Contacts of the helix formed by residues 414 - 425 (chain A) in PDB entry 2V3E
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 GLN 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A VAL* 4.3 7.6 - - + -
352A VAL* 4.1 4.2 - - - +
353A ARG 3.3 5.0 - - - +
354A LEU* 3.3 12.3 - - + -
355A GLY 2.8 29.6 + - - -
356A SER* 4.2 1.7 + - - -
399A ASP* 2.6 33.9 + - - -
400A SER 3.0 11.1 + - - +
401A PRO* 2.8 25.5 + - + +
403A ILE* 3.5 13.4 - - + +
412A TYR 4.1 6.7 - - - +
413A LYS* 1.3 74.3 - - - +
415A PRO* 1.3 73.5 - - + +
416A MET* 4.0 13.2 - - + +
417A PHE* 2.9 19.1 + - - +
418A TYR* 3.3 7.7 - - - -
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Residues in contact with PRO 415 (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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14A VAL 3.6 14.1 - - - +
48A ARG* 4.0 12.1 - - - +
355A GLY* 3.6 32.3 - - - +
356A SER 3.3 26.7 - - - +
357A TRP* 3.8 24.2 - - + -
360A GLY* 4.2 4.0 - - - -
414A GLN* 1.3 83.9 - - + +
416A MET* 1.4 62.1 + - - +
418A TYR* 3.1 10.7 + - + +
419A HIS* 2.9 30.3 + - + -
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Residues in contact with MET 416 (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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343A VAL* 3.5 19.1 - - + -
356A SER 4.9 0.2 + - - -
359A ARG* 3.5 28.3 - - + +
360A GLY* 3.8 7.5 - - - +
363A TYR* 3.4 43.3 - - + -
399A ASP* 3.7 25.6 - - + +
400A SER 3.6 28.7 - - - +
401A PRO* 3.8 17.3 - - + -
414A GLN* 3.0 11.0 + - + +
415A PRO* 1.4 76.5 - - - +
417A PHE* 1.3 62.1 + - - +
419A HIS* 3.9 2.0 - - - +
420A LEU* 2.9 26.0 + - - +
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Residues in contact with PHE 417 (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 PHE* 6.1 1.3 - + - -
107A SER* 3.3 40.4 - - - -
108A TYR* 3.6 32.8 - + - -
113A GLY* 5.5 0.4 - - - -
114A ILE* 3.6 39.3 - - + +
116A TYR* 5.8 0.4 - - - -
401A PRO* 3.6 21.7 - - + +
402A ILE* 4.0 9.9 - - + -
413A LYS* 3.5 23.8 - - + -
414A GLN 2.9 16.9 + - - +
416A MET* 1.3 74.4 - - - +
418A TYR* 1.3 86.2 + + + +
420A LEU* 3.6 5.4 - - - +
421A GLY* 2.8 22.0 + - - -
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Residues in contact with TYR 418 (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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16A CYS* 3.3 16.8 - - - +
24A ASP* 2.5 34.7 + - - -
26A PHE* 6.0 2.5 - + - -
42A SER* 4.1 16.6 - - - +
48A ARG* 3.6 37.0 - - + -
49A MET* 3.8 27.1 - - + +
357A TRP* 6.1 0.4 - - + -
413A LYS* 3.0 38.6 - - + -
414A GLN 3.3 12.6 - - - -
415A PRO* 3.1 6.9 + - + +
417A PHE* 1.3 92.8 - + - +
419A HIS* 1.3 62.1 + - + +
421A GLY* 3.2 1.5 + - - +
422A HIS* 3.0 36.8 + - - -
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Residues in contact with HIS 419 (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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42A SER* 5.6 0.2 - - - -
357A TRP* 3.2 42.3 - + - -
360A GLY* 3.2 27.6 + - - +
361A MET* 3.6 17.9 - - + -
363A TYR* 4.6 1.1 - - + -
364A SER* 2.8 32.6 + - - +
415A PRO 2.9 27.2 + - - +
416A MET* 3.9 4.3 - - - +
418A TYR* 1.3 77.9 - - + +
420A LEU* 1.3 61.9 + - - +
422A HIS* 3.3 8.7 + - - +
423A PHE* 3.1 26.2 - - - -
461A LEU* 3.8 9.0 - - + -
489A ILE* 3.7 24.3 - - + +
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Residues in contact with LEU 420 (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 PHE* 4.4 22.0 - - + -
82A GLY 4.7 1.6 - - - +
114A ILE* 4.6 2.0 - - + -
116A TYR* 3.2 30.7 - - + +
363A TYR* 3.8 29.0 - - + +
367A ILE* 3.7 22.4 - - + +
378A TRP* 3.9 12.1 - - + +
380A ASP* 3.9 20.6 - - + +
401A PRO* 4.8 2.5 - - + -
416A MET 2.9 15.4 + - - +
417A PHE* 3.6 5.8 - - - +
419A HIS* 1.3 77.2 - - - +
421A GLY* 1.3 60.6 + - - +
423A PHE* 3.1 8.5 + - - +
424A SER* 3.0 21.3 + - - -
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Residues in contact with GLY 421 (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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49A MET* 3.6 9.6 - - - +
114A ILE* 3.7 20.6 - - - -
417A PHE 2.8 18.6 + - - -
418A TYR 3.2 3.7 + - - -
420A LEU* 1.3 73.9 - - - +
422A HIS* 1.3 61.8 + - - +
423A PHE 3.0 1.7 + - - -
424A SER* 3.4 11.0 - - - -
425A LYS* 3.1 28.2 + - - +
426A PHE* 4.0 0.2 - - - -
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Residues in contact with HIS 422 (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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40A TYR* 3.1 37.8 - - + +
41A GLU 4.1 0.2 - - - -
42A SER* 2.7 30.7 + - - -
49A MET* 3.7 13.3 - - + +
418A TYR 3.0 27.6 + - - -
419A HIS 3.6 9.6 - - - +
420A LEU 3.2 0.6 - - - -
421A GLY* 1.3 73.9 - - - +
423A PHE* 1.3 59.0 + - + +
426A PHE* 3.5 12.1 - - - +
427A ILE* 5.0 0.3 - - - +
459A VAL* 3.8 7.1 - - + +
489A ILE* 3.3 43.2 + - + -
490A HIS 3.8 1.8 - - - -
491A THR* 2.7 45.8 + - - +
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Residues in contact with PHE 423 (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 PHE* 4.0 17.3 - - + -
364A SER* 3.6 31.2 - - - -
367A ILE* 3.5 32.1 - - + -
368A ILE* 3.7 30.7 - - + -
371A LEU* 4.1 7.4 - - + -
419A HIS 3.1 28.0 - - - -
420A LEU 3.1 4.4 + - - +
421A GLY 3.0 0.4 - - - -
422A HIS* 1.3 77.0 - - - +
424A SER* 1.3 61.5 + - - +
425A LYS 3.3 1.6 - - - -
426A PHE 3.1 1.2 + - - -
427A ILE* 2.9 58.0 + - + +
447A VAL* 4.4 1.1 - - + -
459A VAL* 3.8 25.8 - - + -
489A ILE* 4.1 4.5 - - + -
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Residues in contact with SER 424 (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 PHE* 3.6 34.4 - - - -
114A ILE* 2.7 29.5 + - - +
115A GLY 3.9 4.8 - - - +
116A TYR* 4.0 11.8 - - - -
170A ARG* 2.6 31.4 + - - -
420A LEU* 3.0 15.8 + - - -
421A GLY* 3.4 8.5 - - - -
423A PHE* 1.3 78.4 - - - +
425A LYS* 1.3 52.1 + - - +
426A PHE 3.4 0.3 + - - -
427A ILE 3.9 5.2 + - - +
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Residues in contact with LYS 425 (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 PHE* 3.6 45.3 - - + +
40A TYR* 5.2 3.6 - - - -
49A MET* 4.4 2.0 - - + -
111A GLU* 2.7 32.5 + - - +
113A GLY 2.7 22.2 + - - +
114A ILE* 3.5 13.9 - - - +
170A ARG* 2.8 25.8 + - - +
421A GLY 3.1 19.6 + - - +
424A SER* 1.3 78.9 + - - +
426A PHE* 1.3 90.6 + - + +
428A PRO* 5.5 0.7 - - - +
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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
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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