Contacts of the helix formed by residues 370 - 388 (chain B) in PDB entry 5X1V
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 TYR 370 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LYS* 5.9 10.7 - - + +
199A ASN* 4.2 10.3 - - - -
200A GLY* 4.3 19.8 + - - -
201A GLY* 5.5 0.9 - - - -
334B MET* 3.9 15.0 + - + +
336B LYS 3.4 22.2 + - - -
337B LYS 3.3 25.6 - - - +
338B PRO* 3.7 29.0 - - + +
364B GLU 4.4 2.0 - - - -
368B GLY 3.4 1.0 - - - -
369B ASP* 1.3 101.1 - - + +
371B PRO* 1.4 64.4 - - - +
372B LEU 3.4 2.5 - - - -
373B GLU* 3.4 32.4 + - + +
374B ALA* 3.1 21.3 + - - +
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Residues in contact with PRO 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ALA* 4.0 24.5 - - + +
55B SER* 4.6 2.5 - - - -
60B THR* 4.9 5.6 - - + -
64B MET* 4.3 9.4 - - - -
364B GLU 3.4 20.2 - - - +
365B THR* 3.8 20.7 - - + +
368B GLY 3.9 6.3 - - - +
369B ASP 3.7 7.6 - - - +
370B TYR* 1.4 85.0 - - - +
372B LEU* 1.3 69.3 + - + +
373B GLU* 4.8 0.9 - - - +
374B ALA* 3.3 4.2 + - + +
375B VAL* 3.2 28.4 + - - +
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B THR* 4.1 13.5 - - + +
63B GLU* 3.8 37.9 - - + +
64B MET* 3.8 30.5 - - + +
67B SER* 3.9 7.6 + - - +
370B TYR 3.4 0.6 - - - -
371B PRO* 1.3 81.4 - - + +
373B GLU* 1.3 67.3 + - - +
375B VAL* 3.5 5.6 + - - +
376B ARG* 3.1 55.4 + - - +
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Residues in contact with GLU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LYS* 5.1 8.8 + - - -
199A ASN* 5.0 6.6 - - - +
334B MET* 3.7 15.9 - - + +
338B PRO* 4.2 12.1 - - + +
370B TYR* 3.4 44.8 - - + +
371B PRO* 4.8 0.7 - - - +
372B LEU* 1.3 86.3 + - - +
374B ALA* 1.3 57.6 + - - +
376B ARG* 3.5 22.5 + - - +
377B MET* 3.0 31.0 + - - +
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Residues in contact with ALA 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B LEU* 3.4 9.6 - - + +
334B MET* 3.6 23.2 - - + +
361B LEU* 3.9 12.0 - - + +
364B GLU* 3.9 29.6 - - + +
370B TYR 3.1 14.2 + - - +
371B PRO 3.3 8.9 + - - +
373B GLU* 1.3 73.0 - - - +
375B VAL* 1.3 58.5 + - - +
377B MET 3.3 0.9 + - - -
378B GLN* 3.1 26.2 + - - +
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Residues in contact with VAL 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 3.7 12.1 - - + +
49B CYS* 3.7 22.7 - - - -
64B MET* 3.8 19.7 - - - +
67B SER* 3.4 31.4 - - - +
68B GLY 3.8 4.0 - - - +
69B MET* 3.7 17.7 - - - +
361B LEU* 4.0 6.3 - - + -
365B THR* 3.9 5.4 - - + -
371B PRO 3.2 16.2 + - - +
372B LEU* 3.8 6.1 - - - +
373B GLU 3.5 0.2 - - - -
374B ALA* 1.3 70.8 - - - +
376B ARG* 1.3 60.9 + - - +
377B MET 3.3 0.2 + - - -
378B GLN* 3.4 2.5 + - - -
379B HIS* 3.0 27.5 + - - +
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Residues in contact with ARG 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLU* 4.4 11.1 + - - -
67B SER* 3.2 38.9 + - - +
372B LEU* 3.1 42.8 + - - +
373B GLU* 3.7 22.8 + - - +
374B ALA 3.4 0.2 - - - -
375B VAL* 1.3 77.5 - - - +
377B MET* 1.3 57.3 + - - +
379B HIS* 3.5 6.9 + - + +
380B LEU* 3.0 41.0 + - + +
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Residues in contact with MET 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ALA* 4.9 3.8 - - + -
304A GLU* 4.7 20.6 - - - +
331B LEU* 3.8 11.9 - - + -
334B MET* 4.4 4.7 - - + -
339B ARG* 3.6 27.8 - - - +
340B PRO* 3.9 28.0 - - + -
373B GLU 3.0 16.9 + - - +
374B ALA 3.7 4.7 - - - +
375B VAL 3.2 0.2 - - - -
376B ARG* 1.3 74.5 - - - +
378B GLN* 1.3 59.9 + - - +
380B LEU* 3.3 13.2 + - + +
381B ILE* 2.9 60.8 + - + +
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Residues in contact with GLN 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 3.5 33.6 - - + +
330B MET* 3.7 23.4 - - - +
331B LEU* 3.8 17.9 - - + +
348B VAL* 4.1 12.7 - - + +
359B ILE* 3.7 29.7 - - + +
360B MET 2.8 27.1 + - - -
361B LEU* 3.5 20.4 - - + +
374B ALA 3.1 13.2 + - - +
375B VAL 3.4 1.3 + - - +
377B MET* 1.3 74.5 - - - +
379B HIS* 1.3 54.5 + - - +
381B ILE* 4.0 0.7 - - - +
382B ALA* 3.0 32.7 + - - +
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Residues in contact with HIS 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR 4.7 3.6 - - - -
43B ARG* 3.0 51.5 + - + +
47B ILE* 3.5 10.6 - - + +
67B SER 4.1 15.0 - - - +
68B GLY* 5.6 0.2 - - - -
375B VAL 3.0 17.4 + - - +
376B ARG* 3.7 9.9 - - + +
378B GLN* 1.3 71.7 - - - +
380B LEU* 1.3 76.6 + - + +
383B ARG* 3.3 54.4 + - - +
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU* 3.4 37.2 - - + +
376B ARG* 3.0 28.7 + - + +
377B MET* 3.3 16.5 + - + +
379B HIS* 1.3 84.5 - - + +
381B ILE* 1.3 61.4 + - - +
383B ARG* 3.8 29.8 + - - +
384B GLU* 3.3 26.7 + - - +
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Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ALA 5.4 1.1 - - - +
304A GLU* 3.7 31.6 - - + +
307A PHE* 4.6 1.1 - - + -
331B LEU* 4.7 3.4 - - + -
340B PRO* 5.2 0.9 - - + -
345B GLY* 3.5 40.8 - - - +
348B VAL* 3.8 20.6 - - + -
349B ALA* 3.6 24.2 - - + +
377B MET* 2.9 43.1 + - + +
380B LEU* 1.3 72.3 - - - +
382B ALA* 1.3 58.1 + - - +
384B GLU* 3.4 3.5 + - - +
385B ALA* 3.0 26.9 + - - +
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Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ARG* 4.0 13.2 - - + -
45B THR* 4.0 16.2 - - - +
348B VAL* 4.7 0.8 - - - +
352B VAL* 3.8 17.4 - - + +
359B ILE* 4.3 6.5 - - + -
378B GLN 3.0 19.8 + - - +
380B LEU 3.4 0.2 - - - -
381B ILE* 1.3 73.7 - - - +
383B ARG* 1.3 53.9 + - - +
385B ALA* 3.1 3.3 + - - +
386B GLU* 2.9 52.5 + - - +
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Residues in contact with ARG 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PRO* 3.8 27.7 - - + +
40B ILE 3.3 20.1 + - - +
41B THR* 3.6 34.8 + - - +
42B ALA 3.6 17.2 - - - +
43B ARG* 3.8 6.3 - - + +
379B HIS* 3.3 42.4 + - - +
380B LEU* 3.8 29.4 + - - +
382B ALA* 1.3 78.3 - - - +
384B GLU* 1.3 59.7 + - + +
386B GLU* 3.7 12.6 + - - +
387B ALA* 3.6 13.7 + - - +
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Residues in contact with GLU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLU* 3.5 23.7 - - + +
305A LYS* 2.7 41.6 + - - +
307A PHE* 3.7 19.2 - - + -
308A LEU* 3.7 17.5 - - + +
17B GLN* 4.8 2.8 + - - +
37B SER 4.6 2.9 - - - +
39B PRO* 3.8 24.0 - - + +
380B LEU* 3.3 17.2 + - - +
381B ILE 3.7 5.8 - - - +
382B ALA 3.3 0.4 - - - -
383B ARG* 1.3 75.4 - - - +
385B ALA* 1.3 65.1 + - - +
387B ALA* 3.3 6.8 + - - +
388B ALA* 3.3 19.4 + - - +
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Residues in contact with ALA 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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307A PHE* 3.6 19.3 - - + -
349B ALA* 3.5 29.4 - - - +
352B VAL* 3.9 13.5 - - + -
353B LEU* 3.4 12.7 - - + +
381B ILE 3.0 17.9 + - - +
382B ALA 3.1 3.6 + - - +
384B GLU* 1.3 77.8 - - - +
386B GLU* 1.3 60.5 + - - +
388B ALA 3.3 8.2 + - - +
389B ILE* 3.4 11.8 + - - +
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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
----------------------------------------------------------
42B ALA 4.1 3.3 - - - +
43B ARG* 3.6 8.0 - - - -
44B ASN* 2.8 45.8 + - + +
45B THR* 2.6 35.0 + - - +
352B VAL* 3.8 11.7 - - + -
382B ALA* 2.9 27.7 + - - +
383B ARG* 3.9 8.1 - - - +
384B GLU 3.3 0.2 - - - -
385B ALA* 1.3 74.4 - - - +
387B ALA* 1.3 61.8 + - - +
389B ILE* 3.6 21.6 - - + +
391B HIS* 3.6 15.6 + - - -
447B ARG* 5.7 0.3 - - - +
467B ARG* 4.4 9.0 - - - +
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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
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16B GLN* 3.5 36.9 - - + +
17B GLN* 3.4 23.2 - - + +
21B ALA* 6.1 0.5 - - - +
29B HIS* 5.1 1.2 - - - -
39B PRO* 4.6 9.9 - - + -
40B ILE* 6.5 0.9 - - + -
383B ARG 3.6 9.6 + - - +
384B GLU* 3.3 9.4 + - - +
385B ALA 3.3 0.2 - - - -
386B GLU* 1.3 79.4 - - - +
388B ALA* 1.3 60.4 + - - +
389B ILE 3.5 6.4 + - - +
391B HIS* 5.0 4.2 + - - -
447B ARG* 5.6 4.4 + - - +
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Residues in contact with ALA 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A PHE* 4.0 12.8 - - + -
308A LEU* 3.8 24.2 - - + -
17B GLN* 4.1 1.8 - - - +
29B HIS* 2.6 27.6 + - - -
33B LEU* 3.9 21.4 - - + +
353B LEU* 3.8 11.2 - - + +
384B GLU 3.3 14.1 + - - +
385B ALA 3.9 5.2 - - - +
386B GLU 3.3 0.8 - - - -
387B ALA* 1.3 74.5 - - - +
389B ILE* 1.3 57.4 + - - +
390B TYR 3.5 0.5 + - - -
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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
------------------------------------------------------------
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