Contacts of the helix formed by residues 371 - 387 (chain A) in PDB entry 3H1I
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 GLY 371 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A LEU 3.8 1.8 + - - -
370A ASP* 1.3 74.5 + - - +
372A THR* 1.3 62.5 + - - -
374A PRO* 3.8 4.0 - - - -
375A VAL* 2.9 27.9 + - - +
373B GLU* 4.0 28.6 + - - -
374B THR* 4.6 1.3 - - - -
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Residues in contact with THR 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLN* 4.5 8.7 - - + -
34A THR 4.1 3.4 - - - +
35A CYS* 3.6 14.0 + - - -
36A THR* 3.1 11.7 + - - -
100A LYS* 3.0 11.8 + - - -
200A ALA* 3.3 32.4 - - + +
201A GLY* 3.9 11.2 - - - -
371A GLY* 1.3 70.5 - - - +
373A THR* 1.3 76.3 + - - +
374A PRO* 3.9 0.4 - - - +
375A VAL* 2.9 14.6 + - - +
376A CYS* 3.0 11.2 + - - +
373B GLU* 2.7 33.0 + - + +
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Residues in contact with THR 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A THR* 3.4 14.5 + - + -
40A TRP* 4.9 1.5 - - + -
98A TYR* 3.7 39.9 - - + +
100A LYS* 3.2 34.0 + - + +
372A THR* 1.3 76.4 + - - +
374A PRO* 1.3 76.8 - - + +
376A CYS* 3.1 2.9 + - - +
377A GLU* 2.8 23.6 + - + +
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Residues in contact with PRO 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ALA 5.4 0.2 - - - +
368A GLN 3.0 25.2 - - - +
370A ASP* 3.3 27.6 - - + +
371A GLY* 3.8 8.3 - - - -
372A THR 3.3 4.5 - - - +
373A THR* 1.3 94.5 - - + +
375A VAL* 1.3 62.7 + - - +
377A GLU* 3.1 10.3 + - + +
378A THR* 3.0 23.7 + - - -
373B GLU* 5.6 0.7 - - - +
374B THR* 6.1 0.7 - - + -
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Residues in contact with VAL 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 3.9 26.7 - - - +
200A ALA* 3.9 17.5 - - + -
368A GLN 4.3 0.2 + - - -
369A LEU* 3.8 31.4 - - + +
371A GLY 2.9 23.8 - - - +
372A THR* 2.9 10.1 + - - +
374A PRO* 1.3 71.0 - - - +
376A CYS* 1.3 66.2 + - - +
378A THR* 2.9 6.2 + - - -
379A ILE* 2.9 37.9 + - + +
389A ARG* 4.4 6.7 - - - +
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Residues in contact with CYS 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A THR* 3.8 12.6 - - + +
37A VAL* 4.2 4.0 - - - -
40A TRP* 3.2 33.4 - - + -
198A ALA* 3.1 37.2 - - - +
199A ALA* 3.5 8.3 - - - +
200A ALA* 4.1 8.2 - - + +
372A THR 3.0 7.8 + - - +
373A THR* 3.3 12.3 - - - +
375A VAL* 1.3 81.7 - - - +
377A GLU* 1.3 51.9 + - - +
379A ILE* 3.2 7.2 + - - +
380A GLY 2.6 31.9 + - - -
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Residues in contact with GLU 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 3.4 20.6 + - + -
89A TYR* 2.4 38.4 + - - -
94A GLN* 3.6 0.7 + - - -
98A TYR* 5.5 0.9 - - + -
373A THR* 2.8 15.4 + - + +
374A PRO* 3.1 13.4 + - + +
376A CYS* 1.3 76.0 - - - +
378A THR* 1.3 57.3 + - - +
380A GLY* 3.0 1.4 + - - -
381A SER* 2.5 64.3 + - - -
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Residues in contact with THR 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A GLN* 4.2 9.0 + - - +
369A LEU* 3.1 31.7 - - + +
374A PRO 3.0 5.2 + - - -
375A VAL 2.9 9.3 + - - -
377A GLU* 1.3 80.6 - - - +
379A ILE* 1.3 53.4 + - - +
381A SER* 3.4 3.2 + - - -
382A HIS* 2.5 72.3 + - + +
389A ARG* 4.2 9.9 - - - +
395A TRP* 5.9 0.4 - - - +
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Residues in contact with ILE 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A THR* 3.5 28.0 - - + +
26A ALA* 4.2 13.0 - - + -
27A SER* 4.2 3.6 - - - -
28A GLU* 4.1 13.2 - - + +
198A ALA* 3.9 15.9 - - + -
199A ALA 4.9 1.8 - - - +
375A VAL* 2.9 33.1 + - + +
376A CYS* 3.6 8.3 - - - +
378A THR* 1.3 70.7 - - - +
380A GLY* 1.3 68.7 + - - +
381A SER 3.0 1.3 - - - -
382A HIS* 2.8 17.2 + - - +
383A LEU* 3.1 33.9 + - + +
389A ARG* 3.2 25.4 - - + +
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Residues in contact with GLY 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 3.5 38.4 - - - +
196A VAL* 4.6 7.1 - - - +
198A ALA* 3.9 5.8 - - - +
376A CYS 2.6 20.4 + - - -
377A GLU 3.4 3.4 - - - -
379A ILE* 1.3 73.9 - - - +
381A SER* 1.3 57.4 + - - +
383A LEU* 4.5 1.6 - - - +
384A LEU* 3.3 23.7 + - - +
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Residues in contact with SER 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLN* 2.6 27.8 + - - -
262A TRP* 6.1 3.8 - - - -
377A GLU* 2.5 40.0 + - - -
378A THR* 3.9 3.8 - - - -
380A GLY* 1.3 73.7 - - - +
382A HIS* 1.3 68.0 + - - +
384A LEU* 3.9 5.4 - - - -
385A ASN* 3.2 27.9 + - - +
386A TYR* 4.9 1.7 - - - -
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Residues in contact with HIS 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A THR* 2.5 50.7 + - + +
379A ILE 2.8 7.5 + - - +
381A SER* 1.3 73.9 - - - +
383A LEU* 1.3 57.6 + - + +
386A TYR* 2.8 47.5 + + + -
387A GLY 3.2 4.3 + - - -
388A ARG 3.1 12.5 - - - +
389A ARG* 3.2 15.6 - - + -
390A ILE* 2.7 58.5 + - + +
395A TRP* 4.0 18.7 + + - -
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Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A VAL* 4.3 26.9 - - + -
24A ARG* 3.7 21.6 + - + +
26A ALA* 3.6 25.6 - - + +
196A VAL* 3.3 37.5 - - + -
379A ILE* 3.1 17.8 + - + +
382A HIS* 1.3 80.8 - - + +
384A LEU* 1.3 63.9 + - - +
385A ASN 3.4 0.7 + - - -
387A GLY* 3.4 25.0 + - - +
388A ARG* 3.5 30.7 - - - -
389A ARG* 4.0 5.4 - - + +
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 4.4 16.9 + - - +
40A TRP* 2.8 28.0 - - + +
41A ILE 3.3 17.3 - - - +
42A GLY* 3.6 13.5 - - - -
93A GLU 6.0 0.2 - - - +
94A GLN* 4.0 21.8 - - + +
194A ARG* 3.5 22.7 - - + +
196A VAL* 4.6 4.9 - - + -
380A GLY 3.3 18.6 + - - +
381A SER* 4.1 5.2 - - - +
382A HIS 3.3 0.4 - - - -
383A LEU* 1.3 80.7 - - - +
385A ASN* 1.3 61.4 + - - +
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Residues in contact with ASN 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A GLU* 4.2 14.4 + - - +
94A GLN* 3.3 24.9 + - - -
262A TRP* 3.4 62.4 + - + +
263A ALA* 5.4 1.4 + - - -
315A SER* 4.5 5.2 + - - -
381A SER* 3.2 20.2 + - - +
384A LEU* 1.3 82.0 - - - +
386A TYR* 1.3 63.7 + - + +
387A GLY 3.3 1.9 + - - -
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Residues in contact with TYR 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A TRP* 3.2 73.4 + + + -
263A ALA* 4.8 7.0 - - - +
264A ASP 5.5 0.4 - - - -
267A ASN* 4.8 11.0 - - + +
271A HIS* 5.8 2.9 - - - -
381A SER 4.9 0.7 - - - -
382A HIS* 2.8 34.4 + + - +
385A ASN* 1.3 77.4 - - + +
387A GLY* 1.3 58.0 + - - +
388A ARG* 3.5 16.5 + - - +
390A ILE* 3.4 33.4 - - + -
395A TRP* 3.7 31.0 - + - -
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Residues in contact with GLY 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 4.4 8.6 + - - -
382A HIS 3.2 4.0 + - - -
383A LEU* 3.4 25.7 + - - +
385A ASN 3.3 4.4 + - - -
386A TYR* 1.3 75.9 - - - +
388A ARG* 1.3 61.5 + - - +
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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