +
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Residues in contact with GLU 286 (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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284A PRO 3.8 1.0 + - - -
285A SER* 1.3 72.1 - - - +
287A GLU* 1.3 56.6 + - - +
289A VAL* 3.5 1.1 + - - +
290A ARG* 2.8 49.2 + - + +
332A MET* 4.5 0.9 - - - +
337A PHE* 3.4 42.2 - - + +
338A SER* 2.8 41.6 + - - +
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A SER* 3.9 12.8 - - - +
286A GLU* 1.3 79.8 - - - +
288A ARG* 1.3 59.3 + - + +
290A ARG* 3.5 11.7 - - - +
291A GLU* 3.0 32.0 + - - +
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Residues in contact with ARG 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A TRP* 3.7 26.5 - - - -
219A ALA* 5.9 0.6 - - - +
223A GLU* 2.9 30.8 + - + +
284A PRO* 4.2 11.4 - - + -
285A SER* 2.9 26.1 + - - +
287A GLU* 1.3 79.2 - - + +
289A VAL* 1.3 65.0 + - - +
291A GLU* 3.0 40.7 + - - +
292A ILE* 3.1 38.1 + - + +
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Residues in contact with VAL 289 (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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226A VAL* 4.0 14.4 - - + -
277A PHE* 4.2 4.5 - - + -
284A PRO* 3.9 23.6 - - + -
285A SER 3.0 18.2 + - - +
286A GLU 3.9 2.9 - - - +
288A ARG* 1.3 74.1 - - - +
290A ARG* 1.3 64.8 + - - +
292A ILE* 3.1 9.8 + - + +
293A ILE* 2.9 24.2 + - + +
332A MET* 3.8 19.5 - - - -
335A LEU* 4.0 15.3 - - + -
337A PHE* 3.6 35.4 - - + -
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Residues in contact with ARG 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A GLU* 2.8 40.0 + - + +
287A GLU* 3.5 10.5 - - - +
289A VAL* 1.3 72.4 - - - +
291A GLU* 1.3 57.0 + - - +
293A ILE* 4.0 0.6 - - - +
294A ILE* 2.9 51.4 + - + +
332A MET* 3.7 22.4 - - + +
338A SER* 4.6 4.0 + - - -
339A LYS 3.5 22.4 + - - -
340A VAL* 3.6 36.4 + - + +
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLU* 3.0 19.7 + - + +
288A ARG* 3.0 42.7 + - - +
289A VAL 3.3 0.2 - - - -
290A ARG* 1.3 75.9 - - - +
292A ILE* 1.3 61.1 + - - +
294A ILE* 4.4 5.6 - - - +
295A ASN* 3.3 25.6 + - + +
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Residues in contact with ILE 292 (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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209A TRP* 3.8 28.2 - - + -
213A TRP* 3.9 26.7 - - + -
223A GLU* 4.2 24.2 - - + +
226A VAL* 4.3 13.0 - - + -
227A ALA* 4.2 11.9 - - - -
284A PRO* 6.1 0.4 - - + -
288A ARG* 3.1 41.4 + - + +
289A VAL* 3.1 13.2 + - + +
291A GLU* 1.3 76.3 - - - +
293A ILE* 1.3 61.6 + - + +
295A ASN* 3.4 6.0 - - - +
296A ALA* 3.1 25.3 + - - +
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Residues in contact with ILE 293 (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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226A VAL* 3.9 15.3 - - + -
230A ALA* 3.8 26.2 - - + -
234A ILE* 3.8 5.3 - - + +
289A VAL* 2.9 24.5 + - + +
290A ARG* 4.0 2.2 - - - +
292A ILE* 1.3 76.3 - - + +
294A ILE* 1.3 66.8 + - + +
296A ALA* 3.4 3.8 + - - +
297A VAL* 3.1 24.0 + - + +
328A ALA* 3.7 28.5 - - + +
331A LEU* 3.8 20.4 - - + -
332A MET* 3.7 31.0 - - + -
335A LEU* 5.2 0.9 - - + -
340A VAL* 5.6 1.8 - - + -
341A PHE* 5.4 1.6 - - + -
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Residues in contact with ILE 294 (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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290A ARG* 2.9 41.5 + - + +
291A GLU* 4.4 3.8 - - - +
293A ILE* 1.3 75.1 - - + +
295A ASN* 1.3 64.9 + - - +
297A VAL* 3.2 9.4 + - - +
298A ARG* 3.1 44.4 + - + +
340A VAL* 3.8 33.2 - - + -
341A PHE* 4.3 11.0 - - + -
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Residues in contact with ASN 295 (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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209A TRP* 3.0 30.1 - - - +
291A GLU 3.3 19.2 + - - +
292A ILE* 3.4 6.3 - - - +
294A ILE* 1.3 77.4 - - - +
296A ALA* 1.3 64.3 + - - +
298A ARG* 3.3 7.7 + - - +
299A ILE* 3.1 32.1 + - - +
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Residues in contact with ALA 296 (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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209A TRP* 4.3 8.9 - - + -
230A ALA* 3.9 24.9 - - + -
234A ILE* 3.9 11.7 - - + -
235A PHE* 3.4 29.7 - - + -
292A ILE 3.1 16.5 + - - +
293A ILE 3.8 4.9 - - - +
294A ILE 3.3 0.4 - - - -
295A ASN* 1.3 76.0 - - - +
297A VAL* 1.3 56.9 + - - +
299A ILE* 3.3 2.2 + - - -
300A GLU* 2.9 27.7 + - - +
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Residues in contact with VAL 297 (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 11.2 - - + -
293A ILE 3.1 18.4 + - - +
294A ILE 3.2 10.1 + - - +
296A ALA* 1.3 76.3 - - - +
298A ARG* 1.3 59.7 + - - +
300A GLU* 3.4 1.9 + - - +
301A GLN* 2.8 54.9 + - - +
324A ILE* 4.0 17.0 - - + +
325A GLU* 4.0 12.6 - - + -
328A ALA* 3.4 30.7 - - + -
341A PHE* 4.0 13.5 - - + -
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Residues in contact with ARG 298 (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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294A ILE* 3.1 32.2 + - + +
295A ASN* 3.3 8.9 + - - +
297A VAL* 1.3 73.8 - - - +
299A ILE* 1.3 62.8 + - + +
301A GLN* 2.9 25.3 + - - +
302A GLU* 2.8 31.9 + - - +
325A GLU* 3.0 22.4 + - - -
341A PHE* 3.9 23.1 - - - -
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Residues in contact with ILE 299 (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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205A LYS* 4.2 37.0 - - + +
206A LYS* 3.7 27.6 - - + -
209A TRP* 3.3 40.4 - - + +
212A ARG* 5.6 1.3 - - - +
235A PHE* 4.0 8.1 - - + -
295A ASN* 3.1 24.1 + - - +
296A ALA 3.6 6.5 - - - +
298A ARG* 1.3 77.0 - - + +
300A GLU* 1.3 57.1 + - - +
302A GLU* 3.2 9.4 + - - +
303A PHE* 2.8 27.8 + - - +
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Residues in contact with GLU 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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206A LYS* 2.4 34.7 + - - +
234A ILE* 3.4 28.2 - - + +
235A PHE* 3.2 11.6 - - + +
238A GLY* 3.1 26.2 + - - -
239A SER 4.0 1.4 + - - -
296A ALA 2.9 16.1 + - - +
297A VAL 3.7 3.8 - - - +
299A ILE* 1.3 76.8 - - - +
301A GLN* 1.3 62.6 + - - +
303A PHE* 3.3 5.1 + - - +
304A LEU* 3.1 40.4 + - + +
324A ILE* 3.8 17.0 - - + -
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Residues in contact with GLN 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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297A VAL* 2.8 25.6 + - + +
298A ARG* 2.9 36.4 + - - +
300A GLU* 1.3 69.3 - - - +
302A GLU* 1.3 59.4 + - - +
304A LEU* 3.4 5.2 + - - -
305A THR* 2.7 38.4 + - - +
321A LYS* 2.9 66.6 + - + +
324A ILE* 4.2 6.7 - - + -
325A GLU* 3.1 26.7 + - - +
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Residues in contact with GLU 302 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A CYS 5.4 2.1 - - - +
205A LYS* 3.6 34.0 + - + +
298A ARG 2.8 18.8 + - - +
299A ILE* 3.3 7.1 - - - +
301A GLN* 1.3 76.3 - - - +
303A PHE* 1.3 70.2 + - - +
305A THR* 4.0 4.3 - - - -
306A GLU* 2.9 68.9 + - - +
307A ALA* 3.2 13.0 + - - +
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Residues in contact with PHE 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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130A VAL* 5.4 1.8 - - + -
133A PHE* 4.1 19.7 - + + -
202A CYS* 3.5 47.3 - - + +
203A VAL* 4.4 6.7 - - + -
206A LYS* 3.2 40.6 - - + -
239A SER* 3.9 17.3 - - - -
299A ILE 2.8 17.7 + - - +
300A GLU 3.4 7.9 - - - +
302A GLU* 1.3 80.5 + - - +
304A LEU* 1.3 76.7 + - + +
307A ALA* 3.8 3.1 - - - -
308A LEU* 2.9 55.1 + - + +
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Residues in contact with LEU 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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126A PHE* 5.2 3.4 - - + -
130A VAL* 6.3 0.2 - - + -
238A GLY* 3.6 34.1 - - - -
239A SER* 4.0 2.9 - - - +
242A SER* 4.7 2.0 - - - +
300A GLU* 3.1 41.3 + - - +
301A GLN* 3.4 3.3 + - - +
302A GLU 3.3 0.2 - - - -
303A PHE* 1.3 92.4 - - + +
305A THR* 1.3 61.6 + - + +
306A GLU 3.7 0.2 - - - -
308A LEU 3.8 9.2 - - - +
310A VAL* 3.0 52.5 + - + +
320A MET* 3.7 15.3 - - + -
324A ILE* 3.7 17.0 - - + -
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Residues in contact with THR 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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301A GLN* 2.7 23.2 + - - +
302A GLU* 3.7 4.3 + - - -
304A LEU* 1.3 82.9 - - + +
306A GLU* 1.3 64.4 + - - +
309A PRO* 3.8 16.9 - - - +
317A CYS* 3.8 33.0 - - + +
320A MET* 5.7 1.1 - - + -
321A LYS* 3.8 38.8 + - + +
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Residues in contact with GLU 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 GLU* 2.9 44.2 + - + +
304A LEU 3.7 0.2 - - - -
305A THR* 1.3 86.5 + - - +
307A ALA* 1.3 64.4 + - - +
308A LEU 3.5 0.8 + - - -
309A PRO* 3.9 10.4 - - - +
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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
------------------------------------------------------------
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