Contacts of the helix formed by residues 353 - 366 (chain A) in PDB entry 1V2E
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 THR 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A SER* 4.1 15.5 - - - +
37A ASN* 5.5 5.2 - - + +
286A ARG* 5.0 1.3 - - - +
352A LYS* 1.3 76.5 - - - +
354A GLU* 1.3 66.5 + - - +
355A GLU* 3.5 21.0 - - + +
356A GLU* 2.9 45.2 + - - +
357A LEU* 3.1 12.5 + - - +
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Residues in contact with GLU 354 (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 ARG* 3.3 38.0 + - - +
286A ARG* 4.1 18.7 - - + +
289A LEU* 4.4 19.0 - - + +
352A LYS 3.9 1.0 + - - -
353A THR* 1.3 73.0 - - - +
355A GLU* 1.3 70.6 + - - +
357A LEU* 3.3 11.8 + - - +
358A HIS* 3.0 34.7 + - + +
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Residues in contact with GLU 355 (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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353A THR* 3.5 23.4 - - + +
354A GLU* 1.3 82.0 + - - +
356A GLU* 1.3 55.7 + - + +
358A HIS* 3.9 8.3 - - - +
359A LEU* 3.0 27.2 + - - +
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Residues in contact with GLU 356 (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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28A VAL* 3.9 21.8 - - + +
29A ASN* 5.3 5.5 + - - +
30A LEU* 5.3 0.2 - - - -
36A SER* 2.9 29.8 + - - -
352A LYS* 3.4 19.8 + - + +
353A THR* 2.9 35.7 + - - +
355A GLU* 1.3 74.5 - - - +
357A LEU* 1.3 66.6 + - - +
359A LEU* 3.3 7.2 + - + +
360A ALA* 3.0 23.4 + - - +
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Residues in contact with LEU 357 (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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30A LEU* 3.9 25.6 - - + -
286A ARG* 3.8 46.2 - - + +
289A LEU* 4.0 18.2 - - + -
290A LEU* 4.3 15.2 - - + +
349A ALA 4.1 0.4 - - - +
350A PHE* 3.9 28.5 - - + +
352A LYS* 4.3 5.4 - - + +
353A THR 3.1 11.6 + - - +
354A GLU* 3.3 8.7 + - - +
356A GLU* 1.3 78.0 - - - +
358A HIS* 1.3 57.5 + - - +
360A ALA* 3.2 6.3 + - - +
361A LEU* 2.9 33.3 + - + +
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Residues in contact with HIS 358 (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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289A LEU* 3.9 37.5 - - + +
354A GLU* 3.0 25.7 + - + +
355A GLU* 3.9 7.4 - - - +
357A LEU* 1.3 74.6 - - - +
359A LEU* 1.3 61.9 + - - +
361A LEU* 3.4 11.9 - - + +
362A GLU* 2.9 37.6 + - + +
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Residues in contact with LEU 359 (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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28A VAL* 3.3 25.8 - - + -
355A GLU 3.0 17.7 + - - +
356A GLU* 3.5 8.5 - - + +
357A LEU 3.3 0.2 - - - -
358A HIS* 1.3 75.7 - - - +
360A ALA* 1.3 58.3 + - - +
362A GLU* 3.2 7.5 + - + +
363A ARG* 2.8 73.3 + - + +
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Residues in contact with ALA 360 (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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28A VAL* 4.0 11.8 - - + +
30A LEU* 3.7 28.9 - - + -
290A LEU* 6.5 0.2 - - + -
328A VAL* 4.0 19.2 - - + +
356A GLU 3.0 13.6 + - - +
357A LEU 3.5 8.3 - - - +
359A LEU* 1.3 77.0 - - - +
361A LEU* 1.3 58.5 + - + +
363A ARG* 3.4 0.5 + - - +
364A LEU* 2.8 41.0 + - + +
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Residues in contact with LEU 361 (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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289A LEU* 3.8 30.3 - - + +
290A LEU* 4.1 15.3 - - + -
293A GLY* 3.9 32.3 - - - -
294A LEU* 3.9 28.0 - - + +
297A MET* 3.0 20.4 - - + +
357A LEU 2.9 15.9 + - - +
358A HIS* 3.1 20.6 + - + +
360A ALA* 1.3 79.5 - - + +
362A GLU* 1.3 58.1 + - + +
364A LEU* 4.7 1.6 - - + -
365A GLY* 3.0 20.8 + - - -
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Residues in contact with GLU 362 (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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358A HIS* 2.9 23.1 + - + +
359A LEU* 3.7 10.3 - - + +
361A LEU* 1.3 77.0 - - + +
363A ARG* 1.3 66.8 + - + +
365A GLY* 3.2 8.4 + - - -
366A ARG* 3.2 19.0 + - - +
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Residues in contact with ARG 363 (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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26A GLY 3.2 23.2 + - - -
28A VAL* 3.7 7.9 - - - +
326A ALA* 3.4 17.3 - - - +
327A ARG* 2.9 46.3 + - - +
328A VAL* 3.9 9.1 - - + +
359A LEU* 2.8 61.0 + - + +
362A GLU* 1.3 78.0 - - + +
364A LEU* 1.3 59.0 + - - +
365A GLY 3.3 0.5 + - - -
366A ARG* 3.7 28.8 + - - +
367A VAL* 2.9 29.1 - - - +
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Residues in contact with LEU 364 (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 LEU* 4.2 13.7 - - + -
297A MET* 4.2 12.9 - - + +
299A LEU* 5.9 1.3 - - + -
314A LEU* 4.1 15.7 - - + -
322A LEU* 3.6 31.6 - - + -
326A ALA* 4.6 2.2 - - + -
328A VAL* 4.3 21.5 - - + -
330A LEU* 5.3 0.7 - - + -
348A PHE* 3.8 32.5 - - + -
360A ALA* 2.8 27.8 + - + +
361A LEU* 4.1 4.7 - - + +
363A ARG* 1.3 70.6 - - - +
365A GLY* 1.3 70.1 + - - +
367A VAL* 3.2 20.7 + - + +
368A VAL* 4.6 1.0 - - - -
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Residues in contact with GLY 365 (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 MET* 3.8 19.0 - - - +
361A LEU 3.0 17.7 + - - -
362A GLU* 3.2 5.6 + - - -
363A ARG 3.1 1.0 - - - -
364A LEU* 1.3 78.4 - - - +
366A ARG* 1.3 51.6 + - - +
367A VAL 2.5 15.4 + - - -
368A VAL* 2.9 20.2 + - - +
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Residues in contact with ARG 366 (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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325A GLU 5.7 1.8 + - - -
326A ALA* 5.4 3.4 + - - +
327A ARG* 6.3 1.0 - - - +
362A GLU 3.2 15.2 + - - +
363A ARG* 3.7 33.4 + - - +
365A GLY* 1.3 66.6 - - - +
367A VAL* 1.3 65.6 + - - +
368A VAL* 3.5 7.4 - - - +
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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
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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