Contacts of the helix formed by residues 371 - 385 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329F ALA* 5.1 1.8 - - - +
332F ALA* 4.4 23.1 - - + +
333F ALA* 4.5 3.3 - - - +
369F GLY* 3.3 6.1 - - - +
370F MET* 1.3 81.1 - - - +
372F PHE* 1.3 61.7 + - - +
373F GLU 3.5 0.7 - - - -
374F ARG* 3.8 12.8 + - + +
375F LEU* 3.5 19.1 + - - +
294H GLU* 3.3 14.6 + - - -
295H ASP* 5.6 1.5 + - - +
298H GLY* 5.8 2.9 - - - -
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Residues in contact with PHE 372 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E ASP* 3.2 28.0 - - - -
107E ASN* 3.5 22.7 - - - -
143E ALA* 6.1 0.2 - - + -
144E GLU* 5.5 2.0 - - - -
145E SER* 4.2 7.7 + - - +
148E ALA* 3.5 37.9 - - + -
188E ARG* 4.7 5.8 - - - -
333F ALA* 3.7 18.4 - - + -
370F MET* 3.4 43.3 - - + -
371F ALA* 1.3 77.0 - - - +
373F GLU* 1.3 66.1 + - - +
375F LEU* 3.2 7.5 + - + +
376F ASP* 2.8 29.5 + - - +
291H PRO* 6.4 0.4 - - + -
293H THR* 3.7 20.0 - - + +
294H GLU* 2.9 9.0 + - - +
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Residues in contact with GLU 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E GLU* 5.7 2.1 - - - +
145E SER* 4.7 8.8 + - - -
372F PHE* 1.3 79.1 - - - +
374F ARG* 1.3 63.5 - - - +
376F ASP* 3.7 4.1 - - - +
377F GLN* 3.0 24.9 + - - +
259H ARG* 3.3 31.9 + - - +
291H PRO* 3.6 28.9 - - + +
294H GLU* 3.2 28.7 + - + +
298H GLY 4.3 6.1 - - - +
301H ALA* 5.1 2.2 - - + -
302H SER* 2.8 40.1 + - - +
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Residues in contact with ARG 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329F ALA* 5.5 5.4 - - + -
371F ALA* 3.8 15.8 + - + +
373F GLU* 1.3 78.4 - - - +
375F LEU* 1.3 63.8 + - - +
377F GLN* 3.4 5.7 + - - +
378F LEU* 3.3 31.7 + - + +
294H GLU* 4.6 0.6 + - - -
297H ASP* 4.3 18.8 + - - +
298H GLY* 6.0 1.1 - - - -
301H ALA* 3.8 34.9 - - + +
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Residues in contact with LEU 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E ALA* 3.6 39.0 - - + +
148E ALA* 4.1 7.9 - - + +
320F PHE* 4.1 13.1 - - + -
326F VAL* 4.1 4.5 - - + +
329F ALA* 3.6 31.1 - - + +
330F LEU* 3.9 26.7 - - + +
333F ALA* 4.3 17.3 - - + -
371F ALA 3.5 11.2 + - - +
372F PHE* 3.2 10.3 + - + +
374F ARG* 1.3 80.2 - - - +
376F ASP* 1.3 61.6 + - - +
378F LEU* 3.2 7.9 + - + +
379F ALA* 3.1 18.7 + - - +
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Residues in contact with ASP 376 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E SER* 3.4 28.5 - - - +
146E GLY 4.2 0.3 + - - -
147E ALA* 5.2 1.7 + - - -
266F ARG* 2.7 38.5 + - - -
270F TRP* 3.9 11.3 - - - -
372F PHE 2.8 20.5 + - - +
373F GLU* 3.2 6.5 + - - +
375F LEU* 1.3 75.8 - - - +
377F GLN* 1.3 58.7 + - - +
379F ALA* 3.0 7.0 + - - +
380F MET* 2.8 23.0 + - - +
259H ARG* 2.9 30.0 + - - +
262H ALA* 4.8 0.7 - - - +
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Residues in contact with GLN 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373F GLU 3.0 16.5 + - - +
374F ARG* 3.4 5.4 + - - +
375F LEU 3.3 0.2 - - - -
376F ASP* 1.3 74.3 - - - +
378F LEU* 1.3 61.9 + - - +
380F MET* 3.5 4.1 - - - +
381F ASP* 2.7 59.5 + - - +
259H ARG* 2.9 44.1 - - - +
301H ALA 5.8 2.7 - - - +
305H GLY* 3.8 11.5 - - - -
308H ARG* 3.7 17.6 - - - -
309H ASN* 2.6 36.0 + - - +
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Residues in contact with LEU 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320F PHE* 4.1 2.5 - - + -
325F GLU* 3.8 27.8 - - + +
326F VAL* 3.9 22.4 - - + -
329F ALA* 3.6 30.7 - - + -
374F ARG* 3.3 20.4 + - + +
375F LEU* 3.2 8.6 + - + +
376F ASP 3.2 0.8 - - - -
377F GLN* 1.3 77.0 - - - +
379F ALA* 1.3 63.9 + - - +
381F ASP* 3.7 8.3 - - - +
382F HIS* 3.0 30.2 + - + -
387F ARG* 3.4 33.9 - - - +
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Residues in contact with ALA 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E ALA* 5.4 0.2 - - + -
266F ARG* 4.4 3.3 + - - +
269F PHE* 4.4 9.5 - - + -
270F TRP* 3.6 32.8 - - + -
320F PHE* 3.5 28.2 - - + -
375F LEU 3.1 8.4 + - - +
376F ASP* 3.0 11.3 + - - +
378F LEU* 1.3 79.0 - - - +
380F MET* 1.3 60.8 + - - +
382F HIS* 3.5 1.9 + - - +
383F LEU* 3.1 23.2 + - - +
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Residues in contact with MET 380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266F ARG* 3.7 33.0 - - - +
376F ASP 2.8 13.4 + - - +
377F GLN* 3.5 15.7 - - - +
378F LEU 3.2 0.2 - - - -
379F ALA* 1.3 73.1 - - - +
381F ASP* 1.3 66.9 + - - +
383F LEU* 3.0 6.4 + - - +
384F LEU* 2.9 33.8 + - + +
259H ARG* 4.2 4.0 - - - +
261H GLY* 3.1 36.6 - - - +
262H ALA* 3.9 2.0 - - - +
265H LEU* 3.9 29.2 - - + -
309H ASN* 3.5 30.7 - - - +
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Residues in contact with ASP 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377F GLN* 2.7 42.6 + - - +
378F LEU* 3.4 11.4 + - - +
380F MET* 1.3 76.2 - - - +
382F HIS* 1.3 57.0 + - - +
384F LEU* 3.4 0.8 + - - -
385F GLY* 2.8 10.2 + - - -
386F ALA* 2.7 39.4 + - - +
387F ARG* 3.5 27.3 + - + +
308H ARG* 2.9 32.8 + - - -
312H ILE* 4.0 7.2 - - - +
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Residues in contact with HIS 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269F PHE* 5.5 0.4 - - + -
316F ARG* 3.1 29.6 - - - +
319F ALA* 3.4 31.2 - - + +
320F PHE* 3.7 36.2 + + + -
323F ASP* 2.7 34.6 + - + +
326F VAL* 4.0 4.3 - - + -
378F LEU 3.0 26.7 + - - +
379F ALA 3.9 4.5 - - - +
381F ASP* 1.3 77.3 - - - +
383F LEU* 1.3 61.5 + - - +
385F GLY* 3.2 8.6 + - - -
387F ARG* 3.2 23.1 + - + +
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Residues in contact with LEU 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265F LEU* 4.5 7.2 - - + -
266F ARG* 3.8 22.7 - - + -
269F PHE* 3.6 29.7 - - + -
313F LEU* 3.4 32.1 - - + -
316F ARG* 2.8 32.2 + - + +
379F ALA 3.1 14.2 + - - +
380F MET* 3.0 10.0 + - - +
382F HIS* 1.3 76.8 - - - +
384F LEU* 1.3 59.6 + - + +
265H LEU* 3.8 27.8 - - + -
384H LEU* 3.7 19.2 - - + +
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Residues in contact with LEU 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316F ARG* 4.2 2.9 - - - -
380F MET* 2.9 39.2 + - + +
381F ASP 4.2 1.6 - - - +
383F LEU* 1.3 79.9 - - + +
385F GLY* 1.3 59.4 + - - +
386F ALA* 4.5 4.0 - - + +
265H LEU* 3.7 28.0 - - + -
309H ASN* 4.8 4.0 - - + +
312H ILE* 3.6 37.7 - - + -
313H LEU* 4.4 12.1 - - + -
316H ARG* 2.5 33.3 + - - -
383H LEU* 3.7 33.7 - - + +
384H LEU* 3.9 4.6 - - + +
385H GLY* 4.5 0.3 - - - -
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Residues in contact with GLY 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F ARG* 4.2 11.7 - - - -
381F ASP 2.8 9.1 + - - -
382F HIS* 3.2 11.7 + - - -
383F LEU 3.2 1.0 + - - -
384F LEU* 1.3 78.5 - - - +
386F ALA* 1.3 55.1 + - - -
387F ARG* 3.5 6.5 + - - +
3H TYR* 5.0 0.3 + - - -
316H ARG* 3.3 11.8 + - - -
384H LEU 4.8 0.7 - - - -
385H GLY* 5.8 2.0 - - - -
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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