Contacts of the helix formed by residues 369 - 382 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407B ARG* 2.9 43.7 + - - -
364C TYR* 2.8 24.4 + - + +
367C ASP* 3.0 20.3 + - - +
368C ASN* 1.3 70.1 - - - +
370C ALA* 1.3 56.5 + - - +
371C LEU* 3.8 3.3 + - - +
372C MET* 3.3 20.8 + - - +
373C ALA* 2.9 28.3 + - - +
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Residues in contact with ALA 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A TYR* 5.5 0.9 - - + -
186A PHE* 3.9 17.3 - - + +
189A GLN* 3.5 46.2 - - + +
332B VAL* 4.1 9.5 + - + +
333B THR* 4.0 11.2 - - + +
368C ASN 3.3 6.5 + - - +
369C ASP* 1.3 73.8 + - - +
371C LEU* 1.3 62.9 + - - +
373C ALA* 3.3 2.3 + - - +
374C THR* 3.0 26.3 + - - +
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Residues in contact with LEU 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PHE* 5.6 2.0 - - - -
293B ASP* 4.6 4.5 - - - +
333B THR* 4.0 16.0 - - + +
337B GLU* 3.5 53.8 - - + +
338B SER* 3.6 18.4 - - - +
341B ASN* 3.7 25.1 - - + +
403B VAL* 4.1 17.7 - - + -
407B ARG* 4.2 1.6 - - - +
369C ASP* 3.3 6.3 + - - +
370C ALA* 1.3 79.4 - - - +
372C MET* 1.3 69.0 + - - +
374C THR* 3.3 11.9 - - + +
375C GLU* 3.0 26.1 + - + +
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Residues in contact with MET 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ASN* 5.9 0.2 - - - -
403B VAL* 4.7 9.4 - - - -
407B ARG* 3.3 34.8 - - - +
364C TYR* 3.4 38.5 - - + +
369C ASP* 3.3 17.4 + - - +
371C LEU* 1.3 89.2 - - + +
373C ALA* 1.3 55.9 + - - +
375C GLU* 3.8 10.0 - - + +
376C THR* 2.7 38.4 + - - +
379C ARG* 3.6 34.3 - - - +
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Residues in contact with ALA 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A PRO 4.4 1.6 - - - -
188A GLY 3.5 26.0 - - - +
189A GLN* 3.8 7.2 - - - -
361C LEU* 3.5 15.5 - - + +
364C TYR* 3.8 20.6 - - + +
369C ASP 2.9 19.4 + - - +
370C ALA* 3.6 4.9 - - - +
371C LEU 3.3 0.2 - - - -
372C MET* 1.3 77.5 - - - +
374C THR* 1.3 62.4 + - - +
376C THR* 3.2 12.9 + - - -
377C LEU* 3.3 10.6 + - - +
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Residues in contact with THR 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PHE* 3.7 23.0 - - + +
187A PRO* 2.8 40.5 + - - +
296B ALA* 4.7 9.0 + - + +
300C TYR* 4.5 4.2 + - - -
370C ALA 3.0 14.1 + - - +
371C LEU* 3.3 14.4 - - + +
373C ALA* 1.3 77.1 - - - +
375C GLU* 1.3 72.6 + - + +
377C LEU* 3.2 4.9 + - - +
378C LYS* 3.0 32.3 + - + +
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Residues in contact with GLU 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B ASN* 3.4 32.9 + - - +
345B GLU* 5.3 3.6 - - - +
348B ARG* 5.5 0.4 + - - -
371C LEU* 3.0 24.2 + - + +
372C MET* 3.9 15.0 - - + +
373C ALA 3.3 0.4 - - - -
374C THR* 1.3 83.0 - - + +
376C THR* 1.3 59.8 + - - +
378C LYS* 3.7 12.0 + - - +
379C ARG* 2.9 45.9 + - - +
382C ARG* 2.9 32.1 + - - -
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Residues in contact with THR 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C VAL* 4.6 5.9 - - + +
357C ASP* 3.8 37.1 + - + +
360C ALA* 4.4 2.8 - - + +
361C LEU* 4.0 18.4 - - + +
364C TYR* 3.3 20.7 - - - -
372C MET* 2.7 20.5 + - - +
373C ALA 3.4 10.1 - - - -
374C THR 3.2 0.4 - - - -
375C GLU* 1.3 77.6 - - - +
377C LEU* 1.3 62.9 + - - +
379C ARG* 3.4 20.5 + - - +
380C ALA* 3.7 9.2 + - - +
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Residues in contact with LEU 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A PRO* 3.6 8.3 - - + +
188A GLY* 3.4 32.8 - - - +
300C TYR* 4.0 8.1 - - - +
303C PHE* 3.6 13.7 - - + -
304C LEU* 4.0 22.2 - - + -
307C ASN* 3.6 33.4 - - - +
356C VAL* 3.9 16.6 - - + -
361C LEU* 4.0 18.2 - - + -
373C ALA 3.3 9.6 + - - +
374C THR 3.2 7.5 + - - +
376C THR* 1.3 76.8 - - - +
378C LYS* 1.3 59.8 + - - +
380C ALA* 3.1 7.4 + - - +
381C TYR* 3.0 22.3 + - - +
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Residues in contact with LYS 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B GLY 2.8 32.2 + - - -
296B ALA* 4.2 6.4 - - - +
299B PRO* 4.3 8.7 - - - +
345B GLU* 3.8 21.4 + - - -
300C TYR* 3.5 40.6 - - + +
374C THR* 3.0 23.7 + - + +
375C GLU* 3.7 16.6 + - - +
376C THR 3.3 0.2 - - - -
377C LEU* 1.3 76.4 - - - +
379C ARG* 1.3 59.7 + - - +
381C TYR* 4.1 11.0 - - + -
382C ARG* 2.7 60.0 + - + +
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Residues in contact with ARG 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B ASP* 4.6 13.1 + - - -
36C ARG* 3.3 13.4 + - - +
364C TYR* 5.6 1.0 + - - -
372C MET* 3.6 31.5 - - - +
375C GLU* 2.9 36.2 + - - +
376C THR* 3.7 12.9 + - - +
377C LEU 3.3 0.4 - - - -
378C LYS* 1.3 76.6 - - - +
380C ALA* 1.3 58.2 + - - +
382C ARG* 3.7 25.8 - - - +
383C THR* 2.8 23.2 + - - -
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Residues in contact with ALA 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ARG* 4.1 8.7 - - - +
303C PHE* 4.3 0.7 - - + -
352C GLN* 3.3 34.7 - - - +
355C LEU* 3.8 7.3 - - + +
356C VAL* 3.7 30.1 - - + +
376C THR 3.7 2.5 + - - +
377C LEU 3.1 8.8 + - - +
378C LYS 3.1 0.4 - - - -
379C ARG* 1.3 78.5 - - - +
381C TYR* 1.3 65.2 + - - +
383C THR* 3.1 19.9 + - - -
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Residues in contact with TYR 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B PRO* 3.8 8.5 - - + -
381B TYR* 2.7 35.8 + + - -
299C PRO* 3.2 33.2 - - + +
300C TYR* 3.4 54.3 + + + +
303C PHE* 3.7 16.7 - - + -
352C GLN* 3.2 41.5 - - - +
377C LEU 3.0 15.7 + - - +
378C LYS* 4.0 13.5 - - + +
380C ALA* 1.3 78.3 - - - +
382C ARG* 1.3 66.5 + - + +
383C THR 3.1 0.2 - - - -
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Residues in contact with ARG 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345B GLU* 5.0 3.7 + - - -
348B ARG* 3.6 52.1 - - - +
382B ARG 4.2 5.5 - - - +
384B ASP* 3.4 39.0 + - - +
386B GLU* 5.1 10.9 + - - +
375C GLU* 2.9 27.3 + - - -
378C LYS* 2.7 48.1 + - + +
379C ARG* 3.7 30.6 - - - +
381C TYR* 1.3 78.8 - - + +
383C THR* 1.3 62.8 + - - +
384C ASP 3.4 0.7 + - - -
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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