Contacts of the helix formed by residues 345 - 364 (chain H) in PDB entry 2W3S
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 345 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269H ARG* 4.4 1.2 - - - +
272H PHE* 5.4 0.7 - - - -
307H VAL* 3.6 26.4 - - - +
311H ALA* 3.2 19.6 - - - +
343H GLY 3.4 0.2 - - - -
344H PHE* 1.3 73.2 - - - +
346H GLY* 1.3 62.7 + - - +
348H GLN* 3.2 24.7 + - - +
349H GLY 3.1 19.1 + - - -
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Residues in contact with GLY 346 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310H ARG* 4.0 1.6 - - - +
314H HIS* 3.8 29.3 - - - +
343H GLY 3.0 13.2 + - - -
344H PHE 3.1 3.2 + - - -
345H GLY* 1.3 73.6 - - - +
347H PRO* 1.3 67.7 - - - +
349H GLY 3.5 0.2 + - - -
350H ALA* 3.0 25.5 + - - +
455H PHE* 4.0 6.7 - - - -
734H LEU* 4.0 6.7 - - - -
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Residues in contact with PRO 347 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269H ARG* 4.1 3.8 - - - +
342H ARG 4.1 2.0 - - - +
343H GLY* 3.4 25.4 - - - +
344H PHE 4.1 0.2 - - - +
346H GLY* 1.3 89.7 - - - +
348H GLN* 1.3 64.4 + - - +
350H ALA* 3.2 1.2 + - - +
351H LEU* 2.8 36.7 + - - +
674H TRP* 3.6 29.2 - - + -
733H PHE* 3.6 28.7 - - + -
734H LEU* 3.9 19.0 - - + -
737H ILE* 4.1 2.9 - - + +
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Residues in contact with GLN 348 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H ILE* 4.4 9.0 - - + -
269H ARG* 3.1 30.8 + - - +
270H HIS* 2.9 27.3 + - - +
272H PHE* 3.5 40.3 - - + +
274H ILE* 3.6 11.2 - - - +
307H VAL* 4.7 2.0 - - - +
345H GLY* 3.2 30.2 + - - +
347H PRO* 1.3 82.8 - - - +
349H GLY* 1.3 64.3 + - - +
351H LEU* 3.1 9.7 + - - +
352H GLY 3.2 9.5 + - - -
674H TRP* 3.9 17.9 - - + -
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Residues in contact with GLY 349 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291H PHE* 5.3 0.7 - - - -
293H HIS* 4.2 14.3 + - - -
311H ALA* 3.7 28.4 - - - +
314H HIS 3.9 7.0 - - - -
315H ALA* 4.0 9.4 - - - +
345H GLY 3.1 9.3 + - - -
346H GLY 3.9 1.8 - - - -
348H GLN* 1.3 77.0 - - - +
350H ALA* 1.3 61.0 + - - +
352H GLY* 3.2 12.1 + - - -
353H MET 3.5 8.5 + - - -
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Residues in contact with ALA 350 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314H HIS* 3.6 18.8 + - + +
317H GLY* 4.7 11.8 - - - -
346H GLY 3.0 18.3 + - - +
347H PRO 3.7 2.9 - - - +
349H GLY* 1.3 72.8 - - - +
351H LEU* 1.3 59.8 + - - +
353H MET* 3.3 4.4 + - - +
354H GLU* 2.9 34.7 + - + +
454H LYS 6.1 0.4 - - - +
734H LEU* 3.9 20.0 - - + -
737H ILE* 4.5 5.4 - - + -
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Residues in contact with LEU 351 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166H PHE* 4.0 12.3 - - + -
168H ILE* 3.8 27.4 - - + -
347H PRO 2.8 17.2 + - - +
348H GLN 3.4 5.2 - - - +
350H ALA* 1.3 76.7 - - - +
352H GLY* 1.3 53.5 + - - +
354H GLU* 3.0 5.0 + - + -
355H ARG* 2.8 37.5 + - + +
674H TRP* 3.9 7.2 - - + -
675H LEU* 3.7 34.8 - - + -
737H ILE* 4.0 29.1 - - + +
740H PHE* 4.5 19.5 - - + -
741H LEU* 4.9 2.2 - - + -
759H ALA* 4.9 3.4 - - + -
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Residues in contact with GLY 352 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166H PHE* 4.4 6.5 - - - -
274H ILE* 3.8 31.2 - - - +
276H TYR* 4.6 3.5 - - - -
291H PHE* 3.6 9.8 - - - -
348H GLN 3.2 10.3 + - - -
349H GLY 3.2 6.6 + - - -
351H LEU* 1.3 74.4 - - - +
353H MET* 1.3 56.3 + - - +
355H ARG* 3.8 2.1 - - - +
356H ALA* 2.9 28.1 + - - +
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Residues in contact with MET 353 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278H ILE* 3.7 24.2 - - + -
286H LEU* 5.1 2.9 - - - -
289H ALA* 4.0 8.1 - - + -
291H PHE* 3.7 20.4 - - + -
315H ALA 3.2 37.5 - - - +
316H ASP* 3.8 11.7 - - - +
317H GLY* 4.0 6.7 - - - +
319H TYR* 3.6 30.1 - - + -
321H VAL* 3.7 30.3 - - + -
324H LEU* 4.1 1.3 - - + -
349H GLY 3.5 5.0 + - - +
350H ALA 3.3 8.0 + - - +
352H GLY* 1.3 71.8 - - - +
354H GLU* 1.3 59.7 + - - +
356H ALA* 3.5 0.6 - - - +
357H ILE* 2.8 32.1 + - - +
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Residues in contact with GLU 354 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317H GLY* 5.5 2.3 - - - -
318H SER* 4.9 2.1 + - - -
319H TYR* 2.7 27.4 + - - -
350H ALA* 2.9 23.9 + - + +
351H LEU* 3.0 7.4 + - + +
353H MET* 1.3 75.7 - - - +
355H ARG* 1.3 57.4 + - - +
357H ILE* 3.4 2.4 - - - +
358H GLU* 3.0 16.0 + - - +
372H ARG* 2.7 53.8 + - - +
451H SER* 4.5 3.4 - - - -
452H PRO* 3.0 26.6 - - - +
737H ILE* 4.0 31.6 - - + -
741H LEU* 4.6 3.4 - - + -
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Residues in contact with ARG 355 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165H CYS 3.7 5.9 + - - +
166H PHE* 3.3 71.5 - - + +
276H TYR* 3.2 29.4 + - + -
351H LEU* 2.8 14.7 + - + +
352H GLY 3.8 1.1 - - - +
354H GLU* 1.3 72.7 - - - +
356H ALA* 1.3 68.5 + - - +
358H GLU* 3.1 8.6 + - - +
359H HIS* 2.9 23.8 + - - +
740H PHE* 4.7 14.4 - - + -
741H LEU* 5.2 5.4 - - + -
744H HIS* 6.1 2.2 - - - -
754H TRP* 3.5 21.5 - - - -
756H ASP* 3.5 20.6 + - - -
757H LEU 3.0 35.2 + - - +
758H GLN* 4.1 1.0 - - - +
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Residues in contact with ALA 356 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276H TYR* 3.9 36.5 - - + -
278H ILE* 3.7 27.0 - - + +
291H PHE* 4.3 3.8 - - + -
352H GLY 2.9 19.2 + - - +
353H MET* 3.3 7.6 + - - +
355H ARG* 1.3 75.3 - - - +
357H ILE* 1.3 63.9 + - - +
359H HIS* 2.9 15.4 + - - +
360H LEU 3.0 10.6 + - - -
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Residues in contact with ILE 357 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278H ILE* 4.0 8.7 - - + +
286H LEU* 3.9 35.7 - - + -
319H TYR* 4.0 30.3 - - + +
353H MET* 2.8 16.7 + - - +
354H GLU* 3.4 28.9 - - - +
356H ALA* 1.3 73.2 - - - +
358H GLU* 1.3 59.9 + - - +
360H LEU* 3.4 4.2 + - + +
361H ALA* 2.9 30.3 + - - +
368H PRO* 6.0 0.4 - - + -
371H LEU* 3.9 19.5 - - + +
372H ARG* 3.5 27.1 - - + +
375H ASN* 4.6 3.4 - - + +
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Residues in contact with GLU 358 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354H GLU 3.0 19.4 + - - +
355H ARG* 3.1 10.3 + - - +
357H ILE* 1.3 77.2 - - - +
359H HIS* 1.3 62.3 + - - +
361H ALA* 3.3 5.5 + - - +
362H ARG* 3.0 47.3 + - + +
368H PRO* 3.4 11.3 - - - +
372H ARG* 2.9 31.2 + - - +
741H LEU* 4.1 17.9 - - + +
744H HIS* 3.1 42.9 + - + +
745H ASP* 5.1 0.5 - - - +
754H TRP* 4.8 3.4 - - + -
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Residues in contact with HIS 359 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162H ALA* 3.5 17.8 - - + +
163H GLU 3.2 19.2 + - - -
164H GLY* 4.7 1.6 - - - -
276H TYR* 2.6 35.4 - + + +
355H ARG 2.9 11.3 + - - +
356H ALA 3.2 9.9 - - - +
358H GLU* 1.3 76.3 - - - +
360H LEU* 1.3 57.3 + - - +
362H ARG* 3.1 2.4 + - - +
363H GLY* 2.9 34.0 + - - -
754H TRP* 3.4 53.6 + + + -
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Residues in contact with LEU 360 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160H HIS* 4.0 7.4 - - + -
161H LEU* 3.7 19.3 - - - +
162H ALA* 3.6 30.6 - - - +
278H ILE* 3.7 25.1 - - + +
280H ALA* 3.7 25.4 - - + +
286H LEU* 3.7 25.4 - - + -
356H ALA 3.0 5.4 + - - +
357H ILE* 3.6 9.2 - - + +
359H HIS* 1.3 74.8 - - - +
361H ALA* 1.3 63.4 + - - +
363H GLY* 4.1 0.8 - - - -
364H MET* 3.1 49.4 + - + +
371H LEU* 4.5 4.7 - - + -
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Residues in contact with ALA 361 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357H ILE 2.9 13.8 + - - +
358H GLU 3.4 9.6 - - - +
359H HIS 3.2 0.2 - - - -
360H LEU* 1.3 79.0 - - - +
362H ARG* 1.3 63.5 - - - +
364H MET* 3.2 5.1 + - - +
365H GLY 3.2 4.3 + - - -
366H ARG* 3.2 29.6 + - - +
367H ASP 4.5 0.4 - - - -
368H PRO* 3.5 36.3 - - + -
371H LEU* 3.7 16.5 - - + +
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Residues in contact with ARG 362 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358H GLU* 3.0 43.7 + - - +
359H HIS 3.6 3.1 - - - +
361H ALA* 1.3 71.2 - - - +
363H GLY* 1.3 54.5 + - - +
364H MET 2.8 3.4 + - - -
365H GLY* 2.6 30.1 + - - -
366H ARG 4.9 2.5 - - - +
368H PRO* 4.1 16.8 - - - +
744H HIS* 3.4 13.6 + - + +
745H ASP* 2.9 42.0 + - - +
748H ALA* 3.7 19.8 - - - +
754H TRP* 4.1 26.0 - - + -
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Residues in contact with GLY 363 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160H HIS* 4.8 3.5 + - - -
359H HIS* 2.9 22.7 + - - -
360H LEU* 4.1 1.6 - - - -
362H ARG* 1.3 71.7 - - - +
364H MET* 1.3 56.4 + - - +
365H GLY 3.5 0.2 - - - -
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Residues in contact with MET 364 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160H HIS* 3.3 50.8 - - + +
280H ALA* 4.2 9.0 - - + -
282H ALA 5.9 0.7 - - - +
284H GLY* 5.1 6.1 - - - -
360H LEU* 3.1 59.8 + - + +
361H ALA 3.7 4.3 - - - +
362H ARG 2.8 2.8 + - - -
363H GLY* 1.3 75.0 - - - +
365H GLY* 1.3 68.3 + - - +
366H ARG* 3.8 19.8 - - + +
371H LEU* 3.7 28.7 - - + -
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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