Contacts of the helix formed by residues 284 - 300 (chain A) in PDB entry 2VN9
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 ARG 284 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A TYR* 2.9 20.0 + - + +
109A SER* 4.6 2.2 - - - -
110A GLU* 4.5 24.9 + - - +
208A LEU* 3.0 27.7 + - - +
209A VAL* 4.4 3.6 - - - +
237A GLU* 2.7 32.9 + - - +
240A THR* 2.8 27.2 + - - -
241A VAL* 3.3 22.8 - - - +
280A SER* 5.8 0.6 + - - -
282A MET* 3.3 36.2 - - + +
283A HIS* 1.3 76.7 - - - +
285A GLN* 1.3 65.8 + - - +
286A GLU* 3.1 3.8 - - - -
287A THR* 2.8 29.8 + - - +
288A VAL* 3.2 5.7 + - - +
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Residues in contact with GLN 285 (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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105A ARG 5.5 0.9 - - - +
106A GLU 4.8 0.7 - - - +
283A HIS* 2.7 44.1 + - + +
284A ARG* 1.3 74.3 - - - +
286A GLU* 1.3 57.7 + - - +
288A VAL* 3.1 17.8 + - - +
289A ASP* 2.5 62.4 + - - +
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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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209A VAL 4.9 0.4 - - - -
237A GLU* 5.2 14.1 - - + -
284A ARG* 3.1 2.3 + - - -
285A GLN* 1.3 77.9 - - - +
287A THR* 1.3 56.2 + - - +
289A ASP* 3.4 16.3 + - - +
290A CYS* 2.9 51.6 + - - -
293A LYS* 5.2 5.2 + - - -
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Residues in contact with THR 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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108A TYR* 3.8 14.1 - - + -
207A LEU 3.5 18.6 - - - +
208A LEU 2.6 32.7 + - - +
209A VAL* 3.7 12.1 - - - -
210A GLY 3.7 9.2 - - - +
284A ARG* 2.8 29.3 + - - +
286A GLU* 1.3 75.4 - - - +
288A VAL* 1.3 56.3 + - - +
290A CYS* 3.6 0.9 - - - +
291A LEU* 2.7 40.5 + - + +
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Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ILE* 4.3 9.2 - - + +
103A VAL* 3.6 31.6 - - + +
105A ARG 4.6 7.9 - - - +
108A TYR* 4.0 31.2 - - + -
283A HIS* 4.2 13.0 - - + -
284A ARG 3.9 10.3 - - - +
285A GLN* 3.1 22.5 + - - +
287A THR* 1.3 79.0 - - - +
289A ASP* 1.3 64.4 + - - +
291A LEU* 3.8 7.5 - - - +
292A LYS* 3.0 23.8 + - + +
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Residues in contact with ASP 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLN* 2.5 52.1 + - - +
286A GLU* 3.7 20.5 - - - +
288A VAL* 1.3 78.9 - - - +
290A CYS* 1.3 61.6 + - - +
292A LYS* 3.3 22.9 - - - +
293A LYS* 3.4 20.3 + - - +
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Residues in contact with CYS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A VAL 3.3 24.9 - - - +
210A GLY 3.3 13.4 - - - +
211A TYR* 4.6 12.6 - - + -
286A GLU* 2.9 38.5 + - - +
287A THR 3.7 0.9 - - - +
289A ASP* 1.3 74.8 - - - +
291A LEU* 1.3 53.9 + - - +
293A LYS* 3.0 22.3 + - - +
294A PHE 2.8 30.1 + - - -
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Residues in contact with LEU 291 (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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99A PHE* 3.8 21.8 - - + +
102A ILE* 3.4 41.3 - - + -
103A VAL* 3.6 14.4 - - + -
108A TYR* 4.6 2.7 - - + +
206A ILE* 3.6 37.9 - - + +
207A LEU* 4.8 3.1 - - + +
210A GLY* 3.6 7.4 + - - -
287A THR* 2.7 34.9 + - + +
288A VAL* 3.8 1.8 - - - +
290A CYS* 1.3 68.6 - - - +
292A LYS* 1.3 56.5 + - - +
294A PHE* 3.9 7.0 - - + -
295A ASN* 2.7 40.5 + - - +
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Residues in contact with LYS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 3.5 21.6 - - + +
288A VAL* 3.0 16.0 + - + +
289A ASP* 3.3 17.7 - - - +
291A LEU* 1.3 76.1 - - - +
293A LYS* 1.3 58.1 + - + +
295A ASN* 3.6 3.8 + - - +
296A ALA* 3.1 27.9 + - - +
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Residues in contact with LYS 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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286A GLU* 5.2 4.0 + - - -
289A ASP* 3.6 19.9 - - - +
290A CYS* 3.0 21.7 + - - +
292A LYS* 1.3 75.2 - - + +
294A PHE* 1.3 61.2 + - - +
296A ALA* 3.4 6.8 + - - +
297A ARG* 2.9 30.5 + - - +
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Residues in contact with PHE 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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99A PHE* 3.9 16.2 - + - -
139A PRO* 4.0 2.9 - - + -
180A TYR* 3.5 19.1 - - - -
206A ILE* 3.7 30.5 - - + -
210A GLY 3.4 20.4 - - - +
212A PRO* 4.1 28.5 - - + -
215A TRP* 5.8 0.7 - + - -
290A CYS 2.8 8.9 + - - +
291A LEU* 3.2 8.9 + - + +
293A LYS* 1.3 72.6 - - - +
295A ASN* 1.3 65.3 + - - +
297A ARG* 3.2 9.4 + - + +
298A ARG* 2.9 52.9 + - - +
305A LEU* 3.6 28.0 - - + -
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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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99A PHE* 3.0 38.0 + - - +
100A GLU* 3.6 26.2 + - - +
103A VAL* 3.3 22.8 - - - +
291A LEU* 2.7 19.8 + - - +
292A LYS* 3.8 4.9 - - - +
294A PHE* 1.3 76.4 - - - +
296A ALA* 1.3 60.0 + - - +
298A ARG* 2.6 35.4 + - - +
299A LYS* 3.0 33.1 + - - +
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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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292A LYS 3.1 19.3 + - - +
293A LYS* 3.6 8.5 - - - +
295A ASN* 1.3 73.5 - - - +
297A ARG* 1.3 66.9 + - - +
299A LYS* 3.4 19.5 + - - +
300A LEU* 3.4 19.0 + - - +
277B THR 6.1 0.9 - - - +
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Residues in contact with ARG 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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215A TRP* 3.5 27.8 - - + -
217A GLU* 3.1 38.6 + - - -
293A LYS 2.9 15.5 + - - +
294A PHE* 3.3 12.8 - - + +
296A ALA* 1.3 76.5 - - - +
298A ARG* 1.3 61.6 + - - +
300A LEU* 3.0 29.3 + - - +
301A LYS 3.8 13.3 + - - +
303A ALA* 5.3 4.6 - - - +
304A ILE* 4.3 10.9 - - - +
305A LEU* 3.6 20.0 - - + +
281B MET* 3.7 36.2 - - - +
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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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97A GLU* 2.4 38.4 + - - -
99A PHE* 3.9 9.1 - - - +
100A GLU* 3.9 4.1 + - - -
139A PRO* 3.7 13.8 - - - +
140A GLU* 3.1 33.0 + - - +
180A TYR* 4.6 1.6 - - - -
294A PHE* 2.9 41.6 + - - +
295A ASN* 2.6 46.7 + - - +
297A ARG* 1.3 72.5 - - - +
299A LYS* 1.3 66.8 + - - +
301A LYS* 2.9 28.8 + - - +
305A LEU* 3.5 35.3 - - + +
306A THR* 5.2 0.3 + - - -
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Residues in contact with LYS 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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100A GLU* 4.7 15.5 - - - +
295A ASN* 3.0 17.3 + - + +
296A ALA* 3.5 15.3 - - - +
298A ARG* 1.3 75.6 - - + +
300A LEU* 1.3 65.9 + - + +
301A LYS* 3.2 15.2 + - - +
242B THR* 6.1 1.0 - - - +
280B SER* 5.9 0.3 - - - -
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Residues in contact with LEU 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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296A ALA 3.4 15.9 - - - +
297A ARG* 3.0 19.1 + - - +
299A LYS* 1.3 77.0 - - + +
301A LYS* 1.3 66.5 + - - +
242B THR* 5.9 1.6 - - + -
276B SER 3.6 23.1 - - - +
277B THR* 3.6 26.5 - - - +
278B VAL 3.9 9.2 - - - +
279B ALA 3.8 14.4 - - - +
280B SER* 3.1 11.1 + - - +
281B MET* 2.9 54.6 + - + +
282B MET 3.6 0.2 + - - -
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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