Contacts of the helix formed by residues 371 - 384 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B GLU* 3.4 13.9 + - - -
295B ASP* 5.6 1.7 + - - +
298B GLY* 5.9 1.8 - - - -
329D ALA* 5.0 1.8 - - - +
332D ALA* 4.3 23.1 - - + +
333D ALA* 4.3 3.5 - - - +
369D GLY* 3.3 6.1 - - - +
370D MET* 1.3 81.1 - - - +
372D PHE* 1.3 62.6 + - - +
373D GLU 3.5 1.8 - - - -
374D ARG* 4.1 12.7 + - + +
375D LEU* 3.6 19.6 + - - +
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Residues in contact with PHE 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B PRO* 6.3 0.7 - - + -
293B THR* 3.7 17.7 - - + +
294B GLU* 3.0 7.9 + - - +
101C ASP* 3.4 19.5 - - - -
107C ASN* 3.0 32.8 - - - -
143C ALA* 6.2 0.4 - - + -
144C GLU* 5.5 2.9 - - + -
145C SER* 4.0 13.6 + - - +
148C ALA* 3.3 35.0 - - + -
149C LYS* 5.2 0.7 - - - -
188C ARG* 4.5 9.4 - - - -
333D ALA* 3.7 21.1 - - + -
335D LEU* 4.4 0.2 - - + -
370D MET* 3.6 32.5 - - + -
371D ALA* 1.3 76.6 - - - +
373D GLU* 1.3 60.1 + - + +
375D LEU* 3.3 7.9 - - + +
376D ASP* 2.8 36.6 + - - +
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Residues in contact with GLU 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LEU* 6.0 0.7 - - - +
259B ARG* 3.5 33.9 + - - +
291B PRO* 3.5 30.1 - - + +
294B GLU* 3.3 29.5 + - + +
298B GLY 4.2 11.7 - - - +
301B ALA* 4.9 3.6 - - + +
302B SER* 2.7 33.6 + - - +
144C GLU* 5.6 1.7 - - - +
145C SER* 5.1 5.4 + - - -
372D PHE* 1.3 78.9 - - + +
374D ARG* 1.3 64.8 + - - +
376D ASP* 3.4 6.9 + - - +
377D GLN* 3.0 23.2 + - - +
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Residues in contact with ARG 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B GLU* 4.7 0.8 + - - -
297B ASP* 3.5 34.6 + - - +
298B GLY* 5.2 1.2 - - - -
300B TRP* 6.1 0.2 - - - +
301B ALA* 3.6 24.3 - - + +
325D GLU* 6.1 1.1 - - - -
329D ALA* 6.0 4.0 - - + -
371D ALA* 4.1 13.5 + - + +
372D PHE 3.4 0.4 - - - -
373D GLU* 1.3 77.0 - - - +
375D LEU* 1.3 64.5 + - - +
377D GLN* 3.1 15.4 + - - +
378D LEU* 3.1 25.6 + - + +
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Residues in contact with LEU 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C ALA* 3.9 35.7 - - + +
148C ALA* 4.0 9.4 - - + +
320D PHE* 4.2 12.1 - - + -
326D VAL* 4.3 4.5 - - + +
329D ALA* 3.9 29.3 - - + +
330D LEU* 3.7 27.6 - - + +
333D ALA* 4.3 17.9 - - + -
335D LEU* 4.5 0.9 - - + -
371D ALA 3.6 12.7 + - - +
372D PHE* 3.3 11.0 - - + +
374D ARG* 1.3 80.7 - - - +
376D ASP* 1.3 62.2 + - - +
378D LEU* 3.1 16.0 + - + +
379D ALA* 3.2 11.1 + - - +
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Residues in contact with ASP 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ARG* 2.7 31.6 + - - +
262B ALA* 4.8 0.5 - - - +
145C SER* 3.5 28.6 - - - -
146C GLY 4.3 0.5 + - - -
147C ALA* 5.2 1.9 + - - -
266D ARG* 2.7 34.4 + - - -
270D TRP* 3.9 12.5 + - - -
372D PHE 2.8 21.0 + - - +
373D GLU* 3.8 8.3 - - - +
374D ARG 3.2 0.2 - - - -
375D LEU* 1.3 74.1 - - - +
377D GLN* 1.3 58.9 + - - +
379D ALA* 3.1 7.2 + - - +
380D MET* 2.9 22.5 + - - +
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Residues in contact with GLN 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ARG* 2.8 44.5 - - - +
301B ALA 5.7 3.6 - - - +
305B GLY* 3.9 11.9 - - - -
308B ARG* 3.9 16.0 - - - -
309B ASN* 2.9 34.5 + - - +
373D GLU 3.0 16.9 + - - +
374D ARG* 3.1 7.1 + - - +
376D ASP* 1.3 74.5 - - - +
378D LEU* 1.3 60.6 + - - +
380D MET* 3.5 6.0 - - - +
381D ASP* 2.9 60.2 + - - +
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Residues in contact with LEU 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D PHE* 4.0 1.8 - - + -
325D GLU* 3.9 28.5 - - - +
326D VAL* 3.9 20.6 - - + -
329D ALA* 3.6 30.3 - - + -
374D ARG* 3.1 23.1 + - + +
375D LEU* 3.1 10.8 + - + +
377D GLN* 1.3 77.1 - - - +
379D ALA* 1.3 62.8 + - - +
381D ASP* 3.4 7.5 + - - +
382D HIS* 3.0 32.9 + - - -
387D ARG* 3.4 34.1 - - - +
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Residues in contact with ALA 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D ARG* 4.4 2.9 - - - +
269D PHE* 4.4 8.1 - - + -
270D TRP* 3.6 36.8 - - + -
320D PHE* 3.5 25.0 - - + -
375D LEU 3.2 5.3 + - - +
376D ASP* 3.1 11.6 + - - +
378D LEU* 1.3 80.2 - - - +
380D MET* 1.3 55.8 + - - +
382D HIS* 3.4 2.1 + - - +
383D LEU* 3.0 29.7 + - - +
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Residues in contact with MET 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ARG* 4.0 3.4 - - - +
261B GLY* 3.2 35.9 - - - +
262B ALA* 4.0 1.1 - - - +
265B LEU* 3.9 24.7 - - + -
309B ASN* 3.4 29.8 - - - +
312B ILE* 5.5 0.2 - - + -
266D ARG* 3.6 35.8 - - - +
376D ASP 2.9 14.0 + - - +
377D GLN* 3.5 15.7 - - - +
379D ALA* 1.3 74.1 - - - +
381D ASP* 1.3 65.7 + - - +
383D LEU* 3.3 3.9 + - - +
384D LEU* 2.9 40.3 + - + +
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Residues in contact with ASP 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ARG* 2.8 35.1 + - - -
312B ILE* 4.0 7.0 - - - +
377D GLN* 2.9 41.8 + - - +
378D LEU* 3.8 8.8 - - - +
379D ALA 3.4 0.2 - - - -
380D MET* 1.3 75.7 - - - +
382D HIS* 1.3 58.0 + - - +
384D LEU* 3.4 0.8 + - - -
385D GLY 2.8 8.5 + - - -
386D ALA* 2.6 41.4 + - - +
387D ARG* 3.3 29.8 + - + +
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Residues in contact with HIS 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D PHE* 5.3 0.7 - - + -
316D ARG* 3.5 24.5 - - - +
319D ALA* 3.5 28.9 - - + +
320D PHE* 3.7 37.3 + + + -
323D ASP* 3.0 27.8 + - - -
326D VAL* 3.6 11.6 - - + +
378D LEU 3.0 27.3 + - - +
379D ALA 3.7 3.8 - - - +
381D ASP* 1.3 78.4 - - - +
383D LEU* 1.3 63.6 + - - +
385D GLY* 2.9 13.0 + - - -
387D ARG* 3.1 25.5 + - + +
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Residues in contact with LEU 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LEU* 3.3 32.8 - - + -
384B LEU* 3.5 19.5 - - + +
265D LEU* 4.4 7.2 - - + -
266D ARG* 3.9 20.4 - - + -
269D PHE* 3.6 26.2 - - + -
313D LEU* 3.4 32.8 - - + -
316D ARG* 2.9 29.7 + - + +
379D ALA 3.0 18.0 + - - +
380D MET* 3.3 6.7 + - - +
382D HIS* 1.3 75.1 - - - +
384D LEU* 1.3 59.8 + - + +
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Residues in contact with LEU 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B LEU* 3.9 24.7 - - + -
309B ASN* 5.0 2.7 - - - +
312B ILE* 3.8 34.1 - - + -
313B LEU* 4.2 16.4 - - + -
316B ARG* 2.6 35.3 + - - -
383B LEU* 3.7 31.4 - - + +
384B LEU* 4.0 4.9 - - + +
385B GLY* 4.7 0.2 - - - -
316D ARG* 4.0 3.1 - - - -
380D MET* 2.9 42.4 + - + +
381D ASP* 4.1 2.0 - - - +
383D LEU* 1.3 81.5 - - + +
385D GLY* 1.3 58.1 + - - +
386D ALA* 3.3 2.9 - - + +
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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