Contacts of the helix formed by residues 286 - 302 (chain A) in PDB entry 5VGR
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 ALA 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267A HIS 3.7 11.9 - - - +
268A PRO* 3.0 30.4 + - + +
269A GLY* 3.9 6.7 - - - +
284A ASP 3.7 2.0 + - - -
285A ILE* 1.3 73.7 - - - +
287A GLY* 1.3 65.6 - - - +
288A GLU* 3.4 2.7 - - + +
289A PHE* 3.3 7.3 + - + +
290A LYS* 3.2 19.4 + - - +
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Residues in contact with GLY 287 (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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285A ILE 3.5 1.8 + - - -
286A ALA* 1.3 73.1 - - - +
288A GLU* 1.3 57.8 + - - +
290A LYS* 3.2 17.2 + - - +
291A GLU* 2.9 36.5 + - - +
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Residues in contact with GLU 288 (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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223A TYR* 3.7 31.8 + - + -
266A PRO* 3.6 15.0 - - + -
286A ALA* 3.4 2.7 - - + +
287A GLY* 1.3 74.3 - - - +
289A PHE* 1.3 56.7 + - - +
291A GLU* 3.4 21.5 - - - +
292A GLN* 2.9 37.5 + - + +
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Residues in contact with PHE 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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75A PHE* 4.0 33.7 - + - -
76A ILE* 4.5 2.7 - - + -
79A PHE* 4.3 2.0 - + - -
213A ARG* 4.5 4.3 - - - -
265A LEU* 3.5 34.2 - - + +
266A PRO* 3.1 32.0 - - - +
267A HIS 3.7 15.1 + - - +
268A PRO* 3.8 14.1 - - + -
285A ILE* 3.7 17.5 - - + -
286A ALA* 3.3 9.9 + - - +
287A GLY 3.2 0.4 - - - -
288A GLU* 1.3 75.4 - - - +
290A LYS* 1.3 61.1 + - - +
292A GLN* 3.3 1.7 + - - +
293A LEU* 2.8 61.6 + - + +
501A GDP 4.0 12.8 - - - -
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Residues in contact with LYS 290 (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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79A PHE* 6.2 0.2 - - + -
96A LEU* 4.2 19.6 - - + +
282A LEU* 2.8 47.6 + - + +
283A LYS* 3.5 15.0 + - - +
285A ILE* 3.1 35.1 + - + +
286A ALA 3.2 9.0 + - - +
287A GLY* 3.2 14.1 + - - +
289A PHE* 1.3 77.3 - - + +
291A GLU* 1.3 63.0 + - - +
293A LEU* 3.2 13.2 + - + +
294A GLN* 3.1 29.3 + - - +
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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 GLY* 2.9 19.9 + - - +
288A GLU* 3.4 25.3 - - - +
290A LYS* 1.3 76.2 - - - +
292A GLN* 1.3 73.8 + - - +
294A GLN* 3.2 26.4 + - - +
295A ALA* 3.6 6.1 + - - +
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Residues in contact with GLN 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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223A TYR* 3.6 26.4 + - + +
224A GLY* 3.5 23.0 - - - -
263A PHE* 3.6 8.1 - - + -
265A LEU* 3.7 9.9 - - + -
266A PRO* 3.5 29.6 - - + -
288A GLU* 2.9 23.7 + - - +
289A PHE 4.0 0.2 - - - +
291A GLU* 1.3 84.8 + - - +
293A LEU* 1.3 60.7 + - - +
295A ALA* 3.1 11.5 + - - +
296A LEU* 2.9 29.5 + - - +
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Residues in contact with LEU 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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76A ILE* 3.7 29.8 - - + -
79A PHE* 3.6 36.8 - - + -
95A TRP* 4.0 4.1 - - + -
96A LEU* 4.3 9.9 - - + -
265A LEU* 4.3 4.2 - - + +
289A PHE* 2.8 44.4 + - + +
290A LYS* 3.3 10.3 - - + +
292A GLN* 1.3 77.4 - - - +
294A GLN* 1.3 61.2 + - - +
296A LEU* 4.4 8.5 - - + +
297A ILE* 3.1 49.6 + - + +
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Residues in contact with GLN 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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95A TRP* 4.2 21.8 - - + +
96A LEU* 4.1 26.7 - - + +
290A LYS* 3.1 15.8 + - - +
291A GLU* 3.2 16.1 + - - +
293A LEU* 1.3 76.5 - - - +
295A ALA* 1.3 56.6 + - - +
298A PRO* 3.1 22.1 - - - +
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Residues in contact with ALA 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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224A GLY* 6.1 0.2 - - - -
263A PHE* 4.4 12.6 - - + -
291A GLU 3.6 5.6 + - - +
292A GLN* 3.1 16.4 + - - +
294A GLN* 1.3 80.2 - - - +
296A LEU* 1.3 63.2 + - - +
297A ILE 3.5 0.7 - - - -
298A PRO* 3.8 1.6 - - - +
299A TYR* 3.2 25.1 + - - +
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Residues in contact with LEU 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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76A ILE* 4.4 22.7 - - + -
80A MET* 5.9 2.7 - - + -
171A ILE* 5.7 2.7 - - + -
209A MET* 4.3 14.6 - - + -
211A LEU* 4.0 25.4 - - + -
263A PHE* 3.5 33.7 - - + -
265A LEU* 4.4 13.9 - - + -
292A GLN 2.9 15.8 + - - +
293A LEU* 4.1 7.6 - - + +
295A ALA* 1.3 77.8 - - - +
297A ILE* 1.3 72.7 + - + +
299A TYR* 3.3 4.5 + - + +
300A VAL* 3.2 33.1 + - + +
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Residues in contact with ILE 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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76A ILE* 4.4 6.1 - - + +
79A PHE* 4.1 20.6 - - + +
80A MET* 3.9 24.9 - - + -
83A TYR* 3.7 32.5 - - + -
95A TRP* 3.6 16.2 - - + -
293A LEU* 3.1 30.0 + - + +
296A LEU* 1.3 84.4 - - + +
298A PRO* 1.3 70.0 - - + +
300A VAL* 3.1 6.4 + - - +
301A LEU* 2.9 37.9 + - + +
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Residues in contact with PRO 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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83A TYR* 4.2 19.7 - - + +
95A TRP* 4.2 10.3 - - + +
293A LEU 3.8 0.2 - - - +
294A GLN 3.1 31.0 - - - +
295A ALA* 3.8 1.3 - - - +
297A ILE* 1.3 94.3 - - + +
299A TYR* 1.3 61.5 + - - +
302A ASN* 2.8 46.0 + - + +
305A LYS* 3.7 2.3 - - - +
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Residues in contact with TYR 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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209A MET* 3.3 34.3 - - + -
225A LEU* 3.6 41.2 - - + +
261A THR* 4.2 15.8 + - - +
263A PHE* 5.2 5.4 - + + -
295A ALA 3.2 23.1 + - - +
296A LEU* 3.5 9.4 - - + +
297A ILE 3.2 0.4 - - - -
298A PRO* 1.3 75.8 - - - +
300A VAL* 1.3 60.5 + - + +
305A LYS* 3.3 52.4 + - - +
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Residues in contact with VAL 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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63A VAL* 4.0 32.7 - - + +
80A MET* 4.3 10.1 - - + -
169A VAL* 5.0 13.2 - - + +
171A ILE* 4.2 13.2 - - + -
209A MET* 4.1 25.8 - - + -
296A LEU* 3.2 20.1 + - + +
297A ILE 3.1 6.3 + - - +
298A PRO 3.1 0.4 - - - -
299A TYR* 1.3 81.6 - - + +
301A LEU* 1.3 72.0 + - + +
302A ASN 3.8 0.4 - - - -
305A LYS* 4.3 11.4 - - - +
306A LEU* 4.1 9.0 - - - +
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Residues in contact with LEU 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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63A VAL* 4.1 18.2 - - + -
80A MET* 3.8 46.4 - - + +
83A TYR* 3.7 22.7 - - + -
84A LEU* 4.1 15.9 - - + +
87A GLN* 4.4 4.3 + - - +
138A VAL* 4.3 13.2 - - + -
140A LEU* 5.0 2.7 - - + -
297A ILE* 2.9 20.8 + - + +
300A VAL* 1.3 95.6 - - + +
302A ASN* 1.3 70.0 + - - +
303A PRO* 3.5 2.4 - - - +
306A LEU* 3.5 24.9 - - + +
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Residues in contact with ASN 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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83A TYR* 3.4 14.9 + - - +
298A PRO* 2.8 27.3 + - + +
300A VAL 3.8 0.4 - - - -
301A LEU* 1.3 78.3 - - - +
303A PRO* 1.3 75.8 - - - +
304A SER* 2.5 39.7 + - - -
305A LYS* 2.8 25.6 + - + +
306A LEU* 3.0 10.7 + - - +
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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
------------------------------------------------------------
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