Contacts of the helix formed by residues 371 - 385 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ALA* 4.8 1.9 - - - +
332B ALA* 4.5 21.3 - - + +
333B ALA* 4.2 4.6 - - - +
369B GLY* 3.4 5.1 - - - +
370B MET* 1.3 82.7 - - - +
372B PHE* 1.3 62.1 + - - +
373B GLU 3.4 2.5 - - - -
374B ARG* 4.1 13.1 + - + +
375B LEU* 3.6 18.9 + - - +
294D GLU* 3.3 13.7 + - - +
295D ASP* 5.6 2.2 - - - +
298D GLY* 5.7 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ASP* 3.2 28.9 - - - -
107A ASN* 3.6 19.3 - - - -
144A GLU* 5.4 3.1 - - + -
145A SER* 4.1 12.9 + - - +
148A ALA* 3.5 37.0 - - + -
149A LYS* 5.5 0.4 - - - -
188A ARG* 4.6 7.0 - - - -
333B ALA* 4.0 10.5 - - + -
370B MET* 3.5 38.6 - - + -
371B ALA* 1.3 78.9 - - - +
373B GLU* 1.3 63.4 + - - +
374B ARG 3.5 0.2 - - - -
375B LEU* 3.5 6.4 + - + +
376B ASP* 2.8 30.3 + - - +
291D PRO* 6.1 1.3 - - + -
293D THR* 3.4 25.8 - - + +
294D GLU* 3.0 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLU* 5.9 1.4 - - - +
145A SER* 5.1 4.2 + - - -
372B PHE* 1.3 79.6 - - - +
374B ARG* 1.3 61.0 + - - +
376B ASP* 3.3 4.5 + - - +
377B GLN* 2.8 30.3 + - - +
259D ARG* 3.2 35.3 + - - +
291D PRO* 3.6 24.1 - - + +
294D GLU* 3.3 28.3 + - + +
298D GLY* 4.0 12.6 - - - +
301D ALA* 4.7 2.7 - - + -
302D SER* 2.7 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B GLU* 2.7 45.3 + - - +
328B GLU* 6.0 3.4 - - - +
329B ALA* 4.0 16.5 - - - +
371B ALA* 4.1 15.7 + - + +
372B PHE 3.5 0.2 - - - -
373B GLU* 1.3 77.6 - - - +
375B LEU* 1.3 63.3 + - - +
377B GLN* 3.2 6.0 + - - +
378B LEU* 3.0 45.1 + - + +
294D GLU* 4.9 0.2 + - - -
298D GLY* 5.9 0.8 - - - -
301D ALA* 4.5 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ALA* 3.6 42.6 - - + +
148A ALA* 4.0 8.5 - - + +
320B PHE* 4.1 1.8 - - + -
326B VAL* 4.1 11.4 - - + +
329B ALA* 3.6 32.1 - - + +
330B LEU* 3.8 26.5 - - + +
333B ALA* 4.2 9.2 - - + -
335B LEU* 4.2 7.9 - - + -
371B ALA 3.6 12.3 + - - +
372B PHE* 3.5 11.2 + - + +
373B GLU 3.2 0.2 - - - -
374B ARG* 1.3 79.6 - - - +
376B ASP* 1.3 60.7 + - - +
378B LEU* 3.2 7.6 + - + +
379B ALA* 3.1 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A SER* 3.4 29.3 - - - +
146A GLY 4.3 0.2 + - - -
147A ALA* 5.2 2.6 + - + -
266B ARG* 2.7 39.3 + - - -
270B TRP* 3.9 11.5 - - - -
372B PHE 2.8 21.0 + - - +
373B GLU* 3.8 5.8 - - - +
374B ARG 3.3 0.4 - - - -
375B LEU* 1.3 72.4 - - - +
377B GLN* 1.3 59.7 + - - +
379B ALA* 3.2 6.8 + - - +
380B MET* 2.9 22.3 + - - +
259D ARG* 2.8 30.1 + - - +
262D ALA* 4.9 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B GLU 2.8 17.9 + - - +
374B ARG* 3.2 6.2 + - - +
376B ASP* 1.3 73.3 - - - +
378B LEU* 1.3 62.2 + - + +
380B MET* 3.1 4.2 + - - +
381B ASP* 2.8 53.7 + - - +
259D ARG* 2.8 40.3 - - - +
301D ALA 5.7 3.1 - - - +
305D GLY* 3.5 19.2 - - - -
308D ARG* 3.9 12.6 - - - -
309D ASN* 2.9 35.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B PHE* 4.1 0.9 - - + -
325B GLU* 3.8 24.5 - - + +
326B VAL* 4.1 20.0 - - + -
329B ALA* 3.8 28.9 - - + -
374B ARG* 3.0 35.7 + - + +
375B LEU* 3.4 7.4 - - - +
376B ASP 3.2 0.2 - - - -
377B GLN* 1.3 76.2 - - - +
379B ALA* 1.3 63.3 + - - +
381B ASP* 3.3 8.1 + - - +
382B HIS* 3.0 31.7 + - + -
387B ARG* 3.4 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ARG* 4.3 2.9 - - - +
269B PHE* 4.6 7.6 - - + -
270B TRP* 3.5 33.9 - - + -
320B PHE* 3.3 28.9 - - + -
375B LEU 3.1 9.4 + - - +
376B ASP* 3.3 11.7 - - - +
377B GLN 3.1 0.2 - - - -
378B LEU* 1.3 78.2 - - - +
380B MET* 1.3 56.6 + - - +
382B HIS* 3.5 2.4 + - - +
383B LEU* 3.1 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ARG* 3.7 33.8 - - - +
376B ASP 2.9 13.2 + - - +
377B GLN* 3.1 12.8 + - - +
379B ALA* 1.3 74.4 - - - +
381B ASP* 1.3 65.8 + - - +
383B LEU* 3.3 4.5 + - - +
384B LEU* 3.0 36.0 + - + +
259D ARG* 4.1 4.9 - - - +
261D GLY 2.9 37.2 - - - +
262D ALA* 3.9 2.0 - - - +
265D LEU* 3.9 28.3 - - + -
309D ASN* 3.2 31.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B GLN* 2.8 41.7 + - - +
378B LEU* 3.9 7.8 - - - +
380B MET* 1.3 72.8 - - - +
382B HIS* 1.3 58.9 + - - +
384B LEU* 3.4 0.4 + - - -
385B GLY 2.9 8.0 + - - -
386B ALA* 2.7 49.2 + - - +
387B ARG* 3.5 21.3 + - - +
308D ARG* 2.7 35.5 + - - -
312D ILE* 3.7 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B PHE* 5.7 0.4 - - + -
316B ARG* 3.6 22.7 - - - +
319B ALA* 3.6 27.1 - - + +
320B PHE* 3.6 39.3 + + + -
323B ASP* 2.8 34.5 + - + +
326B VAL* 3.7 5.5 - - + +
378B LEU 3.0 25.8 + - - +
379B ALA 3.7 4.7 - - - +
381B ASP* 1.3 78.1 - - - +
383B LEU* 1.3 62.1 + - - +
385B GLY* 3.0 12.4 + - - -
387B ARG* 3.5 25.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LEU* 4.6 6.3 - - + -
266B ARG* 3.8 23.6 - - + -
269B PHE* 3.9 26.6 - - + -
313B LEU* 3.5 31.9 - - + -
316B ARG* 3.0 29.5 + - + +
379B ALA 3.1 14.6 + - - +
380B MET* 3.3 6.7 + - - +
382B HIS* 1.3 78.9 - - - +
384B LEU* 1.3 59.1 + - + +
385B GLY 3.2 0.2 - - - -
265D LEU* 3.6 29.6 - - + -
384D LEU* 3.7 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ARG* 3.9 3.1 - - - -
380B MET* 3.0 41.9 + - + +
381B ASP 4.2 2.0 - - - +
383B LEU* 1.3 78.1 - - + +
385B GLY* 1.3 59.5 + - - +
386B ALA* 4.4 3.1 - - + -
265D LEU* 4.1 18.2 - - + -
309D ASN* 4.5 8.1 - - - +
312D ILE* 4.0 28.3 - - + -
313D LEU* 4.5 11.9 - - + -
316D ARG* 2.7 36.1 + - + +
383D LEU* 3.5 41.5 - - + +
384D LEU* 4.0 7.9 - - + +
385D GLY* 4.7 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ARG* 3.5 13.7 - - - +
381B ASP 2.9 5.8 + - - -
382B HIS* 3.0 11.4 + - - -
383B LEU 3.2 1.6 + - - -
384B LEU* 1.3 77.8 - - - +
386B ALA* 1.3 58.4 + - - +
387B ARG* 3.5 6.0 + - - +
3D TYR* 4.9 0.3 + - - -
316D ARG* 3.1 12.7 + - - -
384D LEU 4.7 0.7 - - - -
385D GLY* 5.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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