Contacts of the helix formed by residues 371 - 384 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294E GLU* 3.2 14.0 + - - -
295E ASP* 5.9 2.4 + - - -
298E GLY* 5.7 2.2 - - - -
329G ALA* 4.9 2.3 - - - +
332G ALA* 4.4 21.8 - - + +
333G ALA* 4.2 4.3 - - - +
369G GLY* 3.2 6.5 - - - +
370G MET* 1.3 82.7 - - - +
372G PHE* 1.3 62.5 - - - +
373G GLU 3.6 0.9 - - - -
374G ARG* 4.2 12.4 - - + +
375G LEU* 3.7 17.7 + - - +
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Residues in contact with PHE 372 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E PRO* 6.2 1.6 - - + -
293E THR* 3.5 25.1 - - + +
294E GLU* 2.9 9.0 + - - +
333G ALA* 3.8 19.1 - - + -
370G MET* 3.5 28.0 - - + -
371G ALA* 1.3 75.9 - - - +
373G GLU* 1.3 64.0 + - - +
374G ARG 3.3 2.0 - - - -
375G LEU* 3.3 7.0 + - + +
376G ASP* 2.9 29.8 + - - +
101H ASP* 3.3 29.4 - - - -
107H ASN* 3.7 21.5 - - - -
144H GLU* 5.7 1.6 - - - -
145H SER* 4.1 12.3 + - - +
148H ALA* 3.4 39.5 - - + -
149H LYS* 5.6 0.2 - - - -
188H ARG* 4.4 6.3 - - - -
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Residues in contact with GLU 373 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E ARG* 3.1 37.3 + - - +
291E PRO* 3.6 36.5 - - + +
294E GLU* 3.4 19.3 + - + +
298E GLY 4.1 11.9 - - - +
301E ALA* 4.9 3.1 - - + +
302E SER* 2.8 32.5 + - - +
372G PHE* 1.3 79.0 - - - +
374G ARG* 1.3 64.7 + - - +
376G ASP* 3.4 5.7 + - - +
377G GLN* 3.1 23.7 + - - +
144H GLU* 5.9 1.4 - - - +
145H SER* 5.1 5.7 + - - -
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Residues in contact with ARG 374 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294E GLU* 4.7 0.6 + - - -
297E ASP* 3.5 35.2 + - - +
298E GLY* 5.1 2.3 - - - -
301E ALA* 3.7 29.5 - - + +
329G ALA* 5.7 4.0 - - + -
371G ALA* 4.1 17.4 + - + +
372G PHE 3.3 0.6 - - - -
373G GLU* 1.3 77.3 - - - +
375G LEU* 1.3 64.7 + - - +
377G GLN* 3.3 6.9 + - - +
378G LEU* 3.2 31.4 + - + +
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Residues in contact with LEU 375 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320G PHE* 4.1 15.8 - - + -
326G VAL* 4.3 2.7 - - + +
329G ALA* 3.7 30.9 - - + +
330G LEU* 3.8 27.4 - - + -
333G ALA* 4.5 8.7 - - + -
335G LEU* 4.4 8.1 - - + -
371G ALA 3.7 12.1 + - - +
372G PHE* 3.3 9.6 + - + +
373G GLU 3.3 0.2 - - - -
374G ARG* 1.3 79.9 - - - +
376G ASP* 1.3 60.7 + - - +
378G LEU* 3.3 7.4 + - + +
379G ALA* 3.2 17.5 + - - +
147H ALA* 3.6 38.6 - - + +
148H ALA* 4.1 7.2 - - + +
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Residues in contact with ASP 376 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259E ARG* 2.8 29.1 + - - +
262E ALA* 4.8 0.2 - - - +
266G ARG* 2.7 39.9 + - - -
270G TRP* 3.9 12.3 - - - -
372G PHE 2.9 18.1 + - - +
373G GLU* 3.9 4.9 - - - +
374G ARG 3.3 0.2 - - - -
375G LEU* 1.3 77.1 - - - +
377G GLN* 1.3 60.6 + - - +
379G ALA* 3.0 6.9 + - - +
380G MET* 2.8 23.0 + - - +
145H SER* 3.6 27.5 - - - -
146H GLY 4.4 0.5 + - - -
147H ALA* 5.3 2.1 + - - -
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Residues in contact with GLN 377 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E ARG* 2.9 41.8 - - - +
301E ALA 5.6 3.6 - - - +
305E GLY* 3.9 14.7 - - - -
308E ARG* 3.7 13.5 - - - -
309E ASN* 2.6 36.1 + - - +
373G GLU 3.1 16.9 + - - +
374G ARG* 3.3 6.0 + - - +
376G ASP* 1.3 74.5 - - - +
378G LEU* 1.3 57.5 + - - +
380G MET* 3.0 6.5 + - - +
381G ASP* 2.7 64.6 + - - +
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Residues in contact with LEU 378 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320G PHE* 4.1 2.0 - - + -
325G GLU* 3.7 42.2 - - + +
326G VAL* 4.3 15.0 - - + -
329G ALA* 3.8 19.5 - - + -
374G ARG* 3.2 20.0 + - + +
375G LEU* 3.5 8.7 - - + +
376G ASP 3.2 0.4 - - - -
377G GLN* 1.3 77.1 - - - +
379G ALA* 1.3 63.0 + - - +
381G ASP* 3.8 7.4 - - - +
382G HIS* 3.1 29.5 + - - -
387G ARG* 3.4 35.7 - - - +
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Residues in contact with ALA 379 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266G ARG* 4.3 3.4 - - - +
269G PHE* 4.4 8.8 - - + -
270G TRP* 3.8 30.7 - - + -
320G PHE* 3.6 25.3 - - + -
375G LEU 3.2 9.4 + - - +
376G ASP* 3.0 14.2 + - - +
378G LEU* 1.3 77.7 - - - +
380G MET* 1.3 61.9 + - - +
382G HIS* 3.2 4.2 + - - +
383G LEU* 3.0 23.6 + - - +
147H ALA* 5.5 0.4 - - + -
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Residues in contact with MET 380 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E ARG* 4.2 4.5 - - - +
261E GLY 3.3 32.3 - - - +
262E ALA* 4.0 1.3 - - - +
265E LEU* 4.0 20.2 - - - -
309E ASN* 3.3 32.3 - - - +
312E ILE* 5.7 0.2 - - + -
266G ARG* 3.6 33.8 - - - +
376G ASP 2.8 11.0 + - - +
377G GLN* 3.0 17.2 + - - +
379G ALA* 1.3 76.8 - - - +
381G ASP* 1.3 62.5 + - - +
383G LEU* 3.2 6.1 + - - +
384G LEU* 2.9 46.9 + - + +
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Residues in contact with ASP 381 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E ARG* 3.0 29.7 + - - -
312E ILE* 3.9 6.5 - - - +
377G GLN* 2.7 41.5 + - - +
378G LEU* 3.8 9.4 - - - +
380G MET* 1.3 72.2 - - - +
382G HIS* 1.3 58.2 + - - +
384G LEU* 3.3 0.9 + - - -
385G GLY 2.8 9.5 + - - -
386G ALA* 2.6 46.1 + - - +
387G ARG* 3.2 29.3 + - + +
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Residues in contact with HIS 382 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269G PHE* 5.3 0.9 - - + -
316G ARG* 3.2 34.4 + - - +
319G ALA* 3.6 30.4 - - + +
320G PHE* 3.7 30.2 + + + -
323G ASP* 3.0 33.3 + - + +
326G VAL* 4.0 4.5 - - + -
378G LEU 3.1 23.8 + - - +
379G ALA 3.2 4.4 + - - +
381G ASP* 1.3 79.1 - - - +
383G LEU* 1.3 62.3 + - - +
385G GLY* 3.1 10.8 + - - -
387G ARG* 3.3 21.9 + - + +
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Residues in contact with LEU 383 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E LEU* 3.5 29.6 - - + -
384E LEU* 3.7 21.5 - - + +
265G LEU* 4.5 7.2 - - + -
266G ARG* 3.9 20.4 - - + -
269G PHE* 3.8 28.4 - - + -
312G ILE* 6.1 0.2 - - + -
313G LEU* 3.5 31.6 - - + -
316G ARG* 3.0 32.7 + - + +
379G ALA 3.0 12.3 + - - +
380G MET* 3.5 9.2 - - - +
382G HIS* 1.3 76.2 - - - +
384G LEU* 1.3 58.9 + - + +
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Residues in contact with LEU 384 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265E LEU* 4.2 21.3 - - + -
309E ASN* 4.9 3.1 - - + +
312E ILE* 4.1 28.3 - - + -
313E LEU* 4.8 7.2 - - + -
316E ARG* 2.7 31.6 + - - +
383E LEU* 3.3 45.1 - - + +
384E LEU* 4.2 9.7 - - + +
385E GLY* 4.8 0.2 - - - -
380G MET* 2.9 46.8 + - + +
381G ASP 4.2 1.3 - - - +
383G LEU* 1.3 78.1 - - + +
385G GLY* 1.3 64.9 + - - +
386G ALA* 3.3 2.7 - - + +
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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
------------------------------------------------------------
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