Contacts of the helix formed by residues 303 - 317 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LEU* 3.4 33.0 - - + -
32C PHE* 6.1 1.3 - - + -
34C VAL* 4.1 10.3 - - + -
50C GLU* 2.6 28.3 + - - +
302C THR* 1.3 84.0 + - - +
304C GLY* 1.3 66.4 + - - +
305C ILE* 3.0 9.5 + - - +
306C THR* 3.1 13.2 + - - -
307C THR* 3.3 11.8 + - - -
328C TRP* 4.2 4.9 + - - -
331C VAL* 4.8 4.9 - - + -
334C ASP* 3.3 13.2 - - - +
335C ILE* 3.5 17.5 - - + +
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Residues in contact with GLY 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C THR* 1.3 73.4 - - - +
305C ILE* 1.3 63.4 + - - +
306C THR 3.3 0.2 - - - -
307C THR* 3.2 7.1 + - - -
308C CYS* 3.0 29.6 + - - -
328C TRP* 3.9 1.7 - - - +
334C ASP* 2.9 28.6 + - - -
336C VAL* 3.4 8.9 - - - +
341C LEU* 3.5 16.1 - - - +
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Residues in contact with ILE 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 3.5 31.6 - - + -
48C ILE* 4.0 18.6 - - + +
49C GLY* 3.9 23.3 - - - +
50C GLU* 3.7 11.0 - - + +
111C MSE 4.1 5.2 - - - -
303C THR* 3.0 8.9 + - - +
304C GLY* 1.3 76.5 - - - +
306C THR* 1.3 62.8 + - - +
308C CYS* 3.2 5.2 + - - +
309C ALA* 3.1 19.8 + - - +
335C ILE* 3.8 12.8 - - + -
336C VAL* 3.5 2.8 - - + +
356C LEU* 5.0 0.4 - - + -
358C PHE* 3.8 28.3 - - + -
360C LEU* 3.9 24.0 - - + -
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Residues in contact with THR 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLU* 2.6 31.5 + - - +
111C MSE 4.0 15.6 - - + +
272C PRO* 4.9 2.7 - - + -
299C SER* 4.5 1.8 - - - +
300C SER* 4.2 7.2 - - - +
302C THR* 3.2 25.2 + - - +
303C THR 3.1 3.1 + - - -
305C ILE* 1.3 75.3 - - - +
307C THR* 1.3 56.6 + - - +
309C ALA* 3.1 7.7 + - - +
310C GLU* 2.8 68.7 + - + +
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Residues in contact with THR 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C TYR* 4.7 5.7 + - + +
303C THR 3.3 5.3 + - - -
304C GLY* 3.2 13.1 + - - -
306C THR* 1.3 79.3 - - - +
308C CYS* 1.3 56.9 + - - +
310C GLU* 3.4 11.8 + - - +
311C HIS* 2.8 29.4 + - + +
326C ILE* 4.0 20.3 - - + +
327C MSE 4.7 1.9 + - - -
328C TRP* 3.3 44.7 + - + +
341C LEU* 4.0 16.8 - - + -
348C LEU* 4.9 6.3 - - + -
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Residues in contact with CYS 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C GLY 3.0 17.6 + - - -
305C ILE 3.6 7.4 - - - +
307C THR* 1.3 75.1 - - - +
309C ALA* 1.3 65.5 + - - +
311C HIS* 3.1 7.4 + - - +
312C HIS* 3.0 30.7 + - - -
336C VAL* 4.9 0.9 - - - -
339C PRO* 4.5 5.8 - - - -
341C LEU* 3.9 22.4 - - - -
351C PHE* 4.4 7.9 - - + -
356C LEU* 3.6 20.9 - - + +
358C PHE* 3.7 32.8 - - + -
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Residues in contact with ALA 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C MSE 3.7 42.0 - - + -
278C ILE* 4.2 9.7 - - + +
305C ILE 3.1 10.4 + - - +
306C THR 3.1 7.6 + - - +
308C CYS* 1.3 75.5 - - - +
310C GLU* 1.3 59.0 + - + +
312C HIS* 3.3 2.6 + - - +
313C ILE* 2.9 35.5 + - + +
356C LEU* 3.7 17.6 - - + +
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Residues in contact with GLU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C VAL* 5.5 0.5 - - - +
139C TYR* 5.0 4.9 - - + +
272C PRO* 3.9 23.8 - - + +
297C ILE* 3.2 30.3 - - + +
298C HIS 3.3 20.1 - - - +
299C SER* 2.9 28.5 + - - -
300C SER* 4.9 0.3 + - - -
306C THR* 2.8 44.0 + - + +
307C THR* 3.8 8.7 + - - +
309C ALA* 1.3 71.9 - - - +
311C HIS* 1.3 56.1 + - - +
313C ILE* 4.1 7.6 - - - -
314C GLY 2.9 23.9 + - - -
325C GLN 4.1 8.2 - - - +
326C ILE* 5.2 1.4 - - - -
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Residues in contact with HIS 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C VAL* 3.7 13.2 - - + +
139C TYR* 3.1 28.2 + - - +
307C THR* 2.8 18.8 + - + +
308C CYS* 3.1 9.8 + - - +
310C GLU* 1.3 76.5 - - - +
312C HIS* 1.3 66.3 + - - +
314C GLY* 3.1 3.5 + - - -
315C LEU* 3.0 43.9 + - + +
348C LEU* 3.3 30.8 + - + +
349C ASP 3.6 3.2 + - - -
350C ALA* 3.5 2.7 - - - -
351C PHE* 3.1 59.6 - + + +
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Residues in contact with HIS 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C PRO* 3.7 13.7 - - + -
125C VAL* 4.0 21.8 - - + -
126C HIS* 3.1 45.0 + + - +
129C LEU* 4.7 2.3 - - - +
278C ILE* 5.8 0.2 - - + -
308C CYS* 3.0 26.8 + - - +
309C ALA 3.9 3.1 - - - +
311C HIS* 1.3 78.2 - - - +
313C ILE* 1.3 66.3 + - + +
315C LEU* 3.4 5.0 + - - +
316C ALA* 3.2 23.2 + - - +
351C PHE* 3.6 28.5 - + + +
353C LYS 4.9 0.9 - - - -
355C GLY 3.9 2.2 - - - -
356C LEU* 2.9 42.6 + - + -
357C GLY* 4.3 0.6 + - - -
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Residues in contact with ILE 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C LEU* 5.3 0.4 - - - -
272C PRO* 4.0 21.3 - - + -
278C ILE* 3.6 47.6 - - + -
281C MSE 3.9 27.4 - - + -
282C MSE 3.4 22.8 - - + +
297C ILE* 4.2 6.5 - - + -
309C ALA 2.9 24.6 + - - +
310C GLU* 3.5 5.6 - - - +
312C HIS* 1.3 75.8 - - - +
314C GLY* 1.3 64.2 + - - +
316C ALA* 3.3 2.3 + - - -
317C ILE* 3.2 35.5 + - + +
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Residues in contact with GLY 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C ARG* 2.8 21.7 + - - -
137C VAL* 4.3 5.8 - - - -
297C ILE* 3.6 12.8 - - - -
310C GLU 2.9 11.3 + - - -
311C HIS 3.1 4.7 + - - -
313C ILE* 1.3 74.4 - - - +
315C LEU* 1.3 62.4 + - - +
317C ILE 3.2 6.6 + - - +
320C LEU* 3.2 27.9 - - - +
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Residues in contact with LEU 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C HIS* 3.4 33.0 - - + +
132C ALA* 3.4 10.9 - - + -
133C HIS* 2.8 29.4 + - - -
134C ARG* 3.5 36.2 + - + +
136C ALA 4.5 0.7 - - - -
137C VAL* 3.6 22.0 - - + +
311C HIS* 3.0 40.9 + - + +
312C HIS* 3.9 7.0 - - - +
313C ILE 3.4 0.4 - - - -
314C GLY* 1.3 76.3 - - - +
316C ALA* 1.3 60.1 - - - +
317C ILE 3.5 0.3 + - - -
350C ALA* 3.7 23.8 - - + -
351C PHE 4.3 0.4 - - - +
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Residues in contact with ALA 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C HIS* 4.4 4.7 - - + +
129C LEU* 3.8 29.5 - - + +
131C GLY 3.8 12.7 - - - +
133C HIS* 3.1 18.3 + - - -
282C MSE 3.7 22.1 - - - +
312C HIS 3.2 14.9 + - - +
313C ILE 3.7 4.3 - - - +
315C LEU* 1.3 78.9 - - - +
317C ILE* 1.3 58.6 + - - +
318C PRO* 3.5 4.5 - - - +
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Residues in contact with ILE 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C HIS* 3.9 0.9 - - - -
134C ARG* 2.8 28.1 + - - -
281C MSE 4.0 16.8 - - + +
282C MSE 3.5 16.4 - - + -
285C ALA* 3.9 23.1 - - + -
295C ILE* 4.2 5.6 - - + -
297C ILE* 5.3 0.2 - - + -
313C ILE* 3.2 34.6 + - + +
314C GLY 3.2 5.4 + - - +
316C ALA* 1.3 76.2 - - - +
318C PRO* 1.3 68.5 - - + +
319C ASN* 3.4 36.1 - - - +
320C LEU* 3.7 19.1 - - + +
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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