Contacts of the helix formed by residues 355 - 371 (chain B) in PDB entry 4R0C
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 GLN 355 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B ILE* 3.9 16.6 - - + +
56B THR 3.3 26.8 + - - +
57B ALA* 4.5 0.4 - - - -
58B HIS* 4.5 11.0 - - + -
351B PHE 3.6 0.2 + - - -
352B ASN* 2.9 35.4 + - - -
353B TYR* 3.0 15.3 + - - +
354B SER* 1.3 80.1 + - - +
356B LEU* 1.3 57.0 + - - +
357B GLY 3.3 3.1 - - - -
358B LEU* 3.2 29.2 + - - +
359B LEU* 2.8 33.2 + - + +
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Residues in contact with LEU 356 (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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32B LEU* 3.9 12.1 - - + -
35B LEU* 3.8 26.5 - - + -
36B THR* 3.9 10.3 - - + -
39B LEU* 3.6 35.9 - - + -
57B ALA* 4.1 17.5 - - + -
58B HIS 5.3 0.2 - - - +
351B PHE* 3.5 17.3 + - + -
354B SER* 3.1 30.5 - - - +
355B GLN* 1.3 76.4 - - - +
357B GLY* 1.3 56.3 + - - +
359B LEU* 3.6 9.9 - - + +
360B LEU* 2.8 36.4 + - - +
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Residues in contact with GLY 357 (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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193B ILE* 3.5 16.2 - - - +
351B PHE* 3.1 48.1 + - - -
352B ASN* 5.3 0.2 - - - -
356B LEU* 1.3 77.5 - - - +
358B LEU* 1.3 59.6 + - - +
360B LEU* 3.8 3.1 - - - +
361B ALA* 3.2 21.0 + - - +
405B PRO 5.1 0.3 - - - +
409B PRO* 4.7 2.8 - - - +
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Residues in contact with LEU 358 (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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48B HIS* 3.8 28.5 - - + +
55B ILE* 3.7 30.7 - - + -
193B ILE* 3.6 30.4 - - + +
194B ILE* 3.8 21.3 - - + -
352B ASN* 5.7 1.2 + - - +
355B GLN* 3.2 29.7 + - - +
357B GLY* 1.3 72.8 - - - +
359B LEU* 1.3 67.4 + - - +
360B LEU 3.2 0.2 - - - -
361B ALA* 3.2 3.2 + - - +
362B VAL* 3.1 34.4 + - + +
413B LEU* 5.6 0.7 - - + -
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Residues in contact with LEU 359 (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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39B LEU* 6.0 0.4 - - + -
44B VAL* 4.0 17.7 - - + -
45B THR 4.4 2.5 - - - -
46B ALA* 3.6 31.0 - - + +
55B ILE* 3.5 26.2 - - + +
57B ALA* 3.6 39.0 - - + +
355B GLN* 2.8 27.8 + - + +
356B LEU* 3.6 11.7 - - + +
358B LEU* 1.3 72.6 - - - +
360B LEU* 1.3 63.2 + - - +
362B VAL* 3.3 4.2 + - - +
363B LYS* 3.2 35.8 + - - +
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Residues in contact with LEU 360 (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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351B PHE* 4.0 21.8 - - + -
356B LEU 2.8 21.6 + - - +
357B GLY 3.8 4.3 - - - +
359B LEU* 1.3 73.5 - - - +
361B ALA* 1.3 59.0 + - - +
363B LYS* 3.5 5.9 + - + +
364B GLY* 2.9 31.5 + - - +
405B PRO 5.1 0.4 - - - +
406B VAL* 4.0 39.0 - - + +
410B MET* 5.1 4.6 - - - +
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Residues in contact with ALA 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ILE* 3.6 17.5 - - + -
357B GLY 3.2 8.0 + - - +
358B LEU* 3.2 10.4 + - + +
360B LEU* 1.3 80.1 - - - +
362B VAL* 1.3 58.3 + - - +
365B ALA* 3.0 32.7 + - - +
406B VAL 6.0 1.1 - - - -
409B PRO* 3.6 30.7 - - + -
410B MET* 3.5 15.6 - - - +
413B LEU* 3.7 4.2 - - + +
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Residues in contact with VAL 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ALA* 4.6 12.6 - - + -
47B THR 4.0 15.7 - - - +
49B PRO* 3.7 30.6 - - + +
55B ILE* 4.0 17.7 - - + -
358B LEU* 3.1 18.5 + - + +
359B LEU* 3.6 8.1 - - - +
361B ALA* 1.3 76.7 - - - +
363B LYS* 1.3 67.1 + - + +
365B ALA* 3.3 1.7 + - - +
366B ALA* 3.1 23.9 + - + +
413B LEU* 4.1 11.2 - - + -
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Residues in contact with LYS 363 (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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44B VAL* 4.6 17.8 - - - +
45B THR 4.7 5.3 + - - -
46B ALA* 4.6 20.0 - - - -
359B LEU* 3.2 22.4 + - - +
360B LEU* 4.0 6.7 - - + +
362B VAL* 1.3 80.0 - - + +
364B GLY* 1.3 62.9 + - - +
366B ALA* 3.2 9.6 + - - +
367B TRP* 3.1 22.1 + - - +
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Residues in contact with GLY 364 (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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360B LEU* 2.9 21.2 + - - +
361B ALA 3.9 0.9 - - - -
363B LYS* 1.3 77.0 - - - +
365B ALA* 1.3 56.1 + - - +
367B TRP* 3.4 5.5 + - - +
368B LEU* 3.1 35.0 + - - +
410B MET* 4.0 20.0 - - - -
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Residues in contact with ALA 365 (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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361B ALA 3.0 18.6 + - - +
362B VAL 3.9 2.9 - - - +
364B GLY* 1.3 73.9 - - - +
366B ALA* 1.3 58.5 + - - +
369B GLY* 2.8 31.4 + - - -
410B MET* 3.9 13.2 - - + +
413B LEU* 3.6 31.4 - - + -
414B LEU* 3.3 17.0 - - + +
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Residues in contact with ALA 366 (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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362B VAL* 3.1 14.2 + - + +
363B LYS* 3.4 13.0 - - - +
365B ALA* 1.3 76.5 - - - +
367B TRP* 1.3 63.0 + - - +
369B GLY* 4.1 0.4 - - - -
370B ALA* 3.3 20.6 + - - +
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Residues in contact with TRP 367 (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 LYS 3.1 12.2 + - - +
364B GLY* 3.7 9.4 - - - +
365B ALA 3.3 0.2 - - - -
366B ALA* 1.3 74.0 - - - +
368B LEU* 1.3 96.9 + - + +
370B ALA* 3.1 16.8 + - - +
371B LEU* 3.5 36.4 + - + +
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Residues in contact with LEU 368 (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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364B GLY 3.1 15.0 + - - +
367B TRP* 1.3 107.8 - - + +
369B GLY* 1.3 62.3 + - - +
371B LEU* 3.4 24.2 + - + +
372B THR 4.0 2.6 + - - -
373B VAL* 4.3 9.3 + - + +
378B LEU* 4.1 26.0 - - + +
410B MET* 3.4 30.7 - - + -
411B LEU* 4.8 4.0 - - + -
414B LEU* 3.7 25.4 - - + +
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Residues in contact with GLY 369 (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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365B ALA 2.8 23.6 + - - -
366B ALA 4.1 0.4 - - - -
367B TRP 3.1 0.2 - - - -
368B LEU* 1.3 77.7 - - - +
370B ALA* 1.3 61.9 + - - +
372B THR* 3.3 15.2 + - - +
414B LEU* 3.7 14.8 - - - +
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Residues in contact with ALA 370 (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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366B ALA 3.3 17.1 + - - +
367B TRP* 3.1 7.4 + - - +
369B GLY* 1.3 73.9 - - - +
371B LEU* 1.3 60.5 + - + +
372B THR* 3.1 19.9 + - - -
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Residues in contact with LEU 371 (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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367B TRP* 3.6 50.9 - - + +
368B LEU* 3.8 17.5 - - + +
369B GLY 3.3 1.0 - - - -
370B ALA* 1.3 75.8 - - + +
372B THR* 1.3 71.4 + - - +
373B VAL* 3.0 18.5 + - + +
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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
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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