Contacts of the helix formed by residues 271 - 286 (chain A) in PDB entry 2VLH
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 ASP 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A HIS* 4.2 0.4 - - - -
210A LYS* 4.2 22.5 + - - +
249A ASP 4.8 1.2 + - - +
269A MET* 3.6 6.6 - - + +
270A ASN* 1.3 76.3 - - - +
272A ASP* 1.3 62.0 + - - +
273A GLU* 3.0 23.2 - - - +
274A MET* 2.9 37.3 + - + +
275A PHE* 3.0 28.1 + - - +
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Residues in contact with ASP 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LYS* 2.7 35.3 + - - -
92A HIS* 2.7 27.5 + - + -
270A ASN 3.5 0.6 + - - -
271A ASP* 1.3 75.0 + - - +
273A GLU* 1.3 58.1 + - - +
275A PHE* 3.3 5.6 + - - +
276A SER* 3.1 29.1 + - - -
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Residues in contact with GLU 273 (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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271A ASP* 3.0 25.8 - - - +
272A ASP* 1.3 75.8 - - - +
274A MET* 1.3 64.2 + - - +
276A SER* 3.2 7.7 + - - +
277A SER* 3.1 28.7 + - - +
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Residues in contact with MET 274 (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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106A LEU* 3.3 34.8 - - + -
109A LEU* 4.0 30.0 - - + +
110A ALA* 4.8 4.3 - - + -
210A LYS* 5.2 7.0 - - - +
212A PHE* 3.8 26.5 - - + -
267A LEU* 4.8 4.0 - - + -
268A CYS 5.6 0.2 - - - +
269A MET* 3.9 27.4 - - + -
271A ASP* 2.9 28.5 + - + +
272A ASP 3.3 0.2 - - - -
273A GLU* 1.3 76.5 - - - +
275A PHE* 1.3 53.8 + - - +
277A SER* 3.5 5.8 + - - -
278A ALA* 2.8 32.7 + - - +
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Residues in contact with PHE 275 (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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77A PHE* 6.5 0.9 - + - -
81A GLU* 5.6 5.2 - - - -
92A HIS* 3.3 55.2 - + + -
93A ILE 3.8 20.2 - - - -
94A VAL* 3.8 18.6 - - + -
269A MET* 3.8 11.1 - - - +
271A ASP 3.0 14.9 + - - +
272A ASP* 3.4 10.8 - - + +
274A MET* 1.3 73.6 - - - +
276A SER* 1.3 65.1 + - - +
278A ALA* 3.3 0.7 + - - +
279A LYS* 3.0 58.7 + - + +
289A PRO* 5.9 0.7 - - + -
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Residues in contact with SER 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ASP 3.1 14.5 + - - -
273A GLU* 3.2 10.8 + - - -
275A PHE* 1.3 77.3 - - - +
277A SER* 1.3 62.3 + - - +
279A LYS* 3.3 18.7 + - - +
280A GLU* 3.1 18.9 + - - +
445B GLN* 3.4 32.5 + - - +
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Residues in contact with SER 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 3.6 21.0 - - - +
273A GLU* 3.1 16.8 + - - +
274A MET* 3.8 4.9 - - - -
276A SER* 1.3 77.5 - - - +
278A ALA* 1.3 58.1 + - - +
280A GLU* 3.3 10.5 + - - +
281A LEU* 3.0 27.9 + - - +
445B GLN* 4.3 8.9 + - - +
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Residues in contact with ALA 278 (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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94A VAL* 4.1 10.3 - - + -
105A LEU* 4.6 3.6 - - + +
109A LEU* 3.4 23.1 - - + +
267A LEU* 4.0 9.0 - - + -
269A MET* 3.7 18.4 - - + -
274A MET 2.8 19.6 + - - +
275A PHE 3.7 3.6 - - - +
276A SER 3.2 0.4 - - - -
277A SER* 1.3 77.9 - - - +
279A LYS* 1.3 56.3 + - - +
281A LEU* 3.2 3.3 + - - +
282A VAL* 2.8 32.5 + - - +
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 4.5 4.7 - - + -
275A PHE* 3.0 62.7 + - + +
276A SER* 3.6 16.5 + - - +
277A SER 3.3 0.2 - - - -
278A ALA* 1.3 73.6 - - - +
280A GLU* 1.3 65.8 + - - +
282A VAL* 3.3 20.8 - - - +
283A VAL* 3.7 4.3 + - - +
289A PRO* 3.5 33.5 - - + +
446B LEU* 3.8 19.4 - - + +
449B PHE* 4.6 8.2 - - + -
450B THR* 4.6 20.4 + - - +
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Residues in contact with GLU 280 (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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276A SER 3.1 10.0 + - - +
277A SER* 3.4 13.1 - - - +
279A LYS* 1.3 77.6 - - - +
281A LEU* 1.3 57.3 + - + +
283A VAL* 2.9 27.8 - - - +
284A VAL* 4.1 5.2 - - - +
445B GLN* 3.5 44.2 + - + +
446B LEU* 4.6 14.9 + - + +
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Residues in contact with LEU 281 (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 LEU* 3.7 26.0 - - + +
108A GLN* 3.5 44.2 - - + +
109A LEU* 4.0 19.5 - - + -
277A SER 3.0 14.6 + - - +
278A ALA* 3.2 2.9 + - - +
280A GLU* 1.3 74.5 - - + +
282A VAL* 1.3 67.3 + - - +
283A VAL 3.1 2.2 - - - -
284A VAL* 3.0 27.4 + - + +
285A TYR* 3.5 23.7 + - + -
128B TYR* 5.0 4.0 - - - +
132B LYS* 4.7 5.8 - - - +
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 3.5 24.7 - - + -
95A PRO 3.8 9.9 - - - +
105A LEU* 3.7 14.3 - - + +
278A ALA 2.8 19.3 + - - +
279A LYS* 3.3 16.4 - - - +
281A LEU* 1.3 72.3 - - - +
283A VAL* 1.3 59.3 + - - +
286A GLU* 2.6 55.4 + - + +
287A GLY 3.0 18.9 + - - +
289A PRO* 3.8 24.2 - - + -
292A GLY* 4.4 3.1 - - - -
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Residues in contact with VAL 283 (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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279A LYS 4.1 7.2 - - - +
280A GLU 2.9 28.5 - - - +
281A LEU 3.1 0.6 - - - -
282A VAL* 1.3 82.8 - - + +
284A VAL* 1.3 62.0 + - + +
287A GLY 3.3 10.5 - - - +
288A MET* 4.1 27.4 - - + -
100B ARG* 2.7 45.5 + - - +
125B THR* 4.3 5.8 - - + +
446B LEU* 4.3 17.7 - - + -
448B PHE* 5.8 1.8 - - + -
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Residues in contact with VAL 284 (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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280A GLU 4.1 11.7 - - - +
281A LEU* 3.0 17.4 + - + +
283A VAL* 1.3 83.2 - - + +
285A TYR* 1.3 75.9 + - + +
100B ARG* 3.6 13.5 - - - +
125B THR* 5.1 5.2 - - - +
128B TYR* 3.3 51.1 - - + +
129B HIS* 2.8 40.8 + - + -
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Residues in contact with TYR 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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104A ASN* 3.3 25.4 - - - +
105A LEU* 4.6 2.9 - - + -
108A GLN* 3.1 30.3 + - - -
281A LEU* 3.6 31.2 - - + +
282A VAL 3.2 1.6 + - - -
284A VAL* 1.3 95.4 - - + +
286A GLU* 1.3 73.7 + - + +
97B HIS* 3.1 19.1 - - - -
100B ARG* 3.8 8.7 - - - +
101B GLY* 4.5 5.5 + - - -
104B ASN* 3.8 36.6 + - + -
108B GLN* 5.4 1.4 + - - -
129B HIS* 4.1 9.1 - + - -
132B LYS* 3.3 24.9 + - - +
285B TYR* 4.2 11.2 + + + -
286B GLU* 5.0 0.3 - - - +
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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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96A THR* 4.3 9.9 - - + -
97A HIS* 2.7 46.7 + - - +
101A GLY* 3.3 28.6 - - - +
104A ASN* 5.2 1.2 + - - -
105A LEU* 4.9 4.3 - - + -
282A VAL* 2.6 36.0 + - + +
284A VAL 3.8 0.4 - - - -
285A TYR* 1.3 91.9 - - + +
287A GLY* 1.3 57.2 + - - +
292A GLY 3.7 10.7 - - - +
293A GLY* 3.2 11.1 - - - -
97B HIS* 2.7 22.5 + - - -
98B GLN* 3.4 8.1 - - - -
100B ARG* 4.1 4.0 - - - -
285B TYR 4.6 2.1 - - - +
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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