Contacts of the helix formed by residues 371 - 384 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A GLU* 3.3 12.8 + - - -
295A ASP* 5.6 1.7 + - - +
298A GLY* 5.6 3.1 - - - -
329C ALA* 5.1 1.7 - - - +
332C ALA* 4.4 23.3 - - + +
333C ALA* 4.7 1.9 - - + +
369C GLY* 3.2 6.1 - - - +
370C MET* 1.3 79.5 - - - +
372C PHE* 1.3 63.7 + - - +
373C GLU 3.4 3.1 - - - -
374C ARG* 3.7 12.0 + - + +
375C LEU* 3.4 20.1 + - - +
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Residues in contact with PHE 372 (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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291A PRO* 6.3 1.1 - - + -
293A THR* 3.6 20.4 - - + +
294A GLU* 3.1 8.2 + - - +
333C ALA* 3.8 18.8 - - + -
370C MET* 3.1 35.0 - - + -
371C ALA* 1.3 76.9 - - - +
373C GLU* 1.3 58.4 + - - +
375C LEU* 3.1 8.1 + - + +
376C ASP* 2.7 37.4 + - - +
101D ASP* 3.2 28.3 - - - -
107D ASN* 3.4 26.9 - - - -
143D ALA* 6.3 0.2 - - + -
144D GLU* 5.6 1.6 - - - -
145D SER* 4.2 12.8 + - - +
148D ALA* 3.4 34.3 - - + -
149D LYS* 5.2 0.7 - - - -
188D ARG* 4.6 6.5 - - - -
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Residues in contact with GLU 373 (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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259A ARG* 3.1 37.8 + - - +
291A PRO* 3.7 23.6 - - + +
294A GLU* 3.4 30.3 + - + +
298A GLY* 4.1 7.9 - - - +
301A ALA* 5.2 2.9 - - - +
302A SER* 2.7 41.6 + - - +
372C PHE* 1.3 78.8 - - - +
374C ARG* 1.3 60.4 + - - +
376C ASP* 3.4 5.9 + - - +
377C GLN* 2.9 28.6 + - - +
144D GLU* 5.9 1.6 - - - +
145D SER* 5.0 5.4 + - - -
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Residues in contact with ARG 374 (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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294A GLU* 4.9 0.4 + - - -
298A GLY* 5.9 0.8 - - - -
301A ALA* 4.2 22.1 - - + +
325C GLU* 3.4 37.8 + - - +
329C ALA* 5.0 9.2 - - + +
371C ALA* 3.7 13.9 + - + +
372C PHE 3.4 0.4 - - - -
373C GLU* 1.3 78.9 - - - +
375C LEU* 1.3 63.2 + - - +
377C GLN* 3.3 7.3 + - + +
378C LEU* 3.2 44.2 + - + +
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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
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320C PHE* 4.2 14.4 - - + -
326C VAL* 4.4 3.6 - - + +
329C ALA* 3.9 25.3 - - + +
330C LEU* 3.6 35.4 - - + -
333C ALA* 4.2 10.3 - - + -
335C LEU* 4.2 8.7 - - + -
371C ALA 3.4 12.0 + - - +
372C PHE* 3.1 11.6 + - + +
374C ARG* 1.3 80.5 - - - +
376C ASP* 1.3 61.0 + - - +
378C LEU* 3.3 20.2 + - + +
379C ALA* 3.3 10.7 + - - +
145D SER* 6.0 0.2 - - - +
147D ALA* 3.9 26.7 - - + +
148D ALA* 4.0 9.6 - - - +
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Residues in contact with ASP 376 (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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259A ARG* 2.8 28.4 + - - +
262A ALA* 4.9 0.5 - - - +
266C ARG* 2.6 42.4 + - - -
270C TRP* 4.0 11.5 - - - -
372C PHE 2.7 20.3 + - - +
373C GLU* 3.9 4.9 - - - +
375C LEU* 1.3 72.0 - - + +
377C GLN* 1.3 61.0 + - - +
379C ALA* 3.1 5.3 + - - +
380C MET* 3.0 22.3 + - - +
145D SER* 3.5 30.9 - - - +
146D GLY 4.4 0.5 + - - -
147D ALA* 5.3 2.2 + - - -
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Residues in contact with GLN 377 (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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259A ARG* 2.8 42.9 - - - +
301A ALA 5.2 6.7 - - - +
305A GLY* 3.9 13.3 - - - -
308A ARG* 3.7 14.3 - - - -
309A ASN* 2.7 35.3 + - - +
373C GLU 2.9 18.2 + - - +
374C ARG* 3.3 7.4 + - + +
376C ASP* 1.3 74.3 - - - +
378C LEU* 1.3 60.2 + - - +
380C MET* 3.9 3.3 - - - +
381C ASP* 3.0 49.7 + - - +
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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
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320C PHE* 3.9 8.3 - - + -
325C GLU* 4.2 15.5 - - + +
326C VAL* 4.1 20.2 - - + +
329C ALA* 3.6 31.2 - - + -
374C ARG* 3.2 36.7 + - + +
375C LEU* 3.4 9.0 - - + +
376C ASP 3.2 0.2 - - - -
377C GLN* 1.3 76.6 - - + +
379C ALA* 1.3 62.9 + - - +
381C ASP* 3.4 9.9 + - - +
382C HIS* 3.1 29.2 + - + -
387C ARG* 3.8 27.3 - - - +
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Residues in contact with ALA 379 (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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266C ARG* 4.2 4.3 - - - +
269C PHE* 4.5 7.4 - - + -
270C TRP* 3.8 27.4 - - + -
320C PHE* 3.4 31.8 - - + -
375C LEU 3.3 4.7 + - - +
376C ASP* 3.1 12.2 + - - +
378C LEU* 1.3 78.1 - - - +
380C MET* 1.3 60.2 + - - +
382C HIS* 3.1 3.3 + - - +
383C LEU* 2.9 29.6 + - - +
147D ALA* 5.5 0.4 - - + -
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Residues in contact with MET 380 (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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259A ARG* 4.2 3.4 - - - +
261A GLY 3.4 31.9 - - - +
262A ALA* 4.1 1.3 - - - +
265A LEU* 4.1 16.2 - - + -
309A ASN* 3.4 28.5 - - - +
266C ARG* 3.4 48.6 - - - +
376C ASP 3.0 12.8 + - - +
377C GLN* 3.6 15.5 - - - +
378C LEU 3.3 0.2 - - - -
379C ALA* 1.3 77.6 - - - +
381C ASP* 1.3 57.2 + - - +
383C LEU* 3.4 3.8 + - - +
384C LEU* 2.9 55.6 + - + +
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Residues in contact with ASP 381 (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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308A ARG* 3.0 39.9 + - - -
312A ILE* 3.9 7.7 - - - +
377C GLN* 3.0 36.2 + - - +
378C LEU* 3.8 11.2 - - - +
379C ALA 3.3 0.4 - - - -
380C MET* 1.3 75.8 - - - +
382C HIS* 1.3 56.8 + - - +
384C LEU* 3.6 0.6 + - - -
385C GLY 2.9 5.9 + - - -
386C ALA* 2.6 42.9 + - - +
387C ARG* 3.7 20.5 + - - -
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Residues in contact with HIS 382 (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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269C PHE* 5.3 1.1 - - + -
316C ARG* 3.2 26.1 + - - +
319C ALA* 3.3 33.3 - - + +
320C PHE* 3.7 37.5 + + + -
323C ASP* 3.1 29.8 + - + +
326C VAL* 4.1 3.1 - - + -
378C LEU 3.1 23.4 + - - +
379C ALA 3.1 7.1 + - - +
381C ASP* 1.3 75.2 - - - +
383C LEU* 1.3 66.7 + - - +
385C GLY* 2.9 11.9 + - - -
387C ARG* 3.3 28.1 + - + +
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Residues in contact with LEU 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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265A LEU* 3.6 31.4 - - + -
384A LEU* 3.9 21.3 - - + +
265C LEU* 4.7 4.0 - - + -
266C ARG* 3.8 27.1 - - + -
269C PHE* 3.6 27.8 - - + -
313C LEU* 3.5 31.6 - - + -
316C ARG* 3.1 29.7 + - + +
379C ALA 2.9 16.1 + - - +
380C MET* 3.7 6.5 - - - +
382C HIS* 1.3 75.5 - - - +
384C LEU* 1.3 59.5 + - + +
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Residues in contact with LEU 384 (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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265A LEU* 4.0 24.0 - - + -
309A ASN* 4.8 4.3 - - + +
312A ILE* 3.8 33.9 - - + -
313A LEU* 4.6 6.7 - - + -
316A ARG* 2.7 27.1 + - - -
383A LEU* 3.4 40.6 - - + +
384A LEU* 4.1 6.5 - - + +
380C MET* 2.9 45.1 + - + +
381C ASP 4.2 1.8 - - - +
383C LEU* 1.3 80.4 - - + +
385C GLY* 1.3 65.0 + - - +
386C ALA* 3.2 3.8 - - + -
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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