Contacts of the helix formed by residues 349 - 368 (chain B) in PDB entry 4RUH
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 THR 349 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 3.5 4.0 - - - -
348B MET* 1.3 80.9 - - - +
350B PRO* 1.3 74.7 - - - +
351B GLU* 4.0 6.4 + - - +
352B VAL* 3.1 33.1 + - + +
353B VAL* 2.9 24.7 + - - +
383B LYS* 4.1 22.4 - - + +
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Residues in contact with PRO 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ILE 4.9 0.7 - - - +
214B CYS* 3.5 19.7 - - - -
344B LEU* 3.5 7.8 - - + -
349B THR* 1.3 87.4 - - - +
351B GLU* 1.3 66.3 + - + +
353B VAL* 3.3 0.5 + - - +
354B GLY* 2.7 34.1 + - - -
378B MET* 3.7 14.4 - - + +
381B GLY* 4.7 4.3 - - - +
382B GLY* 3.3 33.4 - - - +
383B LYS* 3.5 23.6 - - + -
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Residues in contact with GLU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B THR* 3.2 7.8 - - - +
350B PRO* 1.3 86.4 - - + +
352B VAL* 1.3 66.1 + - + +
354B GLY* 4.3 0.4 - - - -
355B GLU* 3.4 26.6 + - - +
378B MET* 3.6 18.9 - - - +
383B LYS* 6.1 3.4 - - - -
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Residues in contact with VAL 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B THR* 3.1 24.4 + - - +
351B GLU* 1.3 79.2 - - + +
353B VAL* 1.3 60.4 + - + +
355B GLU* 3.5 11.0 + - - +
356B GLN* 3.1 47.9 + - + +
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Residues in contact with VAL 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B CYS* 3.8 21.3 - - + -
216B PHE* 4.1 3.8 - - + -
262B ILE* 4.2 10.3 - - + -
342B ILE* 4.0 16.4 - - + -
344B LEU* 4.0 22.4 - - + -
348B MET* 4.3 14.8 - - + -
349B THR 2.9 20.2 + - - +
352B VAL* 1.3 76.8 - - + +
354B GLY* 1.3 64.2 + - - +
356B GLN* 3.9 13.1 - - - +
357B VAL* 3.0 40.5 + - + +
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Residues in contact with GLY 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B PHE* 3.6 19.5 - - - -
350B PRO 2.7 21.3 + - - -
351B GLU 4.3 1.3 - - - -
353B VAL* 1.3 72.7 - - - +
355B GLU* 1.3 54.9 + - - +
357B VAL* 3.9 0.3 - - - +
358B THR* 2.8 39.5 + - - +
378B MET* 4.2 11.7 - - - -
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Residues in contact with GLU 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B GLU* 3.4 17.2 + - - +
352B VAL* 3.6 15.4 - - - +
354B GLY* 1.3 75.1 - - - +
356B GLN* 1.3 58.9 + - + +
358B THR* 3.2 7.1 + - - -
359B SER* 2.9 38.2 + - - +
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Residues in contact with GLN 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ILE* 3.8 15.5 - - + +
260B PRO* 3.6 15.9 + - + +
261B GLY* 4.2 11.1 + - - +
262B ILE* 3.5 28.8 - - + +
352B VAL* 3.1 34.2 + - + +
353B VAL* 3.3 9.8 + - - +
355B GLU* 1.3 76.9 - - + +
357B VAL* 1.3 57.4 + - - +
359B SER* 4.0 4.2 - - - -
360B TYR* 3.1 29.6 + - - +
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Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B PHE* 3.5 31.4 - - + -
259B ILE* 3.6 20.0 - - + -
262B ILE* 4.3 4.0 - - + -
340B PHE* 3.8 20.0 - - + -
342B ILE* 3.6 30.3 - - + -
353B VAL* 3.0 23.6 + - + +
356B GLN* 1.3 73.3 - - - +
358B THR* 1.3 66.6 + - - +
360B TYR* 3.5 2.5 + - - +
361B LEU* 3.1 34.4 + - + +
376B VAL* 4.8 0.4 - - + -
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Residues in contact with THR 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B PHE* 4.3 9.9 - - + -
354B GLY* 2.8 26.5 + - - +
355B GLU* 3.2 11.6 + - - -
357B VAL* 1.3 77.1 - - - +
359B SER* 1.3 57.6 + - - +
362B THR* 3.0 35.7 + - - +
376B VAL* 3.7 42.6 - - + +
377B TYR* 4.8 3.1 - - - -
378B MET* 5.2 1.6 - - + +
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Residues in contact with SER 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLU* 2.9 23.7 + - - +
356B GLN* 4.0 4.7 - - - -
358B THR* 1.3 76.1 + - - +
360B TYR* 1.3 64.6 + - - +
362B THR* 3.0 17.9 + - - -
363B LYS* 3.3 21.0 + - - +
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Residues in contact with TYR 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B SER* 2.4 43.3 + - - -
250B LEU* 4.3 5.8 - - + -
258B LEU* 3.5 33.2 - - - +
259B ILE* 4.0 21.3 - - + -
260B PRO* 4.1 14.6 - - + -
356B GLN 3.1 19.0 + - - +
357B VAL 3.9 2.5 - - - +
359B SER* 1.3 78.3 - - - +
361B LEU* 1.3 69.1 + - + +
363B LYS* 3.5 19.6 + - + +
364B LYS* 3.0 63.5 + - + +
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ILE* 3.8 26.0 - - + -
246B LEU* 3.6 47.7 - - + +
249B SER* 4.1 5.8 - - - +
250B LEU* 3.8 16.2 - - + -
340B PHE* 4.2 11.7 - - + -
357B VAL* 3.1 23.6 + - + +
358B THR 4.2 1.8 - - - +
360B TYR* 1.3 78.3 - - + +
362B THR* 1.3 53.6 + - - +
364B LYS* 3.1 2.3 + - + +
365B PHE* 2.7 36.2 + - - +
374B PHE* 4.0 12.1 - - + -
376B VAL* 3.9 22.9 - - + -
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Residues in contact with THR 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B THR* 3.0 25.4 + - - +
359B SER* 3.0 14.0 + - - -
361B LEU* 1.3 76.6 - - - +
363B LYS* 1.3 58.1 + - - +
365B PHE* 3.6 3.6 + - - +
366B ALA* 3.0 24.9 + - - +
374B PHE* 3.5 28.5 - - + -
376B VAL* 4.1 7.2 - - + -
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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
----------------------------------------------------------
260B PRO* 6.1 3.0 - - - +
359B SER* 3.3 20.2 + - - +
360B TYR* 3.7 20.5 - - + +
361B LEU 3.2 0.6 - - - -
362B THR* 1.3 81.1 + - - +
364B LYS* 1.3 60.3 + - + +
366B ALA* 3.2 17.3 - - + +
367B GLU* 3.1 35.3 - - + +
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Residues in contact with LYS 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B LEU* 4.0 11.1 - - + +
249B SER* 4.0 21.7 - - - +
360B TYR* 3.0 65.6 + - + +
361B LEU* 3.1 7.8 + - - +
363B LYS* 1.3 78.5 - - + +
365B PHE* 1.3 62.8 + - - +
366B ALA 3.2 0.2 - - - -
367B GLU* 3.3 41.4 + - - +
368B LEU* 3.6 13.5 + - - +
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Residues in contact with PHE 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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220B VAL* 4.8 2.2 - - + -
242B ASP* 3.8 22.9 - - + -
246B LEU* 3.6 18.3 - - + +
361B LEU 2.7 19.9 + - - +
362B THR 3.9 5.2 - - - +
364B LYS* 1.3 70.7 - - - +
366B ALA* 1.3 70.5 + - - +
368B LEU* 3.0 30.3 + - + +
369B ARG 3.9 1.4 + - - -
370B SER* 3.8 29.9 + - - -
372B ASN* 3.3 28.0 - - + -
374B PHE* 3.7 47.6 - + + -
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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 THR 3.0 17.0 + - - +
363B LYS* 3.2 17.5 - - + +
365B PHE* 1.3 81.1 - - - +
367B GLU* 1.3 57.6 + - + +
369B ARG* 2.9 26.5 + - - +
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Residues in contact with GLU 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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253A LYS* 4.4 11.4 - - + +
363B LYS* 3.1 30.3 + - + +
364B LYS* 3.6 39.9 + - - +
365B PHE 3.2 0.8 - - - -
366B ALA* 1.3 76.8 - - + +
368B LEU* 1.3 61.9 + - + +
369B ARG* 3.1 5.0 + - - +
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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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253A LYS* 3.3 33.9 - - + +
254A ARG* 5.3 0.5 - - - -
237B HIS* 5.7 1.6 + - - -
242B ASP* 3.2 49.8 - - + +
245B LEU* 3.9 29.8 - - + -
246B LEU* 4.6 4.9 - - + -
364B LYS 3.7 11.9 - - - +
365B PHE* 3.0 27.2 + - + +
366B ALA 3.0 0.2 + - - -
367B GLU* 1.3 76.8 - - + +
369B ARG* 1.3 71.0 + - - +
370B SER* 3.2 11.6 + - - -
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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