Contacts of the helix formed by residues 303 - 317 (chain H) in PDB entry 2PGW
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 303 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H LEU* 3.4 32.8 - - + -
32H PHE* 6.4 0.2 - - + -
34H VAL* 3.9 12.3 - - + -
50H GLU* 2.6 26.7 + - - +
302H THR* 1.3 83.0 + - - +
304H GLY* 1.3 65.3 + - - +
305H ILE* 3.0 14.0 + - - +
306H THR* 3.2 12.1 + - - -
307H THR* 3.4 12.0 + - - -
328H TRP* 4.2 4.7 + - - +
331H VAL* 4.8 4.7 - - + -
334H ASP* 3.4 12.3 - - - +
335H ILE* 3.6 15.8 - - + +
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Residues in contact with GLY 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303H THR* 1.3 74.1 - - - +
305H ILE* 1.3 63.3 + - - +
306H THR 3.4 0.2 - - - -
307H THR* 3.3 8.8 - - - -
308H CYS* 3.0 28.8 + - - -
328H TRP* 3.9 2.0 - - - +
334H ASP* 2.8 28.7 + - - -
336H VAL* 3.5 8.9 - - - +
341H LEU* 3.5 14.7 - - - +
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Residues in contact with ILE 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H LEU* 3.4 32.5 - - + -
48H ILE* 3.9 13.5 - - + +
49H GLY* 4.0 19.1 - - - -
50H GLU* 3.6 17.0 - - + +
111H MSE 4.0 5.8 - - - -
303H THR* 3.0 7.9 - - - +
304H GLY* 1.3 77.6 - - - +
306H THR* 1.3 64.7 + - - +
308H CYS* 3.1 13.9 + - - +
309H ALA* 3.2 11.6 + - - +
335H ILE* 3.7 14.6 - - + -
336H VAL* 3.7 4.2 - - + +
356H LEU* 5.0 0.4 - - + -
358H PHE* 4.0 24.1 - - + -
360H LEU* 3.8 26.2 - - + -
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Residues in contact with THR 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H GLU* 2.6 28.4 + - - +
111H MSE 4.2 12.3 - - + +
272H PRO* 4.7 8.3 - - + -
299H SER* 4.5 2.7 - - - +
300H SER* 4.1 6.5 - - - +
302H THR* 3.2 27.4 + - - +
303H THR 3.2 3.4 + - - -
305H ILE* 1.3 78.8 - - - +
307H THR* 1.3 58.9 + - - +
309H ALA* 3.1 6.9 + - - +
310H GLU* 2.8 66.3 + - + +
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Residues in contact with THR 307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H TYR* 4.7 5.2 + - + +
303H THR 3.4 11.3 + - - -
304H GLY* 3.3 12.7 + - - -
305H ILE 3.1 0.4 - - - -
306H THR* 1.3 79.0 - - - +
308H CYS* 1.3 57.9 + - - +
310H GLU* 3.4 10.3 + - - +
311H HIS* 2.9 27.8 + - + +
326H ILE* 3.9 30.6 - - + +
327H MSE 4.8 1.7 + - - -
328H TRP* 3.5 27.0 + - + +
341H LEU* 4.2 17.3 - - + -
348H LEU* 4.9 6.3 - - + -
351H PHE* 5.5 0.4 - - + -
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Residues in contact with CYS 308 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304H GLY 3.0 18.3 + - - -
305H ILE 3.1 7.1 + - - +
307H THR* 1.3 73.2 - - - +
309H ALA* 1.3 66.3 + - - +
311H HIS* 3.2 6.4 + - - +
312H HIS* 3.0 31.5 + - - -
336H VAL* 4.9 0.9 - - - -
339H PRO* 4.6 3.4 - - - -
341H LEU* 3.8 22.9 - - - -
351H PHE* 4.4 9.4 - - + -
356H LEU* 3.4 22.2 - - + +
358H PHE* 3.8 33.9 - - + -
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Residues in contact with ALA 309 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H MSE 3.9 37.7 - - + -
272H PRO* 5.3 0.7 - - + -
278H ILE* 4.6 8.2 - - + +
305H ILE 3.2 6.4 + - - +
306H THR 3.1 8.2 + - - +
308H CYS* 1.3 77.2 - - - +
310H GLU* 1.3 58.1 + - + +
312H HIS* 3.2 4.5 + - - +
313H ILE* 2.9 36.4 + - + +
356H LEU* 3.8 21.7 - - + +
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Residues in contact with GLU 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H VAL* 5.5 1.2 - - - +
139H TYR* 5.0 5.2 - - + +
272H PRO* 3.6 25.3 - - + +
297H ILE* 3.8 25.9 - - + +
298H HIS 3.4 6.2 - - - +
299H SER* 3.0 38.1 + - - -
300H SER* 4.7 0.7 + - - -
306H THR* 2.8 45.5 + - + +
307H THR* 3.9 7.8 - - - +
309H ALA* 1.3 71.9 - - - +
311H HIS* 1.3 56.7 + - - +
313H ILE* 3.5 9.8 - - - +
314H GLY* 2.9 25.6 + - - -
325H GLN 4.3 8.9 - - - +
326H ILE* 5.2 1.4 - - - -
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Residues in contact with HIS 311 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H VAL* 3.6 15.4 - - + +
139H TYR* 3.0 27.8 + - - +
307H THR* 2.9 18.4 + - + +
308H CYS* 3.4 9.2 - - - +
309H ALA 3.1 0.2 - - - -
310H GLU* 1.3 77.6 - - - +
312H HIS* 1.3 61.6 + - - +
314H GLY* 3.1 3.1 + - - -
315H LEU* 3.0 47.2 + - + +
348H LEU* 3.4 31.7 + - + +
349H ASP 3.6 3.6 + - - -
350H ALA* 3.6 1.7 - - - -
351H PHE* 3.1 57.4 - + + +
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Residues in contact with HIS 312 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H PRO* 3.8 13.2 - - + -
125H VAL* 4.0 21.3 - - + -
126H HIS* 3.0 50.1 + + - +
129H LEU* 4.7 2.7 - - - +
278H ILE* 5.9 0.2 - - + -
308H CYS* 3.0 28.2 + - - +
309H ALA 3.7 3.4 - - - +
311H HIS* 1.3 76.8 - - - +
313H ILE* 1.3 66.0 + - + +
315H LEU* 3.4 2.4 + - - +
316H ALA* 3.2 20.4 + - - +
351H PHE* 3.7 27.3 - + + +
353H LYS 4.8 0.9 - - - -
355H GLY 3.8 4.5 - - - -
356H LEU* 2.9 42.2 + - + -
357H GLY* 4.7 0.2 - - - -
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Residues in contact with ILE 313 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H PRO* 4.1 20.0 - - + -
278H ILE* 3.9 41.1 - - + -
281H MSE 3.9 28.0 - - + -
282H MSE 3.3 22.8 - - + +
297H ILE* 3.9 5.6 - - + -
309H ALA* 2.9 24.8 + - + +
310H GLU* 3.5 11.7 - - - +
312H HIS* 1.3 76.4 - - - +
314H GLY* 1.3 65.3 + - - +
316H ALA* 3.3 2.6 + - - -
317H ILE* 3.2 35.4 + - + +
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Residues in contact with GLY 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H ARG* 2.8 22.5 + - - -
137H VAL* 4.3 7.2 - - - -
297H ILE* 4.8 3.1 - - - -
310H GLU 2.9 14.7 + - - -
311H HIS 3.1 4.2 + - - -
313H ILE* 1.3 79.7 - - - +
315H LEU* 1.3 58.7 + - - +
317H ILE* 3.3 7.4 + - - +
320H LEU* 3.2 31.9 - - - +
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Residues in contact with LEU 315 (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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126H HIS* 3.4 35.7 - - + +
132H ALA* 3.3 8.1 - - + -
133H HIS* 2.7 32.6 + - - +
134H ARG* 3.3 34.9 + - + +
136H ALA 4.6 0.7 - - - -
137H VAL* 3.7 21.3 - - + +
311H HIS* 3.0 41.4 + - + +
312H HIS* 3.9 5.2 - - - +
313H ILE 3.3 0.2 - - - -
314H GLY* 1.3 75.9 - - - +
316H ALA* 1.3 59.3 + - - +
317H ILE 3.6 0.2 + - - -
350H ALA* 3.6 23.1 - - + -
351H PHE 4.3 0.2 - - - +
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Residues in contact with ALA 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H HIS* 4.3 5.4 - - + +
129H LEU* 3.8 30.5 - - + +
131H GLY 3.6 13.4 - - - +
133H HIS* 3.3 15.3 + - - -
282H MSE 3.7 24.6 - - - +
312H HIS 3.2 14.2 + - - +
313H ILE 3.8 1.1 - - - +
314H GLY 3.2 0.4 - - - -
315H LEU* 1.3 79.0 - - - +
317H ILE* 1.3 57.8 + - - +
318H PRO* 3.6 5.2 - - - +
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Residues in contact with ILE 317 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H HIS* 4.0 1.1 - - - -
134H ARG* 2.8 28.9 + - - -
281H MSE 4.1 15.5 - - + +
282H MSE 3.6 15.7 - - + -
285H ALA* 3.8 24.0 - - + -
295H ILE* 4.3 5.6 - - + -
313H ILE* 3.2 34.6 + - + +
314H GLY 3.3 4.8 + - - +
316H ALA* 1.3 78.1 - - - +
318H PRO* 1.3 63.4 - - + +
319H ASN* 3.3 39.0 - - - +
320H LEU* 3.7 18.6 - - + +
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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