Contacts of the helix formed by residues 369 - 382 (chain A) in PDB entry 3ITX
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 ASP 369 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A TYR* 2.8 23.9 + - + +
367A ASP* 3.3 25.0 - - - +
368A ASN* 1.3 69.6 - - - +
370A ALA* 1.3 62.8 + - - +
371A LEU* 3.8 3.3 + - - +
372A MET* 3.4 21.7 + - - +
373A ALA* 2.9 23.1 + - - +
189C GLN 6.1 0.2 - - - -
407D ARG* 2.8 45.1 + - - -
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Residues in contact with ALA 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ASN 3.2 8.0 + - - +
369A ASP* 1.3 73.5 + - - +
371A LEU* 1.3 58.2 + - - +
373A ALA* 3.3 2.7 + - - +
374A THR* 3.0 31.4 + - - +
143C TYR* 5.4 0.2 - - + -
186C PHE* 4.0 9.8 - - + +
189C GLN* 3.5 44.9 - - + +
332D VAL* 4.1 8.9 + - + +
333D THR* 4.0 18.4 - - + +
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Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ASP* 3.3 6.1 + - - +
370A ALA* 1.3 77.7 - - - +
372A MET* 1.3 68.7 + - - +
374A THR* 3.3 11.9 - - + +
375A GLU* 2.9 28.3 + - + +
186C PHE* 5.7 1.6 - - - -
293D ASP* 4.5 5.2 - - - +
333D THR* 4.0 16.2 - - + +
337D GLU* 3.5 53.2 - - + +
338D SER* 3.5 17.7 - - - +
341D ASN* 3.5 26.0 - - + +
403D VAL* 4.0 19.1 - - + -
407D ARG* 4.4 1.3 - - - +
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Residues in contact with MET 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A TYR* 3.5 37.4 - - + +
369A ASP* 3.4 15.1 + - - +
371A LEU* 1.3 91.1 - - - +
373A ALA* 1.3 56.0 + - - +
375A GLU* 3.7 10.8 - - + +
376A THR* 2.7 39.7 + - - +
379A ARG* 3.8 35.0 - - - +
341D ASN* 5.8 0.2 - - - -
403D VAL* 4.6 11.0 - - - -
407D ARG* 3.4 33.0 - - - +
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Residues in contact with ALA 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A LEU* 3.6 15.9 - - + +
364A TYR* 3.9 22.6 - - + +
369A ASP 2.9 19.1 + - - +
370A ALA* 3.5 5.2 - - - +
372A MET* 1.3 77.4 - - - +
374A THR* 1.3 62.7 + - - +
376A THR* 3.2 13.1 + - - -
377A LEU* 3.3 11.4 + - - +
187C PRO 4.3 1.6 - - - -
188C GLY 3.5 22.0 - - - +
189C GLN* 3.8 9.9 - - - -
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Residues in contact with THR 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A TYR* 4.5 3.5 + - - -
370A ALA 3.0 14.3 + - - +
371A LEU* 3.3 15.3 - - + +
373A ALA* 1.3 76.1 - - - +
375A GLU* 1.3 63.9 + - + +
377A LEU* 3.1 6.5 + - - +
378A LYS* 3.0 32.7 + - + +
186C PHE* 3.6 27.2 - - + +
187C PRO* 2.8 36.0 + - - +
296D ALA* 4.7 8.6 + - + +
341D ASN* 6.3 0.4 - - - +
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Residues in contact with GLU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A LEU 2.9 18.4 + - - +
372A MET* 3.8 15.5 - - + +
374A THR* 1.3 76.6 - - + +
376A THR* 1.3 60.7 + - - +
378A LYS* 3.2 6.0 + - - +
379A ARG* 2.9 62.5 + - - +
382A ARG* 2.9 41.5 + - - -
341D ASN* 4.7 18.7 + - - +
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Residues in contact with THR 376 (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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356A VAL* 4.3 6.3 - - + +
357A ASP* 3.7 38.2 + - + +
360A ALA* 4.6 2.3 - - + +
361A LEU* 4.0 17.3 - - + +
364A TYR* 3.4 20.4 - - - -
372A MET* 2.7 25.6 + - - +
373A ALA* 3.3 9.2 - - - -
374A THR 3.1 0.2 - - - -
375A GLU* 1.3 78.8 - - - +
377A LEU* 1.3 61.5 + - - +
379A ARG* 3.5 19.2 + - - +
380A ALA* 3.7 9.5 + - - +
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Residues in contact with LEU 377 (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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300A TYR* 4.0 8.1 - - - +
303A PHE* 3.5 13.2 - - + -
304A LEU* 4.0 22.2 - - + -
307A ASN* 3.6 32.5 - - - +
356A VAL* 3.9 22.9 - - + -
361A LEU* 4.0 11.2 - - + -
373A ALA 3.3 9.8 + - - +
374A THR 3.1 7.4 + - - +
376A THR* 1.3 79.5 - - - +
378A LYS* 1.3 57.8 + - - +
380A ALA* 3.1 7.4 + - - +
381A TYR* 2.9 22.9 + - - +
187C PRO* 3.5 8.1 - - + +
188C GLY* 3.4 33.0 - - - +
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Residues in contact with LYS 378 (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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300A TYR* 3.5 38.8 - - + +
374A THR* 3.0 22.6 + - + +
375A GLU* 3.6 11.7 - - - +
377A LEU* 1.3 74.9 - - - +
379A ARG* 1.3 57.6 + - - +
381A TYR* 4.1 11.2 - - + -
382A ARG* 2.7 63.2 + - + +
295D GLY 2.8 32.3 + - - -
296D ALA* 4.2 6.6 - - - +
299D PRO* 4.2 10.6 - - - +
345D GLU* 3.9 22.0 + - - -
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Residues in contact with ARG 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 3.1 20.9 + - - +
364A TYR* 5.4 2.0 + - - -
372A MET* 3.8 26.7 - - - +
375A GLU* 2.9 51.0 + - - +
376A THR* 3.8 12.9 + - - +
377A LEU 3.3 0.6 - - - -
378A LYS* 1.3 75.6 - - - +
380A ALA* 1.3 58.0 + - - +
382A ARG* 3.7 15.1 + - - +
383A THR* 2.8 22.5 + - - -
401D ASP* 3.8 21.4 + - - -
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Residues in contact with ALA 380 (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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36A ARG* 4.3 2.5 - - - +
303A PHE* 4.3 0.9 - - + -
352A GLN* 3.3 35.4 - - - +
355A LEU* 3.9 10.6 - - + +
356A VAL* 3.6 30.7 - - + +
376A THR 3.7 3.8 + - - +
377A LEU 3.1 9.0 + - - +
378A LYS 3.0 0.4 - - - -
379A ARG* 1.3 77.9 - - - +
381A TYR* 1.3 65.3 + - - +
383A THR* 3.2 21.1 + - - -
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Residues in contact with TYR 381 (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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299A PRO* 3.3 32.9 - - + +
300A TYR* 3.5 47.5 + + + +
303A PHE* 3.7 24.2 - - + -
352A GLN* 3.1 42.2 + - - -
377A LEU 2.9 15.7 + - - +
378A LYS* 3.9 14.1 - - + +
380A ALA* 1.3 78.4 - - - +
382A ARG* 1.3 63.7 + - + +
299D PRO* 3.8 9.2 - - + -
381D TYR* 2.6 35.2 + + - -
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Residues in contact with ARG 382 (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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375A GLU* 2.9 40.2 + - - -
378A LYS* 2.7 55.2 + - + +
379A ARG* 3.7 17.1 - - - +
381A TYR* 1.3 77.6 - - + +
383A THR* 1.3 64.1 + - - +
384A ASP 3.4 2.4 + - - -
345D GLU* 4.9 5.0 + - - +
348D ARG* 3.5 54.1 - - - +
382D ARG 4.2 5.9 - - - +
384D ASP* 3.4 36.5 + - - +
386D GLU* 4.7 14.1 + - - +
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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