Contacts of the helix formed by residues 374 - 389 (chain B) in PDB entry 1NTZ
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 SER 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* 3.3 35.2 - - - -
371A GLY* 4.6 1.6 - - - -
370B MET 5.7 0.2 + - - -
371B SER 4.7 1.7 + - - -
372B VAL 3.8 0.2 - - - +
373B GLU* 1.3 81.0 - - - +
375B SER* 1.3 59.2 + - - +
376B GLU* 3.8 6.0 + - - +
377B GLY* 3.3 16.5 + - - -
378B PHE* 2.9 31.6 + - - +
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Residues in contact with SER 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ASP* 2.8 27.7 + - - -
40B ASN* 4.6 5.2 + - - -
46B ARG* 3.6 27.8 + - - -
209B LEU* 3.7 22.6 - - - +
374B SER* 1.3 70.3 - - - +
376B GLU* 1.3 56.4 + - - -
378B PHE* 4.5 2.0 - - - -
379B LEU* 2.9 35.2 + - - +
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Residues in contact with GLU 376 (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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370A ASP* 4.0 2.1 + - - +
46B ARG* 3.4 33.7 + - - +
374B SER* 3.3 6.2 + - - +
375B SER* 1.3 79.5 - - - +
377B GLY* 1.3 61.5 + - - +
379B LEU* 4.2 1.9 - - - +
380B ASP* 3.2 24.8 + - - +
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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
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371B SER* 3.2 25.6 + - - +
372B VAL* 3.6 2.3 - - - +
374B SER* 3.3 10.7 + - - -
375B SER 3.3 0.6 - - - -
376B GLU* 1.3 77.3 - - - +
378B PHE* 1.3 64.5 + - - +
380B ASP* 3.6 4.8 + - - +
381B GLU* 3.2 24.4 + - - +
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Residues in contact with PHE 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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24B LEU* 3.9 17.5 - - + -
38B LEU* 3.7 32.3 - - + -
207B ILE* 6.2 0.7 - - + -
209B LEU* 3.7 26.2 - - + -
372B VAL* 3.8 32.6 - - + +
374B SER 2.9 18.7 + - - +
375B SER* 3.8 3.8 - - - +
377B GLY* 1.3 76.8 - - - +
379B LEU* 1.3 60.1 + - - +
381B GLU* 3.0 5.1 + - + +
382B VAL* 2.9 51.8 + - + +
392B TYR* 3.8 20.4 - + - -
395B PRO* 6.3 1.3 - - + -
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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* 3.8 35.7 - - + +
47B ILE 4.4 2.5 - - - -
48B GLY* 4.0 14.6 - - - +
50B PHE* 3.4 8.7 - - + -
108B THR* 4.0 27.6 - - + -
207B ILE* 3.7 28.4 - - + +
208B GLY 4.3 0.7 - - - -
209B LEU* 3.9 21.8 - - + -
375B SER 2.9 18.8 + - - +
376B GLU 4.2 2.2 - - - +
378B PHE* 1.3 81.0 - - - +
380B ASP* 1.3 58.4 + - - +
382B VAL* 3.5 4.4 + - - +
383B GLY* 2.9 23.9 + - - -
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Residues in contact with ASP 380 (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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50B PHE* 3.9 17.3 - - + -
376B GLU* 3.2 17.1 + - + +
377B GLY* 4.0 5.6 - - - +
378B PHE 3.2 0.8 - - - -
379B LEU* 1.3 79.5 - - - +
381B GLU* 1.3 58.0 + - - +
383B GLY 3.9 0.2 - - - -
384B SER* 2.8 46.1 + - - -
3I SER* 3.3 16.0 + - - -
5I ALA* 5.5 4.2 - - - +
6I ALA* 4.5 8.8 + - - +
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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
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368B TYR* 2.9 39.4 + - - +
372B VAL* 3.7 16.1 - - + +
377B GLY 3.2 17.0 + - - +
378B PHE* 3.0 6.6 + - + +
380B ASP* 1.3 75.1 - - - +
382B VAL* 1.3 67.3 + - + +
384B SER* 4.1 0.3 - - - -
385B GLN* 3.0 44.8 + - - +
392B TYR* 5.7 2.5 - - + -
1I MET* 3.9 0.9 - - - -
2I LEU 2.8 36.9 + - - +
3I SER* 3.1 13.0 - - - +
6I ALA* 5.1 4.1 - - + +
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Residues in contact with VAL 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* 3.9 13.0 - - + -
26B PHE* 5.7 1.3 - - + -
36B ALA* 3.9 21.5 - - + -
207B ILE* 3.7 22.9 - - + -
378B PHE* 2.9 54.6 + - + +
379B LEU 4.0 3.1 - - - +
381B GLU* 1.3 80.3 - - + +
383B GLY* 1.3 62.0 + - - +
385B GLN* 3.6 5.4 - - - +
386B ALA* 3.0 22.8 + - + +
391B SER 5.1 0.3 - - - +
392B TYR* 3.9 19.3 - - + -
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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
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50B PHE* 3.7 38.9 - - - +
205B ALA* 4.6 0.2 - - - +
207B ILE* 3.7 11.1 - - - +
379B LEU 2.9 11.4 + - - -
382B VAL* 1.3 77.1 - - - +
384B SER* 1.3 60.8 + - - +
386B ALA* 3.2 13.0 + - - +
387B LEU* 3.2 17.0 + - - +
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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
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50B PHE* 4.2 3.7 - - - -
104B ASN* 4.4 17.9 + - - +
380B ASP* 2.8 34.8 + - - -
381B GLU 4.1 0.2 - - - -
383B GLY* 1.3 76.0 - - - +
385B GLN* 1.3 56.1 + - - +
387B LEU* 3.4 2.5 + - - +
388B ALA* 2.9 31.9 + - - +
2I LEU* 4.6 2.0 - - - -
3I SER* 3.3 34.8 - - - -
4I VAL* 4.9 2.0 - - - -
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Residues in contact with GLN 385 (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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368B TYR* 3.8 2.9 + - - -
381B GLU* 3.0 48.4 + - - +
382B VAL* 3.6 4.7 - - - +
384B SER* 1.3 73.1 - - - +
386B ALA* 1.3 61.7 + - - +
389B ALA* 2.8 30.8 + - - +
390B GLY 3.2 4.5 + - - -
391B SER* 3.5 8.6 + - - +
392B TYR* 3.4 15.6 - - - +
393B THR* 2.7 56.1 + - - +
398B VAL* 5.3 0.2 - - - +
1I MET 4.9 4.0 + - - -
2I LEU* 3.7 27.9 - - + +
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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
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26B PHE* 4.4 4.5 - - + -
28B ARG* 5.6 0.3 + - - -
34B VAL* 3.6 34.1 - - + +
205B ALA* 3.8 12.1 - - + -
207B ILE* 4.3 5.4 - - + -
382B VAL 3.0 13.8 + - - +
383B GLY 3.4 9.4 - - - +
385B GLN* 1.3 77.5 - - - +
387B LEU* 1.3 60.2 + - - +
390B GLY* 2.9 28.0 + - - +
391B SER 3.9 8.9 + - - +
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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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50B PHE* 3.6 35.9 - - + +
51B ILE 3.8 4.7 - - - +
52B LYS* 3.3 40.9 + - + -
104B ASN* 3.5 34.8 - - - +
203B ARG 4.0 18.2 - - - +
204B MET* 4.1 5.8 - - - +
205B ALA* 3.9 21.5 - - + -
233B SER* 5.2 0.2 + - - -
383B GLY 3.2 5.5 + - - +
384B SER 3.7 7.0 - - - +
386B ALA* 1.3 82.3 - - - +
388B ALA* 1.3 64.6 + - - +
390B GLY* 4.6 0.7 + - - -
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Residues in contact with ALA 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* 5.4 1.1 + - - +
264B ILE* 4.3 19.7 - - + -
317B SER* 6.1 5.4 - - - -
384B SER 2.9 17.5 + - - +
387B LEU* 1.3 79.6 - - - +
389B ALA* 1.3 59.0 + - - +
2I LEU* 3.7 19.5 - - + -
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Residues in contact with ALA 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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265B GLY* 6.5 0.4 - - - -
385B GLN* 2.8 14.2 + - - +
388B ALA* 1.3 74.0 - - - +
390B GLY* 1.3 60.3 + - - +
391B SER* 3.4 19.4 + - - +
393B THR* 5.7 1.8 - - - +
2I LEU* 3.5 22.9 - - + -
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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
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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