Contacts of the helix formed by residues 383 - 403 (chain B) in PDB entry 2ZXI
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 383 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B LYS* 3.9 0.7 - - - -
377B ASN* 3.9 0.7 + - - +
381B THR* 5.3 0.2 + - - -
382B THR* 1.3 75.2 + - - +
384B TYR* 1.3 65.1 + - - +
385B GLU 3.4 2.2 - - - -
386B GLU* 3.5 9.1 - - - +
387B ALA* 3.3 23.4 + - - +
618B FAD 2.8 44.4 + - - +
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Residues in contact with TYR 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B HIS* 3.4 47.7 - + + +
46B MET* 3.4 24.9 - - + +
47B SER 4.1 4.0 - - - -
48B CYS* 2.7 29.8 + - + -
49B ASN* 2.9 28.6 + - + -
51B ALA 3.6 19.7 - - - -
52B ILE* 4.0 10.1 - - + -
71B MET* 3.9 10.3 - - + -
383B GLY* 1.3 72.3 - - - -
385B GLU* 1.3 67.0 + - - +
387B ALA* 3.2 4.3 + - - +
388B ALA* 2.9 29.5 + - - +
618B FAD 3.7 30.5 + - - -
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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
----------------------------------------------------------
51B ALA 3.8 5.4 - - - +
52B ILE* 3.2 11.6 - - + -
53B GLY 2.8 26.0 + - - +
57B LYS* 3.0 53.2 + - + +
60B VAL* 3.7 13.7 - - + +
61B VAL* 3.5 27.4 - - + -
71B MET* 4.0 13.7 - - - -
384B TYR* 1.3 81.7 + - - +
386B GLU* 1.3 63.6 + - - +
388B ALA* 3.3 1.2 + - - +
389B GLY* 2.9 27.9 + - - -
435B LEU* 4.4 0.7 - - + -
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Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS* 2.7 32.6 + - - +
381B THR* 4.0 11.4 - - - -
382B THR 2.8 39.1 - - - +
383B GLY* 3.5 5.5 - - - +
385B GLU* 1.3 79.6 - - - +
387B ALA* 1.3 56.7 + - - +
390B GLN* 2.7 25.9 + - - +
420B MET* 3.2 38.3 - - - +
433B TYR* 4.5 2.0 - - + +
434B ARG* 3.8 2.1 - - - +
435B LEU* 3.0 42.0 + - + +
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Residues in contact with ALA 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B HIS* 4.1 0.4 - - + -
18B ALA* 3.4 18.6 - - - +
376B GLY* 3.8 17.9 - - - -
377B ASN* 4.8 0.4 - - - +
381B THR* 4.5 1.5 + - - +
383B GLY 3.3 10.2 + - - +
384B TYR 3.4 8.5 - - - +
385B GLU 3.1 0.2 - - - -
386B GLU* 1.3 77.1 - - - +
388B ALA* 1.3 60.3 + - - +
390B GLN* 3.1 12.1 + - - +
391B GLY 2.8 24.3 + - - -
618B FAD 3.4 26.9 - - - +
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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
----------------------------------------------------------
17B HIS 3.4 17.4 + - - +
18B ALA* 4.3 0.4 - - - +
21B GLU* 3.5 26.0 - - + +
64B ILE* 3.6 18.4 - - + +
71B MET* 3.8 17.7 - - + -
384B TYR 2.9 16.5 + - - +
385B GLU 4.0 0.9 - - - +
387B ALA* 1.3 76.1 - - - +
389B GLY* 1.3 63.2 + - - +
392B ILE* 3.2 21.7 + - - +
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Residues in contact with GLY 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 4.4 0.9 - - - -
64B ILE* 3.7 11.6 - - - +
385B GLU 2.9 16.5 + - - -
386B GLU 4.0 2.0 - - - -
387B ALA 3.2 0.2 - - - -
388B ALA* 1.3 77.9 - - - +
390B GLN* 1.3 59.7 + - - +
392B ILE* 3.3 17.5 - - - +
393B VAL* 3.6 3.1 - - - +
417B ILE* 3.6 33.0 - - - +
420B MET* 4.2 7.2 - - - -
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Residues in contact with GLN 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B LEU* 3.2 18.9 - - + +
375B ALA* 3.8 11.4 - - + -
376B GLY 3.2 17.8 + - - +
379B ASN* 3.0 29.9 + - - +
381B THR* 2.8 33.3 + - - +
386B GLU 2.7 23.5 + - - +
387B ALA 3.1 3.7 + - - +
389B GLY* 1.3 74.4 - - - +
391B GLY* 1.3 61.0 + - - +
393B VAL* 3.2 3.8 + - - -
394B ALA* 2.9 26.5 + - - +
420B MET* 3.8 12.4 - - + -
421B ILE* 4.5 9.9 - - + -
424B LEU* 3.8 15.2 - - + +
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Residues in contact with GLY 391 (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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18B ALA* 3.3 24.2 - - - -
21B GLU* 4.4 0.2 - - - -
22B ALA* 3.2 17.0 - - - +
375B ALA* 4.0 9.3 - - - +
387B ALA 2.8 14.6 + - - -
388B ALA 3.4 2.2 + - - -
389B GLY 3.3 0.4 - - - -
390B GLN* 1.3 77.6 - - - +
392B ILE* 1.3 57.1 + - - +
394B ALA 3.3 1.1 + - - -
395B GLY 2.8 26.5 + - - -
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Residues in contact with ILE 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLU* 3.6 17.5 - - + +
25B ALA* 4.2 12.8 - - + +
64B ILE* 3.9 8.3 - - + +
67B LEU* 3.7 43.1 - - + -
69B GLY* 3.8 29.2 - - - +
388B ALA 3.2 12.4 + - - +
389B GLY* 3.3 15.9 - - - +
391B GLY* 1.3 75.1 - - - +
393B VAL* 1.3 65.7 + - + +
395B GLY* 3.9 0.3 - - - -
396B ILE* 2.9 45.2 + - + +
417B ILE* 4.6 6.3 - - + -
464B LEU* 4.4 8.1 - - + -
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Residues in contact with VAL 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 5.5 1.1 - - + -
362B PRO 4.6 3.4 - - - +
363B THR* 4.0 5.2 - - - +
364B LEU* 3.9 16.8 - - + -
389B GLY 3.6 14.4 - - - +
390B GLN 3.2 7.9 + - - +
392B ILE* 1.3 87.3 - - + +
394B ALA* 1.3 57.4 + - - +
396B ILE* 3.3 10.8 + - + +
397B ASN* 3.0 44.5 + - - +
408B ILE* 4.9 5.6 - - + +
409B TYR* 5.3 5.4 - - - -
410B LEU* 4.1 18.2 - - + -
417B ILE* 4.0 9.0 - - + -
421B ILE* 3.7 20.9 - - + -
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Residues in contact with ALA 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 3.8 25.6 - - + +
364B LEU* 4.0 13.4 - - + +
373B PHE* 4.1 24.3 - - + -
374B HIS 4.4 0.9 - - - +
375B ALA* 4.3 8.1 - - + -
390B GLN 2.9 15.9 + - - +
391B GLY 3.8 2.5 - - - +
393B VAL* 1.3 74.4 - - - +
395B GLY* 1.3 61.4 + - - +
397B ASN* 4.0 1.1 - - - +
398B ALA* 2.9 30.5 + - - +
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Residues in contact with GLY 395 (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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22B ALA* 3.4 31.6 - - - +
25B ALA* 4.6 0.7 - - - -
26B ALA* 3.7 14.5 - - - +
153B VAL* 4.6 1.6 - - - -
391B GLY 2.8 16.2 + - - -
392B ILE 3.9 0.7 - - - -
394B ALA* 1.3 77.6 - - - +
396B ILE* 1.3 62.1 + - - +
398B ALA* 3.2 7.0 + - - +
399B ALA* 3.1 19.1 + - - +
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Residues in contact with ILE 396 (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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25B ALA* 4.2 4.4 - - + +
29B MET* 3.7 14.8 - - - +
67B LEU* 4.9 9.2 - - + -
392B ILE* 2.9 40.6 + - + +
393B VAL* 3.5 9.2 - - + +
395B GLY* 1.3 76.7 - - - +
397B ASN* 1.3 59.8 + - - +
399B ALA* 3.4 3.3 + - - +
400B LEU* 3.0 32.7 + - + +
408B ILE* 3.7 28.3 - - + -
458B LEU* 6.1 0.4 - - + -
462B LEU* 3.5 32.8 - - + -
464B LEU* 3.8 25.4 - - + -
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Residues in contact with ASN 397 (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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363B THR* 2.6 30.3 + - - +
373B PHE* 3.4 20.9 - - + -
393B VAL* 3.0 23.1 + - - +
394B ALA 4.1 0.7 - - - +
396B ILE* 1.3 74.4 - - - +
398B ALA* 1.3 60.6 + - - +
400B LEU* 3.6 7.2 - - - +
401B ARG* 2.9 32.6 + - - +
407B PRO* 3.5 8.8 - - + +
408B ILE* 2.8 56.1 + - - +
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Residues in contact with ALA 398 (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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10B VAL* 3.7 18.6 - - + -
151B ALA* 3.7 13.9 - - + +
153B VAL* 3.7 22.2 - - + -
373B PHE* 3.9 15.9 - - + -
394B ALA 2.9 19.2 + - - +
395B GLY 3.2 4.5 + - - +
397B ASN* 1.3 73.1 - - - +
399B ALA* 1.3 60.5 + - - +
401B ARG* 3.2 4.2 + - - +
402B ALA* 2.9 27.4 + - - +
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Residues in contact with ALA 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 3.7 10.4 - - - +
26B ALA* 3.8 24.2 - - + +
29B MET* 4.1 14.1 - - + -
31B ALA* 3.9 11.7 - - + -
395B GLY 3.1 9.7 + - - +
396B ILE 3.7 7.6 - - - +
398B ALA* 1.3 75.9 - - - +
400B LEU* 1.3 67.1 + - - +
402B ALA* 3.0 6.1 + - - +
403B PHE* 3.0 33.8 + - + -
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Residues in contact with LEU 400 (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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29B MET* 3.9 16.4 - - + -
396B ILE* 3.0 32.2 + - + +
397B ASN* 3.6 21.5 - - - +
399B ALA* 1.3 76.0 - - - +
401B ARG* 1.3 62.2 + - - +
403B PHE* 3.0 17.8 + - + +
405B LYS* 3.0 56.7 + - + +
406B GLU 3.7 18.2 - - - +
407B PRO* 4.1 3.4 - - + -
408B ILE* 4.2 11.9 - - + -
462B LEU* 4.4 8.3 - - + -
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Residues in contact with ARG 401 (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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150B LYS* 5.5 2.6 - - - +
151B ALA* 4.6 8.3 - - + -
365B GLU* 2.8 40.5 + - - +
370B ARG* 3.7 55.2 + - - +
371B GLY* 4.6 4.7 - - - +
373B PHE* 3.9 10.5 - - + -
397B ASN 2.9 16.2 + - - +
398B ALA* 3.4 11.0 - - - +
400B LEU* 1.3 75.1 - - - +
402B ALA* 1.3 58.5 + - - +
404B GLY* 2.9 20.7 + - - -
405B LYS 3.7 12.6 + - - -
406B GLU* 3.7 15.8 + - - -
407B PRO* 3.1 34.4 - - + +
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Residues in contact with ALA 402 (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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9B ASP* 3.8 41.7 - - + +
150B LYS* 3.5 32.6 - - + +
151B ALA* 5.0 1.1 - - + +
398B ALA 2.9 12.7 + - - +
399B ALA* 3.0 15.0 + - - +
401B ARG* 1.3 75.3 - - - +
403B PHE* 1.3 64.0 + - + +
404B GLY 3.8 0.3 + - - -
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Residues in contact with PHE 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASP* 4.6 8.1 - - - -
29B MET* 3.4 24.7 - - + -
30B GLY* 3.7 5.6 - - - -
31B ALA* 3.5 43.3 - - + -
399B ALA* 3.2 23.6 - - + -
400B LEU* 3.0 13.8 + - + +
402B ALA* 1.3 85.5 - - + +
404B GLY* 1.3 62.8 + - - +
405B LYS* 3.6 29.1 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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