Contacts of the helix formed by residues 373 - 389 (chain B) 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 GLY 373 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B GLU* 5.0 8.1 - - - -
370B PRO* 4.4 7.5 + - - -
372B SER* 1.3 70.7 - - - +
374B THR* 1.3 62.7 - - - -
375B LEU* 3.4 2.2 - - - -
376B GLU* 4.1 18.1 + - - +
377B LYS* 3.7 29.3 + - - +
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Residues in contact with THR 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B HIS* 3.7 29.8 - - + -
311B GLU* 4.6 2.8 + - - -
372B SER* 3.0 12.3 + - - -
373B GLY* 1.3 71.9 - - - -
375B LEU* 1.3 61.4 + - - +
376B GLU 3.2 0.2 - - - -
377B LYS* 3.3 7.5 + - - +
378B LEU* 2.9 45.8 + - + +
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PHE* 4.2 14.8 - - + -
110B HIS* 3.6 23.8 - - + +
111B PHE* 4.0 19.1 - - + -
304B PHE* 3.7 32.3 - - + +
305B TRP* 3.5 27.1 - - + -
311B GLU* 3.5 42.6 + - + +
373B GLY* 5.6 0.7 - - - -
374B THR* 1.3 81.8 - - - +
376B GLU* 1.3 55.7 + - - +
378B LEU* 4.3 3.8 - - + -
379B VAL* 2.9 35.3 + - - +
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Residues in contact with GLU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A VAL* 4.1 21.1 - - - +
383A LYS* 4.1 18.6 + - - +
387A ARG* 3.2 40.6 + - - +
305B TRP* 3.6 18.0 - - + -
373B GLY* 4.1 18.6 + - - +
374B THR 3.2 0.6 - - - -
375B LEU* 1.3 79.8 - - - +
377B LYS* 1.3 64.8 + - + +
379B VAL* 3.5 2.4 + - - +
380B SER* 2.9 29.7 + - - -
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Residues in contact with LYS 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B SER* 6.0 5.2 - - - -
373B GLY 3.7 19.7 - - - +
374B THR* 3.3 7.2 + - - +
376B GLU* 1.3 80.9 + - + +
378B LEU* 1.3 62.8 + - + +
380B SER* 3.2 6.9 + - - -
381B GLU* 2.9 31.5 + - - +
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Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B GLN* 4.3 0.9 - - - +
106B SER* 4.3 33.0 - - - +
107B PHE* 3.4 23.9 - - + +
110B HIS* 4.2 22.7 - - + +
374B THR* 2.9 39.2 + - + +
375B LEU* 3.9 4.0 - - - +
377B LYS* 1.3 78.2 - - + +
379B VAL* 1.3 56.7 + - - +
381B GLU* 3.5 6.6 + - + +
382B ALA* 2.9 29.3 + - - +
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Residues in contact with VAL 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PHE* 3.7 18.4 - - + -
301B THR* 4.2 14.4 - - + -
304B PHE* 3.6 33.2 - - + -
305B TRP* 3.9 20.0 - - + +
375B LEU* 2.9 22.6 + - + +
376B GLU 3.9 2.9 - - - +
378B LEU* 1.3 74.0 - - - +
380B SER* 1.3 61.2 + - - +
382B ALA* 3.6 3.1 - - - +
383B LYS* 2.9 49.3 + - + +
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Residues in contact with SER 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B GLU* 2.9 19.2 + - - -
377B LYS* 3.5 8.3 - - - -
379B VAL* 1.3 76.0 - - - +
381B GLU* 1.3 60.4 + - - +
383B LYS* 3.2 9.2 + - - +
384B ALA* 3.0 28.6 + - - +
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Residues in contact with GLU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B GLN* 3.3 23.6 + - - +
377B LYS 2.9 17.2 + - - +
378B LEU* 3.9 7.2 - - + +
380B SER* 1.3 76.2 - - - +
382B ALA* 1.3 57.1 + - - +
384B ALA* 3.4 7.9 + - - +
385B GLN* 2.9 59.1 + - - +
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Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B GLN* 3.2 24.8 + - - +
107B PHE* 3.7 16.4 - - + -
223B PHE* 4.7 9.9 - - + -
227B LEU* 6.5 0.2 - - + -
378B LEU 2.9 18.9 + - - +
379B VAL* 3.6 5.6 - - - +
380B SER 3.2 0.2 - - - -
381B GLU* 1.3 74.5 - - - +
383B LYS* 1.3 59.3 + - - +
385B GLN* 3.4 0.7 + - - +
386B LEU* 2.9 43.8 + - + +
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Residues in contact with LYS 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A ARG* 4.6 12.9 - - - +
295A ASP* 5.2 10.7 + - - -
390A GLN* 4.0 19.4 + - - +
298B VAL* 4.0 32.6 - - + +
301B THR* 4.0 22.1 + - + +
305B TRP* 6.2 0.2 - - - +
379B VAL* 2.9 32.8 + - + +
380B SER* 3.6 7.9 - - - +
382B ALA* 1.3 74.6 - - + +
384B ALA* 1.3 58.1 + - - +
386B LEU* 4.0 3.2 - - - +
387B ARG* 2.9 33.5 + - - +
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Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B SER 3.0 13.4 + - - +
381B GLU* 3.6 13.5 - - - +
383B LYS* 1.3 76.7 - - - +
385B GLN* 1.3 64.0 + - - +
387B ARG* 3.2 6.0 + - - +
388B ASP* 3.0 30.4 + - - +
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Residues in contact with GLN 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B MET* 3.3 38.3 - - + +
103B GLN* 3.9 10.8 - - - +
381B GLU* 2.9 48.7 + - - +
382B ALA* 4.0 3.4 - - - +
384B ALA* 1.3 81.5 - - - +
386B LEU* 1.3 61.3 + - + +
388B ASP* 3.5 11.2 + - - +
389B VAL* 3.3 25.3 + - - +
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Residues in contact with LEU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B MET* 4.6 7.2 - - + -
100B LEU* 4.1 23.3 - - + -
103B GLN* 5.9 2.2 - - + -
223B PHE* 5.0 7.4 - - + -
227B LEU* 4.5 10.8 - - + -
294B LEU* 3.4 26.4 - - + +
297B MET* 3.9 37.5 - - + -
298B VAL* 4.1 26.0 - - + +
382B ALA* 2.9 27.8 + - + +
383B LYS* 4.1 2.0 - - - +
385B GLN* 1.3 76.3 - - + +
387B ARG* 1.3 66.6 + - - +
389B VAL* 3.2 13.0 + - + +
390B GLN* 3.3 11.9 + - - +
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Residues in contact with ARG 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B ASP* 3.2 16.4 + - - +
298B VAL* 4.6 24.1 - - - +
383B LYS 2.9 21.9 + - - +
384B ALA* 3.2 5.4 + - - +
386B LEU* 1.3 76.8 - - - +
388B ASP* 1.3 62.9 + - - +
389B VAL 3.5 0.2 + - - -
390B GLN* 3.1 45.3 + - - +
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Residues in contact with ASP 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B ALA 3.0 16.8 + - - +
385B GLN* 3.7 13.5 + - - +
386B LEU 3.2 0.2 - - - -
387B ARG* 1.3 79.6 - - - +
389B VAL* 1.3 64.9 + - + +
390B GLN 3.4 0.9 + - - -
391B ASP* 3.6 14.4 - - - +
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Residues in contact with VAL 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 3.6 28.3 - - + -
99B MET* 3.9 15.7 - - + -
290B TRP* 3.2 19.4 + - + +
294B LEU* 4.1 8.1 - - + -
385B GLN 3.3 18.8 - - - +
386B LEU* 3.4 15.3 - - + +
388B ASP* 1.3 84.5 - - + +
390B GLN* 1.3 65.3 + - - +
391B ASP* 3.2 3.6 - - - -
392B PHE* 3.1 26.5 + - + +
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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