Contacts of the helix formed by residues 259 - 274 (chain A) in PDB entry 2VMX
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 LEU 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLN 5.3 1.2 + - - -
92A HIS* 3.7 38.8 + - + +
232A ARG 5.9 0.9 - - - +
257A GLY 4.7 2.0 - - - +
258A PRO* 1.3 72.0 - - - +
260A MET* 1.3 60.3 + - - +
261A HIS* 3.2 19.1 - - + +
262A VAL* 3.0 31.7 + - + +
263A ILE* 2.9 31.4 + - - +
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Residues in contact with MET 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 3.7 26.0 + - + +
50A LYS 4.2 8.9 + - - +
52A ALA* 3.9 23.1 - - + -
59A ARG* 4.0 3.1 - - - +
67A VAL* 3.6 39.0 - - + +
70A VAL* 4.3 4.0 - - + +
71A GLU* 3.6 27.4 - - + +
258A PRO* 3.2 34.3 + - - +
259A LEU* 1.3 72.3 - - - +
261A HIS* 1.3 59.9 + - - +
263A ILE* 3.6 18.6 - - + +
264A ALA* 2.9 28.2 + - - +
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Residues in contact with HIS 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA 3.4 27.5 - - - +
43A GLN* 3.3 23.3 - - + +
45A SER* 3.8 7.9 - - - +
47A LEU* 3.6 8.3 - - - +
48A THR* 3.4 51.0 + - - +
259A LEU* 3.8 31.9 - - + +
260A MET* 1.3 82.3 + - - +
262A VAL* 1.3 73.4 + - + +
264A ALA* 3.4 3.3 + - - +
265A ALA* 3.1 21.5 + - - +
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Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLN* 3.5 30.1 - - - +
231A PRO* 4.0 7.2 - - + -
232A ARG 3.6 21.1 - - - +
233A GLY* 5.1 0.4 - - - -
259A LEU* 3.0 36.4 + - + +
261A HIS* 1.3 89.8 - - + +
263A ILE* 1.3 55.7 + - + +
265A ALA* 3.1 4.0 + - - +
266A LYS* 2.8 47.7 + - - +
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Residues in contact with ILE 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A VAL* 4.2 0.7 - - + -
71A GLU* 3.7 34.1 - - + +
74A ALA* 3.9 2.9 - - + +
89A VAL* 3.5 32.8 - - + +
90A GLN* 3.8 19.5 - - + +
258A PRO* 3.8 29.4 - - + -
259A LEU 2.9 12.8 + - - +
260A MET* 3.3 25.3 + - + +
262A VAL* 1.3 74.5 - - + +
264A ALA* 1.3 59.5 + - - +
266A LYS* 3.2 11.6 + - - +
267A ALA* 3.0 27.4 + - - +
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Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA* 3.9 16.2 - - + +
45A SER* 5.1 0.7 - - - +
47A LEU* 3.9 13.2 - - + -
70A VAL* 3.4 23.9 - - + +
260A MET 2.9 14.2 + - - +
261A HIS* 3.4 10.8 - - - +
263A ILE* 1.3 75.9 - - - +
265A ALA* 1.3 61.0 + - - +
267A ALA* 3.2 6.5 + - - +
268A VAL* 3.1 25.5 + - + +
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Residues in contact with ALA 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 3.5 14.7 - - + +
42A ALA* 3.7 9.3 - - + +
43A GLN* 3.4 33.4 - - + -
231A PRO* 3.6 20.3 - - + +
261A HIS 3.1 9.1 + - - +
262A VAL 3.1 8.5 + - - +
264A ALA* 1.3 72.4 - - - +
266A LYS* 1.3 60.6 + - - +
268A VAL* 3.3 5.6 + - - +
269A ALA* 3.0 23.7 + - - +
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Residues in contact with LYS 266 (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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74A ALA* 4.7 2.5 - - + -
89A VAL* 2.7 35.8 + - + +
90A GLN 4.3 0.8 - - - -
91A PRO 3.0 17.4 + - - -
224A THR* 3.8 27.8 - - + -
231A PRO* 3.7 15.0 - - + -
233A GLY* 4.2 2.0 - - - -
234A GLY 2.8 24.8 + - - +
235A MET* 5.6 0.2 - - + -
262A VAL* 2.8 37.1 + - - +
263A ILE* 3.2 14.9 + - - +
265A ALA* 1.3 73.6 - - - +
267A ALA* 1.3 57.3 + - - +
269A ALA* 3.1 2.8 + - - +
270A PHE* 2.8 50.8 + - + -
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Residues in contact with ALA 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A VAL* 4.1 9.0 - - + +
73A LEU* 4.3 6.7 - - + -
74A ALA* 3.8 31.9 - - + +
77A ARG* 2.8 29.0 + - - +
263A ILE 3.0 12.2 + - - +
264A ALA* 3.4 11.4 - - - +
266A LYS* 1.3 73.4 - - - +
268A VAL* 1.3 58.6 + - + +
270A PHE* 3.3 2.9 + - - +
271A GLY 2.9 18.5 + - - -
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Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA* 3.8 21.3 - - + +
39A VAL* 3.7 12.8 - - + +
42A ALA* 4.0 18.4 - - + -
77A ARG* 4.2 6.3 - - - +
264A ALA* 3.1 16.0 + - + +
265A ALA* 3.5 7.4 - - - +
266A LYS 3.2 0.2 - - - -
267A ALA* 1.3 76.4 - - + +
269A ALA* 1.3 57.0 + - - +
271A GLY* 3.1 3.1 + - - -
272A GLU* 2.9 47.0 + - + +
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Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 4.1 9.4 - - + -
228A LEU* 4.7 6.3 - - + +
229A ARG 4.2 4.3 - - - +
230A GLY* 3.5 33.2 - - - +
231A PRO* 3.8 3.1 - - + -
265A ALA 3.0 12.9 + - - +
266A LYS* 3.5 8.7 - - - +
268A VAL* 1.3 76.6 - - - +
270A PHE* 1.3 63.3 + - + +
272A GLU* 3.2 10.4 + - - +
273A ALA* 3.0 28.1 + - - +
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Residues in contact with PHE 270 (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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74A ALA* 3.3 31.4 - - - -
77A ARG* 3.7 14.8 - - + -
78A ALA* 3.9 5.2 - - + -
81A LEU* 3.9 23.8 - - + +
89A VAL* 4.1 6.3 - - + -
224A THR* 3.7 26.7 - - + -
228A LEU* 3.9 20.9 - - + -
235A MET* 3.6 33.7 - - + -
266A LYS* 2.8 38.2 + - + +
267A ALA 3.7 3.8 - - - +
269A ALA* 1.3 78.1 - - + +
271A GLY* 1.3 66.1 + - - +
273A ALA* 3.1 2.9 + - - +
274A LEU* 3.0 29.4 + - - +
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Residues in contact with GLY 271 (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 ARG* 4.0 20.1 - - - +
267A ALA 2.9 15.3 + - - -
268A VAL 3.5 4.5 - - - -
270A PHE* 1.3 75.8 - - - +
272A GLU* 1.3 61.3 + - - +
274A LEU* 3.3 20.5 + - - +
275A GLN* 3.6 15.7 - - - +
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Residues in contact with GLU 272 (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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36A SER* 2.6 38.1 + - - -
38A ALA* 4.2 4.7 - - - +
39A VAL* 4.2 9.9 - - - +
229A ARG* 4.7 19.5 + - - +
268A VAL* 2.9 28.8 + - + +
269A ALA* 3.5 10.1 - - - +
271A GLY* 1.3 76.0 - - - +
273A ALA* 1.3 61.3 + - - +
275A GLN* 3.1 36.1 + - - +
277A ASP* 4.4 0.3 - - - +
278A PHE* 3.3 18.1 - - + +
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Residues in contact with ALA 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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81A LEU* 3.7 26.2 - - + +
206A ALA* 4.9 0.8 - - + +
228A LEU* 4.1 12.6 - - + +
269A ALA 3.0 16.1 + - - +
270A PHE 3.1 5.3 + - - +
272A GLU* 1.3 76.3 - - - +
274A LEU* 1.3 58.2 + - - +
275A GLN 3.2 0.7 + - - -
278A PHE* 3.5 41.9 - - + +
279A LYS* 2.8 18.4 + - - -
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 3.8 34.5 - - + +
80A GLN* 3.6 45.3 - - + +
81A LEU* 3.7 26.0 - - + +
270A PHE 3.0 17.9 + - - +
271A GLY* 3.5 11.2 - - - +
272A GLU 3.2 0.4 - - - -
273A ALA* 1.3 76.4 - - - +
275A GLN* 1.3 59.6 + - - +
276A ASP* 4.0 2.4 + - - +
279A LYS* 3.2 15.8 + - - +
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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
------------------------------------------------------------
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