Contacts of the helix formed by residues 373 - 390 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C SER* 1.3 80.8 + - - +
374C THR* 1.3 66.3 + - - -
375C LEU 3.3 2.7 - - - -
376C GLU* 3.1 11.9 + - - +
377C LYS* 3.0 31.4 + - - +
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Residues in contact with THR 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C HIS* 3.6 31.0 - - + +
373C GLY* 1.3 70.5 - - - -
375C LEU* 1.3 57.3 + - - +
377C LYS* 3.1 13.3 + - - +
378C LEU* 2.9 39.9 + - + +
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Residues in contact with LEU 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C PHE* 4.5 14.4 - - + -
110C HIS* 3.6 31.7 + - + +
111C PHE* 3.9 26.9 - - + -
114C LEU* 5.4 4.9 - - + -
304C PHE* 4.0 19.3 - - + -
305C TRP* 3.8 32.8 - - + +
312C SER* 4.4 15.3 - - - +
373C GLY 3.3 0.4 - - - -
374C THR* 1.3 78.9 - - - +
376C GLU* 1.3 59.0 + - - +
378C LEU* 3.3 4.7 + - + +
379C VAL* 2.9 36.0 + - + +
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Residues in contact with GLU 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C TRP* 4.0 22.7 - - + +
372C SER* 3.7 30.4 + - - +
373C GLY 3.1 13.7 + - - +
375C LEU* 1.3 78.0 - - - +
377C LYS* 1.3 58.6 + - + +
379C VAL* 3.3 6.1 + - + +
380C SER* 2.9 28.7 + - - -
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Residues in contact with LYS 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C SER* 3.7 21.5 + - - +
373C GLY* 3.0 20.0 + - - +
374C THR* 3.4 11.2 - - - +
376C GLU* 1.3 74.9 - - + +
378C LEU* 1.3 68.1 + - + +
380C SER* 3.2 8.5 + - - -
381C GLU* 3.0 24.2 + - - +
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Residues in contact with LEU 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C GLN* 4.6 0.5 - - - +
106C SER* 4.4 20.4 - - - +
107C PHE* 3.5 31.8 - - + -
110C HIS* 4.0 37.5 - - + -
374C THR* 2.9 24.8 + - + +
375C LEU* 3.6 6.7 - - + +
377C LYS* 1.3 77.0 - - + +
379C VAL* 1.3 57.8 + - - +
381C GLU* 3.4 7.2 + - + +
382C ALA* 2.9 30.8 + - - +
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Residues in contact with VAL 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C PHE* 4.2 9.0 - - + -
301C THR* 3.9 15.9 - - + +
304C PHE* 3.6 36.6 - - + -
305C TRP* 4.2 14.6 - - + -
375C LEU* 2.9 22.4 + - + +
376C GLU* 3.5 8.7 - - + +
377C LYS 3.2 0.2 - - - -
378C LEU* 1.3 77.9 - - - +
380C SER* 1.3 57.0 + - - +
382C ALA* 3.4 3.3 + - - +
383C LYS* 2.9 53.9 + - + +
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Residues in contact with SER 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C GLU* 2.9 14.5 + - - -
377C LYS* 3.2 11.0 + - - -
379C VAL* 1.3 77.9 - - - +
381C GLU* 1.3 62.6 + - - +
383C LYS* 3.3 9.6 + - - +
384C ALA* 3.0 23.2 + - - +
387C ARG* 5.5 0.3 + - - -
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Residues in contact with GLU 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C GLN* 4.2 17.7 + - - +
377C LYS 3.0 13.1 + - - +
378C LEU* 3.6 11.4 - - + +
380C SER* 1.3 76.9 - - - +
382C ALA* 1.3 63.6 + - - +
384C ALA* 3.1 10.3 + - - +
385C GLN* 2.9 53.9 + - - +
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Residues in contact with ALA 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C GLN* 3.7 22.4 + - + +
107C PHE* 4.0 15.9 - - + -
223C PHE* 4.1 15.3 - - + -
227C LEU* 6.2 0.9 - - + -
378C LEU 2.9 19.0 + - - +
379C VAL* 3.6 4.7 - - - +
381C GLU* 1.3 76.4 - - - +
383C LYS* 1.3 61.9 + - + +
385C GLN* 3.2 2.5 + - - +
386C LEU* 2.9 35.8 + - + +
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Residues in contact with LYS 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298C VAL* 4.0 32.5 + - + -
301C THR* 3.6 26.3 + - + -
302C ASP* 4.6 7.5 + - - -
379C VAL* 2.9 33.1 + - + +
380C SER* 3.5 8.1 - - - +
382C ALA* 1.3 75.2 - - + +
384C ALA* 1.3 64.2 + - - +
386C LEU* 4.0 0.3 - - - +
387C ARG* 2.9 50.4 + - - +
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Residues in contact with ALA 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C SER 3.0 13.8 + - - +
381C GLU* 3.3 15.7 - - - +
383C LYS* 1.3 76.7 - - - +
385C GLN* 1.3 64.3 + - - +
387C ARG* 3.8 18.6 - - - +
388C ASP* 2.9 29.5 + - - +
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Residues in contact with GLN 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C MET* 3.3 38.6 - - + +
103C GLN* 4.1 17.2 + - - +
381C GLU* 2.9 39.8 + - - +
382C ALA* 3.7 5.4 - - - +
384C ALA* 1.3 80.2 - - - +
386C LEU* 1.3 58.6 + - + +
388C ASP* 3.1 13.4 + - - +
389C VAL* 2.9 34.3 + - - +
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Residues in contact with LEU 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C MET* 5.0 3.4 - - + -
100C LEU* 4.5 21.1 - - + -
103C GLN* 6.3 1.3 - - + -
223C PHE* 5.0 10.8 - - + -
227C LEU* 4.8 10.5 - - + -
294C LEU* 3.4 36.5 - - + +
297C MET* 4.2 23.6 - - + -
298C VAL* 3.7 29.6 - - + +
382C ALA* 2.9 25.6 + - + +
383C LYS 4.0 2.0 - - - +
385C GLN* 1.3 75.1 - - + +
387C ARG* 1.3 60.7 + - - +
389C VAL* 3.2 6.9 + - + -
390C GLN* 2.9 27.3 + - - +
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Residues in contact with ARG 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298C VAL* 5.5 8.3 - - + -
380C SER 5.5 0.4 + - - -
383C LYS* 2.9 51.9 + - - +
384C ALA* 3.9 18.9 - - - +
386C LEU* 1.3 77.5 - - - +
388C ASP* 1.3 61.5 - - - +
390C GLN* 3.4 34.9 + - - +
391C ASP* 4.6 1.7 - - - +
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Residues in contact with ASP 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384C ALA 2.9 14.8 + - - +
385C GLN* 3.2 18.3 + - - +
386C LEU 3.1 0.2 - - - -
387C ARG* 1.3 78.9 - - - +
389C VAL* 1.3 64.3 + - + +
390C GLN 3.4 0.2 - - - -
391C ASP* 3.1 27.5 - - - +
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Residues in contact with VAL 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C LEU* 3.6 30.1 - - + -
99C MET* 3.8 20.6 - - + -
100C LEU* 5.5 0.7 - - + -
290C TRP* 3.1 21.1 + - + -
294C LEU* 4.2 7.4 - - + -
385C GLN* 2.9 20.2 + - - +
386C LEU* 3.6 14.8 - - + +
388C ASP* 1.3 84.6 - - - +
390C GLN* 1.3 61.0 + - - +
391C ASP* 3.0 10.7 + - - -
392C PHE* 3.2 16.5 + - + +
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Residues in contact with GLN 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C ASP* 4.2 2.1 - - - +
290C TRP* 3.8 7.9 - - - +
291C ARG* 3.5 50.0 + - + +
294C LEU* 3.7 17.5 - - + -
295C ASP* 5.1 6.9 - - - +
386C LEU 2.9 13.0 + - - +
387C ARG* 3.4 32.0 + - - +
388C ASP 3.4 0.2 - - - -
389C VAL* 1.3 77.4 - - - +
391C ASP* 1.3 66.2 + - + +
392C PHE 3.3 1.9 + - - -
393C TRP 5.3 0.2 + - - -
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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
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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