Contacts of the helix formed by residues 371 - 384 (chain E) in PDB entry 4HHM
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 ALA 371 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329E ALA* 5.0 2.2 - - - +
332E ALA* 4.5 22.7 - - + +
333E ALA* 4.4 3.2 - - - +
369E GLY* 3.3 4.8 - - - +
370E MET* 1.3 81.6 - - - +
372E PHE* 1.3 63.8 + - - +
373E GLU 3.4 1.6 - - - -
374E ARG* 4.0 12.3 + - + +
375E LEU* 3.6 19.4 + - - +
294G GLU* 3.4 13.1 + - - +
295G ASP* 6.1 0.2 - - - -
298G GLY* 5.7 2.7 - - - -
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Residues in contact with PHE 372 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333E ALA* 3.8 23.6 - - + -
370E MET* 3.6 33.2 - - + -
371E ALA* 1.3 77.4 - - - +
373E GLU* 1.3 65.3 + - - +
375E LEU* 3.4 7.0 + - + +
376E ASP* 2.9 28.4 + - - +
101F ASP* 2.9 34.3 - - - -
107F ASN* 3.8 5.2 - - - -
143F ALA* 6.2 0.4 - - + -
144F GLU* 5.5 2.0 - - - -
145F SER* 4.1 13.1 + - - +
148F ALA* 3.5 43.5 - - + -
149F LYS* 5.1 1.3 - - - -
188F ARG* 4.7 6.3 - - - -
291G PRO* 6.3 1.1 - - + -
293G THR* 3.4 22.4 - - + +
294G GLU* 2.9 10.3 + - - +
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Residues in contact with GLU 373 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372E PHE* 1.3 80.0 - - + +
374E ARG* 1.3 59.0 + - - +
376E ASP* 3.3 5.4 + - - +
377E GLN* 2.9 30.3 + - - +
144F GLU* 5.5 2.4 - - - +
145F SER* 4.8 6.9 + - - -
258G LEU* 5.9 2.0 - - - +
259G ARG* 2.7 37.2 + - - +
291G PRO* 3.8 29.7 - - + +
294G GLU* 3.1 28.8 + - + +
298G GLY 4.2 5.8 - - - +
301G ALA* 4.9 2.8 - - + +
302G SER* 3.1 36.3 + - - +
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Residues in contact with ARG 374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325E GLU* 3.6 30.3 + - - +
328E GLU* 5.9 2.6 - - - +
329E ALA* 3.9 16.5 - - + +
371E ALA* 4.0 15.0 + - + +
372E PHE 3.4 0.2 - - - -
373E GLU* 1.3 78.5 - - - +
375E LEU* 1.3 63.4 + - - +
377E GLN* 3.4 6.2 + - + +
378E LEU* 3.2 47.4 + - + +
294G GLU* 4.6 1.0 + - - -
298G GLY* 6.0 0.6 - - - -
301G ALA* 4.4 20.4 - - + +
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Residues in contact with LEU 375 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320E PHE* 4.0 12.2 - - + -
326E VAL* 4.5 2.9 - - + -
329E ALA* 4.2 21.5 - - + +
330E LEU* 3.7 27.8 - - + +
333E ALA* 4.2 17.9 - - + -
335E LEU* 4.4 0.2 - - + -
371E ALA 3.6 11.4 + - - +
372E PHE* 3.4 11.6 + - + +
373E GLU 3.2 0.2 - - - -
374E ARG* 1.3 81.4 - - - +
376E ASP* 1.3 62.4 + - - +
378E LEU* 3.3 12.5 + - + +
379E ALA* 3.2 18.4 + - - +
145F SER* 5.9 0.2 - - - +
147F ALA* 3.7 42.2 - - + +
148F ALA* 3.9 9.4 - - - +
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Residues in contact with ASP 376 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E ARG* 2.6 37.7 + - - -
270E TRP* 4.0 11.8 - - - -
372E PHE 2.9 18.2 + - - +
373E GLU* 3.3 4.7 + - - +
375E LEU* 1.3 80.5 - - + +
377E GLN* 1.3 57.3 + - - +
379E ALA* 3.1 5.3 + - - +
380E MET* 2.9 25.6 + - - +
145F SER* 3.5 28.6 - - - -
146F GLY 4.3 0.5 + - - -
147F ALA* 5.3 1.9 + - - -
259G ARG* 2.9 28.0 + - - +
262G ALA* 4.8 1.0 - - - +
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Residues in contact with GLN 377 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373E GLU 2.9 17.6 + - - +
374E ARG* 3.8 7.9 - - - +
375E LEU 3.3 0.2 - - - -
376E ASP* 1.3 77.5 - - - +
378E LEU* 1.3 57.7 + - + +
380E MET* 3.2 4.2 + - - +
381E ASP* 2.9 55.8 + - - +
259G ARG* 2.9 36.6 - - - +
301G ALA 5.5 5.4 - - - +
305G GLY* 3.8 16.7 - - - -
308G ARG* 3.6 14.1 - - - -
309G ASN* 3.0 32.5 + - - +
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Residues in contact with LEU 378 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320E PHE* 4.2 1.3 - - + -
325E GLU* 4.1 22.9 - - + +
326E VAL* 4.2 19.3 - - + -
329E ALA* 3.8 19.1 - - + -
374E ARG* 3.2 46.5 + - + +
375E LEU* 3.5 8.3 - - + +
376E ASP 3.2 0.2 - - - -
377E GLN* 1.3 74.3 - - + +
379E ALA* 1.3 61.0 + - - +
381E ASP* 3.5 8.7 + - - +
382E HIS* 3.0 36.8 + - - -
387E ARG* 3.6 30.5 - - - +
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Residues in contact with ALA 379 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E ARG* 4.3 4.0 + - - +
269E PHE* 4.4 7.2 - - + -
270E TRP* 3.7 31.9 - - + -
320E PHE* 3.6 27.7 - - + -
375E LEU 3.2 9.1 + - - +
376E ASP* 3.1 11.8 + - - +
378E LEU* 1.3 78.0 - - - +
380E MET* 1.3 58.4 + - - +
382E HIS* 3.4 2.5 + - - +
383E LEU* 3.0 28.4 + - - +
147F ALA* 5.4 0.2 - - + -
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Residues in contact with MET 380 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266E ARG* 3.4 41.9 - - - +
376E ASP 2.9 12.4 + - - +
377E GLN* 3.2 15.2 + - - +
379E ALA* 1.3 74.5 - - - +
381E ASP* 1.3 66.4 + - - +
383E LEU* 3.2 4.8 + - - +
384E LEU* 3.0 50.8 + - + +
259G ARG* 4.3 3.1 - - - +
261G GLY 3.6 30.1 - - - +
262G ALA* 4.1 1.3 - - - +
265G LEU* 3.9 17.5 - - + -
309G ASN* 3.2 32.3 - - - +
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Residues in contact with ASP 381 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377E GLN* 2.9 36.1 + - - +
378E LEU* 3.8 6.8 - - - +
380E MET* 1.3 76.4 - - - +
382E HIS* 1.3 60.8 + - - +
384E LEU* 5.0 0.7 - - - -
385E GLY* 3.0 2.1 + - - -
386E ALA* 2.6 41.0 + - - +
387E ARG* 3.4 31.9 + - + +
308G ARG* 2.8 35.1 + - - -
309G ASN* 4.9 0.2 + - - -
312G ILE* 3.8 10.3 - - - +
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Residues in contact with HIS 382 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E PHE* 5.3 0.9 - - + -
316E ARG* 3.2 29.4 - - - +
319E ALA* 3.4 33.2 - - + +
320E PHE* 3.5 38.3 + + + -
323E ASP* 2.8 32.5 + - + +
326E VAL* 3.9 4.0 - - + -
378E LEU* 3.0 26.2 + - - +
379E ALA 3.7 4.9 - - - +
381E ASP* 1.3 78.1 - - - +
383E LEU* 1.3 60.6 + - - +
385E GLY* 3.2 7.6 + - - -
387E ARG* 3.2 23.4 + - + +
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Residues in contact with LEU 383 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E LEU* 4.6 7.0 - - + -
266E ARG* 3.9 22.2 - - + +
269E PHE* 3.4 39.2 - - + -
313E LEU* 3.5 21.8 - - + -
316E ARG* 2.9 29.1 + - + +
379E ALA 3.0 17.6 + - - +
380E MET* 3.2 6.7 + - - +
382E HIS* 1.3 77.3 - - - +
384E LEU* 1.3 56.4 + - + +
265G LEU* 3.8 27.6 - - + -
384G LEU* 3.3 23.1 - - + +
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Residues in contact with LEU 384 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316E ARG* 3.9 3.8 - - - +
380E MET* 3.0 39.4 + - + +
381E ASP 4.4 1.6 - - - +
383E LEU* 1.3 78.1 - - + +
385E GLY* 1.3 61.8 + - - +
386E ALA* 4.5 2.7 - - + +
265G LEU* 3.9 26.0 - - + -
309G ASN* 4.6 3.8 - - + +
312G ILE* 3.8 31.9 - - + -
313G LEU* 4.8 7.0 - - + -
316G ARG* 2.6 34.9 + - - +
383G LEU* 3.7 38.7 - - + +
384G LEU* 4.2 7.9 - - + -
385G GLY* 4.4 0.5 + - - -
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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
------------------------------------------------------------
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