Contacts of the helix formed by residues 374 - 389 (chain B) in PDB entry 3H1J
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 THR 374 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A ASP* 3.2 34.3 - - + +
371A GLY* 5.0 0.7 - - - -
374A PRO* 5.9 1.6 - - + -
370B MET 4.6 0.2 + - - -
371B SER 4.0 5.5 + - - -
373B GLU* 1.3 80.8 - - + +
375B ALA* 1.3 65.9 + - - +
376B GLN* 4.3 4.5 - - - +
377B GLY* 2.8 30.1 + - - -
378B LEU* 3.0 11.8 + - - +
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Residues in contact with ALA 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ASP* 3.1 25.9 + - - +
46B ARG* 3.8 9.0 - - + -
110B GLU* 3.8 21.1 - - - +
209B ILE* 3.7 12.8 - - + +
373B GLU 3.7 2.0 + - - -
374B THR* 1.3 70.6 - - - +
376B GLN* 1.3 59.6 + - - +
378B LEU* 3.7 4.8 + - - +
379B LEU* 3.1 24.4 + - - +
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Residues in contact with GLN 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ASP* 4.6 1.0 + - - +
46B ARG* 3.1 33.6 + - - +
99B TYR* 3.6 33.3 + - + -
110B GLU* 5.1 0.4 + - - +
374B THR* 3.1 5.4 - - - +
375B ALA* 1.3 76.4 - - - +
377B GLY* 1.3 62.6 + - - +
379B LEU* 3.2 1.7 + - + +
380B ASN* 2.8 40.0 + - + +
77I ARG* 3.1 32.7 - - - +
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Residues in contact with GLY 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B SER* 3.2 25.9 + - - +
372B VAL* 4.0 2.7 - - - +
374B THR* 2.8 14.8 + - - -
376B GLN* 1.3 79.7 - - - +
378B LEU* 1.3 56.3 + - - -
380B ASN* 3.4 5.6 + - - +
381B GLU* 2.9 28.8 + - - +
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Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LEU* 4.5 20.4 - - + -
40B ASN* 4.9 9.2 - - + +
209B ILE* 3.6 26.0 - - + -
372B VAL* 3.5 32.2 - - + +
373B GLU 5.6 0.2 - - - +
374B THR 3.0 10.8 + - - +
375B ALA* 4.0 4.7 - - - +
377B GLY* 1.3 76.2 - - - +
379B LEU* 1.3 58.8 + - - +
381B GLU* 3.0 6.1 + - + +
382B ILE* 2.9 52.0 + - + +
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Residues in contact with LEU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ARG* 3.4 53.8 - - + +
47B ILE 4.2 10.3 - - - +
50B PHE* 3.0 25.2 - - + -
106B THR* 6.0 0.2 - - + -
108B CYS* 4.6 6.3 - - + -
207B VAL* 3.4 29.8 - - + -
208B GLY* 3.8 5.8 - - - +
209B ILE* 3.3 27.9 - - + +
375B ALA 3.1 12.6 + - - +
376B GLN 3.2 3.3 + - - +
378B LEU* 1.3 78.8 - - - +
380B ASN* 1.3 59.8 + - - +
382B ILE* 4.0 3.4 - - - -
383B GLY 3.3 10.7 + - - -
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Residues in contact with ASN 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 3.9 8.3 - - + -
104B LYS* 3.3 26.3 + - - -
106B THR* 4.9 1.9 + - - +
376B GLN* 2.8 25.3 + - + +
377B GLY* 3.8 6.0 + - - +
379B LEU* 1.3 75.6 - - - +
381B GLU* 1.3 68.8 + - - +
384B SER* 2.4 39.8 + - - -
77I ARG* 5.5 9.6 - - - +
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Residues in contact with GLU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B TYR* 3.3 36.7 + - - +
371B SER* 5.6 1.0 + - - -
372B VAL* 3.8 23.4 - - + +
377B GLY 2.9 14.4 + - - +
378B LEU* 3.4 10.5 - - + +
380B ASN* 1.3 82.1 + - - +
382B ILE* 1.3 66.6 + - + +
384B SER* 3.8 5.1 - - - -
385B GLU* 3.7 17.0 + - - +
392B HIS* 5.8 2.4 - - + +
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Residues in contact with ILE 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LEU* 4.4 25.4 - - + -
36B ALA* 4.1 18.4 - - + +
38B LEU* 4.2 19.1 - - + -
207B VAL* 3.5 17.3 - - + -
208B GLY 4.9 2.5 - - - +
209B ILE* 4.4 14.1 - - + -
378B LEU* 2.9 47.8 + - + +
379B LEU 4.0 3.4 - - - +
381B GLU* 1.3 79.7 - - + +
383B GLY* 1.3 67.5 + - - +
384B SER 3.0 0.3 + - - -
385B GLU* 3.1 4.3 + - - +
386B ALA* 3.0 19.4 + - + +
391B THR 5.2 0.5 - - - +
392B HIS* 4.9 14.7 - - + +
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Residues in contact with GLY 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 3.9 12.7 - - - -
207B VAL* 3.1 31.5 - - - +
379B LEU 3.3 11.4 + - - -
382B ILE* 1.3 80.6 - - - +
384B SER* 1.3 62.8 + - - +
386B ALA* 3.7 4.2 - - - -
387B LEU* 3.0 26.3 + - - +
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Residues in contact with SER 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 4.2 0.8 - - - -
104B LYS* 3.5 23.8 + - - +
380B ASN* 2.4 47.8 + - - -
381B GLU* 3.8 8.1 - - - -
382B ILE 3.0 0.4 + - - -
383B GLY* 1.3 76.9 - - - +
385B GLU* 1.3 61.4 + - - +
387B LEU* 3.7 1.9 - - - +
388B LEU* 3.1 32.7 + - - +
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Residues in contact with GLU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLU* 3.7 8.6 + - - +
382B ILE 3.1 6.5 + - - +
384B SER* 1.3 76.4 - - - +
386B ALA* 1.3 53.3 + - - +
387B LEU 2.5 17.1 + - - -
388B LEU* 2.7 17.7 + - - +
389B SER* 2.9 18.0 + - - +
390B GLY 3.6 0.9 + - - -
391B THR* 3.4 25.7 + - - +
392B HIS* 2.8 33.0 - - - +
393B THR* 2.7 38.9 + - - +
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Residues in contact with ALA 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 4.5 1.3 - - + -
34B ILE* 2.8 39.0 - - + +
36B ALA* 3.9 28.7 - - + -
205B ALA* 4.0 2.0 - - + +
207B VAL* 4.5 4.3 - - + -
382B ILE* 3.0 17.3 + - + +
383B GLY* 3.7 10.1 - - - -
385B GLU* 1.3 76.1 - - - +
387B LEU* 1.3 55.9 + - - +
390B GLY* 3.4 7.1 - - - -
391B THR 3.9 14.8 + - - +
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ILE* 4.4 8.7 - - + +
50B PHE* 3.6 14.6 - - + +
51B ILE 3.8 26.2 - - - +
52B LYS* 3.3 29.3 + - + -
104B LYS* 4.8 14.1 - - + -
202B ALA 5.7 0.2 - - - +
203B ARG 3.2 24.9 - - - +
204B MET 3.6 8.3 - - - +
205B ALA* 3.4 24.0 - - + -
383B GLY 3.0 16.3 + - - +
384B SER 3.7 3.8 - - - +
385B GLU 2.5 6.3 + - - -
386B ALA* 1.3 76.5 - - - +
388B LEU* 1.3 66.8 + - + +
389B SER 3.4 0.2 - - - -
390B GLY 4.5 0.4 - - - -
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Residues in contact with LEU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LYS* 4.6 19.7 + - + +
104B LYS* 6.3 3.6 - - + -
264B VAL* 3.3 39.5 - - + -
317B SER* 6.0 5.2 - - - -
384B SER* 3.1 18.5 + - - +
385B GLU* 2.7 12.5 + - - +
387B LEU* 1.3 83.6 - - + +
389B SER* 1.3 61.9 + - - +
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Residues in contact with SER 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LYS* 5.9 1.3 - - - -
385B GLU* 2.9 13.3 + - - +
388B LEU* 1.3 82.7 - - - +
390B GLY* 1.3 52.9 + - - +
391B THR* 2.4 53.5 + - - +
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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