Contacts of the helix formed by residues 374 - 390 (chain A) in PDB entry 4AD7
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 374 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A HIS* 3.2 36.3 - - + +
311A GLU* 5.8 0.9 - - - -
373A GLY* 1.3 71.7 - - - -
375A LEU* 1.3 56.0 + - - +
377A LYS* 2.6 42.7 + - - +
378A LEU* 2.9 20.8 + - + +
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Residues in contact with LEU 375 (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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107A PHE* 3.8 26.2 - - + -
110A HIS* 3.4 29.4 - - + +
111A PHE* 4.0 21.3 - - + -
114A LEU* 5.0 1.3 - - + -
304A PHE* 4.1 13.2 - - + -
305A TRP* 3.7 18.2 - - + -
311A GLU* 3.8 42.8 - - + +
373A GLY 3.1 2.0 + - - -
374A THR* 1.3 79.4 - - - +
376A GLU* 1.3 56.5 + - - +
378A LEU* 4.1 7.2 - - + -
379A VAL* 2.9 39.2 + - + +
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Residues in contact with GLU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A TRP* 3.5 27.7 - - + -
311A GLU* 5.5 0.4 + - - -
373A GLY* 3.6 23.9 + - - +
374A THR 2.9 0.8 + - - -
375A LEU* 1.3 77.3 - - - +
377A LYS* 1.3 59.9 + - + +
379A VAL* 3.3 4.3 + - - +
380A SER* 2.9 28.3 + - - -
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Residues in contact with LYS 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A GLY* 3.7 24.8 - - - +
374A THR* 2.6 24.7 + - - +
376A GLU* 1.3 72.2 - - + +
378A LEU* 1.3 61.0 + - + +
380A SER* 3.2 7.5 + - - -
381A GLU* 2.9 30.5 + - - +
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Residues in contact with LEU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLN* 3.9 4.9 + - - +
106A SER* 4.5 26.7 - - - +
107A PHE* 3.5 22.8 - - + +
110A HIS* 4.3 30.7 - - + +
374A THR* 2.9 20.9 + - + +
375A LEU* 3.7 9.6 - - - +
377A LYS* 1.3 77.9 - - + +
379A VAL* 1.3 58.0 + - - +
381A GLU* 3.4 6.8 + - + +
382A ALA* 2.9 30.0 + - - +
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Residues in contact with VAL 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PHE* 3.7 19.5 - - + -
301A THR* 3.8 25.6 - - + +
304A PHE* 3.5 32.1 - - + -
305A TRP* 3.8 17.7 - - + +
375A LEU* 2.9 21.9 + - + +
376A GLU 3.6 4.7 - - - +
378A LEU* 1.3 74.2 - - - +
380A SER* 1.3 61.6 + - - +
382A ALA* 3.4 2.9 + - - +
383A LYS* 2.9 42.4 + - + +
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Residues in contact with SER 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A GLU* 2.9 15.2 + - - -
377A LYS* 3.2 11.2 + - - -
379A VAL* 1.3 78.3 - - - +
381A GLU* 1.3 57.3 + - - +
383A LYS* 3.2 11.8 + - - +
384A ALA* 3.0 26.6 + - - +
387A ARG* 5.6 0.3 + - - -
369B ARG* 5.7 6.2 - - - +
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Residues in contact with GLU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLN* 4.2 11.7 - - - +
377A LYS 2.9 16.9 + - - +
378A LEU* 3.8 8.5 - - + +
380A SER* 1.3 76.2 - - - +
382A ALA* 1.3 57.7 + - - +
384A ALA* 3.2 11.2 + - - +
385A GLN* 2.9 58.1 + - + +
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Residues in contact with ALA 382 (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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103A GLN* 3.4 26.4 - - + +
107A PHE* 3.8 16.4 - - + -
223A PHE* 4.4 13.5 - - + -
227A LEU* 6.3 0.2 - - + -
378A LEU 2.9 19.8 + - - +
379A VAL* 3.5 4.7 - - - +
381A GLU* 1.3 73.8 - - - +
383A LYS* 1.3 59.9 + - - +
385A GLN* 3.3 2.4 + - - +
386A LEU* 2.9 39.9 + - + +
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Residues in contact with LYS 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A VAL* 4.1 28.8 - - + +
301A THR* 3.7 23.8 - - + +
302A ASP* 4.2 12.7 + - - -
305A TRP* 6.1 0.8 - - - +
379A VAL* 2.9 28.1 + - + +
380A SER* 3.4 12.1 - - - +
382A ALA* 1.3 75.2 - - + +
384A ALA* 1.3 57.7 + - - +
386A LEU* 3.9 4.6 - - - +
387A ARG* 2.9 50.7 + - - +
376B GLU* 4.1 24.9 + - - +
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Residues in contact with ALA 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A SER 3.0 13.6 + - - +
381A GLU* 3.2 18.1 + - - +
383A LYS* 1.3 77.5 - - - +
385A GLN* 1.3 60.1 + - + +
387A ARG* 3.4 14.5 + - - +
388A ASP* 2.9 29.4 + - - +
306B GLY 5.6 1.7 + - - -
369B ARG* 4.4 29.4 - - - +
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Residues in contact with GLN 385 (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 MET* 3.4 37.2 - - - +
103A GLN* 4.0 17.3 - - + +
381A GLU* 2.9 43.3 + - + +
382A ALA* 3.7 5.2 - - - +
384A ALA* 1.3 77.1 - - - +
386A LEU* 1.3 59.3 + - + +
388A ASP* 3.0 15.0 + - - +
389A VAL* 2.9 34.1 + - - +
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Residues in contact with LEU 386 (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 MET* 5.1 2.2 - - + -
100A LEU* 4.2 24.5 - - + -
103A GLN* 6.2 2.9 - - + -
223A PHE* 4.8 9.4 - - + -
227A LEU* 4.7 10.3 - - + -
294A LEU* 3.3 33.8 - - + +
297A MET* 4.1 33.7 - - + -
298A VAL* 4.5 19.7 - - + +
382A ALA* 2.9 24.2 + - + +
383A LYS* 4.0 3.8 - - - +
385A GLN* 1.3 77.9 - - + +
387A ARG* 1.3 59.3 + - - +
389A VAL* 3.3 7.2 + - + -
390A GLN* 2.9 26.2 + - - +
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Residues in contact with ARG 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A VAL* 5.3 8.5 - - + -
380A SER 5.6 0.4 + - - -
383A LYS* 2.9 37.5 + - - +
384A ALA* 3.9 18.1 - - - +
386A LEU* 1.3 75.7 - - - +
388A ASP* 1.3 58.5 + - - +
390A GLN* 3.1 34.9 + - - +
391A ASP* 4.8 1.7 - - - +
302B ASP 5.0 1.0 - - - +
305B TRP* 3.6 61.2 - - + +
369B ARG* 4.9 15.8 - - - +
376B GLU* 3.2 38.6 + - - +
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Residues in contact with ASP 388 (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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384A ALA 2.9 13.9 + - - +
385A GLN* 3.0 20.6 + - - +
387A ARG* 1.3 78.9 - - - +
389A VAL* 1.3 66.9 + - - +
391A ASP* 3.1 27.7 - - - +
305B TRP* 4.9 0.8 - - - +
306B GLY* 3.8 27.1 - - - +
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Residues in contact with VAL 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 3.6 29.4 - - + -
99A MET* 3.9 19.3 - - + -
100A LEU* 5.4 0.2 - - + -
290A TRP* 3.1 22.8 + - + -
294A LEU* 4.2 8.1 - - + -
385A GLN* 2.9 23.9 + - - +
386A LEU* 3.7 15.5 - - + +
388A ASP* 1.3 85.6 - - - +
390A GLN* 1.3 63.9 + - - +
391A ASP* 3.0 6.1 - - - -
392A PHE* 3.1 18.8 + - + +
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Residues in contact with GLN 390 (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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287A ASP* 4.3 1.7 - - - +
290A TRP* 3.8 13.0 - - - +
291A ARG* 3.3 46.9 + - + +
294A LEU* 3.6 18.2 - - + -
386A LEU 2.9 13.4 + - - +
387A ARG* 3.1 29.3 + - - +
389A VAL* 1.3 77.8 - - - +
391A ASP* 1.3 66.7 + - + +
392A PHE 3.2 0.8 + - - -
393A TRP 5.1 0.3 + - - -
302B ASP* 3.5 11.5 - - + +
305B TRP* 3.1 37.1 + - - +
383B LYS* 4.0 14.3 + - - +
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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
------------------------------------------------------------
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