Contacts of the helix formed by residues 292 - 307 (chain C) in PDB entry 3NZG
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 292 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C TRP* 2.8 28.9 + - - -
104C MSE 3.5 17.7 - - - -
107C LEU* 4.2 2.0 - - - -
108C SER* 2.8 20.8 + - - -
111C ASP* 3.7 2.4 - - - +
290C ARG 3.5 0.2 + - - -
291C CYS* 1.3 74.8 - - - +
293C GLY* 1.3 68.1 + - - +
296C GLU* 3.5 13.1 + - - -
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Residues in contact with GLY 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C SER* 3.3 14.8 + - - -
111C ASP* 3.4 5.8 - - - -
112C MSE 5.0 3.4 - - - -
288C TYR* 3.1 25.9 + - - -
291C CYS* 4.3 0.8 - - - -
292C GLY* 1.3 78.5 - - - +
294C LEU* 1.3 65.7 + - - -
296C GLU* 4.0 0.2 - - - +
297C LEU* 3.1 29.4 + - - +
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Residues in contact with LEU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ASP* 2.8 4.0 + - - -
112C MSE 4.7 12.8 - - + +
115C TYR* 3.7 43.1 - - + -
126C ALA* 5.6 0.9 - - + -
130C LEU* 4.3 21.8 - - + +
288C TYR* 4.0 15.5 - - + +
293C GLY* 1.3 70.5 - - - -
295C THR* 1.3 66.6 + - - +
297C LEU* 3.3 4.6 + - - +
298C ARG* 3.0 23.7 + - - +
324C ALA* 3.8 37.2 - - + +
327C HIS* 5.7 0.9 - - + -
328C TYR* 3.9 23.1 - - + -
332C VAL* 5.7 0.9 - - - +
374C LEU* 4.7 9.6 - - + -
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Residues in contact with THR 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ILE* 3.3 9.2 - - - +
84C ASN* 4.0 14.7 + - + +
87C TRP* 3.7 15.9 - - + -
111C ASP* 2.7 29.0 + - - -
115C TYR* 2.5 24.4 + - - +
294C LEU* 1.3 79.5 - - - +
296C GLU* 1.3 62.4 + - - +
298C ARG* 3.3 13.0 + - - +
299C ARG* 3.4 42.4 + - + +
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Residues in contact with GLU 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C TRP* 3.6 14.1 - - + -
268C THR* 3.5 6.6 - - - -
269C ARG* 2.8 53.7 + - - +
291C CYS* 3.5 17.3 - - - +
292C GLY* 3.5 27.1 + - - +
293C GLY 3.4 2.2 + - - +
295C THR* 1.3 76.5 - - - +
297C LEU* 1.3 60.6 + - - +
299C ARG* 2.7 43.4 + - - +
300C ILE* 2.9 39.7 + - + +
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Residues in contact with LEU 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C SER* 3.5 27.1 - - - +
288C TYR* 3.3 53.2 - - + +
291C CYS* 3.8 14.4 - - - -
293C GLY 3.1 21.5 + - - +
294C LEU* 3.3 6.7 + - - +
296C GLU* 1.3 77.1 - - - +
298C ARG* 1.3 56.1 + - - +
300C ILE* 3.8 6.4 - - + +
301C THR* 2.7 38.0 + - - -
311C VAL* 4.5 9.4 - - + -
313C PRO* 3.9 15.3 - - + -
328C TYR* 3.9 13.9 - - + -
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Residues in contact with ARG 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C TYR* 5.8 1.1 - - - -
129C LEU 4.1 6.7 + - - -
130C LEU* 3.8 47.3 + - + +
131C GLY* 4.4 7.1 - - - +
294C LEU 3.0 13.0 + - - +
295C THR* 3.5 11.2 - - - +
296C GLU 3.1 0.2 - - - -
297C LEU* 1.3 75.4 - - - +
299C ARG* 1.3 67.5 + - + +
301C THR* 3.4 0.9 + - - -
302C GLU* 3.1 50.3 + - - +
332C VAL* 3.8 24.8 - - + +
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Residues in contact with ARG 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ASN* 2.9 31.4 - - - +
87C TRP* 3.3 36.7 - - - -
88C ASP* 4.2 10.5 + - - -
269C ARG* 3.7 34.2 - - - +
295C THR* 3.4 18.6 + - + +
296C GLU* 2.7 35.4 + - - +
298C ARG* 1.3 80.8 - - + +
300C ILE* 1.3 63.6 + - - +
302C GLU* 4.1 5.8 - - - +
303C MSE 3.1 24.1 + - - +
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Residues in contact with ILE 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C THR 4.0 6.3 - - - +
269C ARG* 3.7 28.7 - - + -
272C ALA* 3.9 19.7 - - + -
284C LEU* 3.7 26.2 - - + -
286C SER* 4.0 22.9 - - - +
291C CYS* 4.3 8.1 - - + -
296C GLU* 2.9 29.8 + - + +
297C LEU* 3.8 7.0 - - + +
299C ARG* 1.3 78.0 - - - +
301C THR* 1.3 58.7 + - - +
303C MSE 3.3 11.7 + - + +
304C ALA* 2.8 26.2 + - - +
311C VAL* 4.6 11.0 - - + -
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Residues in contact with THR 301 (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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297C LEU 2.7 27.1 + - - -
299C ARG 3.3 0.2 - - - -
300C ILE* 1.3 71.8 - - - +
302C GLU* 1.3 61.8 + - + +
304C ALA* 3.6 0.5 - - - +
305C THR* 2.8 35.5 + - - +
311C VAL* 3.8 15.0 - - + +
328C TYR* 2.7 26.4 + - - +
332C VAL* 3.2 35.4 - - + +
334C ASN* 3.8 26.0 - - + +
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Residues in contact with GLU 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C ARG* 3.1 47.5 + - + +
299C ARG* 4.2 5.1 - - - +
301C THR* 1.3 78.5 - - + +
303C MSE 1.3 60.6 + - - +
305C THR* 3.6 6.7 + - - -
306C ALA* 3.3 21.7 + - - +
332C VAL* 5.6 2.7 - - + -
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Residues in contact with MSE 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C ARG* 3.8 13.9 - - + +
272C ALA* 4.0 9.6 - - + -
273C GLU* 3.6 54.3 - - - +
276C ILE* 3.6 15.3 - - + -
299C ARG 3.1 15.5 + - - +
300C ILE* 3.6 13.7 - - + +
302C GLU* 1.3 75.8 - - - +
304C ALA* 1.3 64.3 + - - +
306C ALA* 3.3 5.5 + - - +
307C ASN* 2.8 41.7 + - - +
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Residues in contact with ALA 304 (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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276C ILE* 4.0 7.2 - - - -
284C LEU* 4.1 8.1 - - + -
300C ILE 2.8 18.5 + - - +
301C THR 3.6 2.7 - - - +
303C MSE 1.3 77.6 - - - +
305C THR* 1.3 57.5 + - - +
307C ASN* 3.1 8.4 + - - -
309C VAL* 2.7 55.7 + - + +
311C VAL* 3.4 22.7 - - + -
334C ASN* 4.2 0.2 - - - +
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Residues in contact with THR 305 (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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301C THR* 2.8 16.2 + - - +
302C GLU* 3.8 8.2 - - - -
304C ALA* 1.3 77.2 - - - +
306C ALA* 1.3 62.5 + - - +
308C ASN* 3.1 17.8 + - - +
309C VAL 4.2 0.9 - - - -
334C ASN* 2.9 34.2 + - + +
602C GOL 4.5 15.1 - - - +
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Residues in contact with ALA 306 (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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302C GLU 3.3 11.7 + - - +
303C MSE 3.3 9.4 + - - +
305C THR* 1.3 80.1 - - - +
307C ASN* 1.3 64.5 + - - +
308C ASN* 3.4 7.4 + - - -
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Residues in contact with ASN 307 (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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276C ILE* 3.8 29.4 - - + +
277C THR* 5.6 3.0 - - - +
303C MSE 2.8 38.4 + - - +
304C ALA 3.1 4.8 + - - +
305C THR 3.0 0.8 - - - -
306C ALA* 1.3 84.4 - - - +
308C ASN* 1.3 75.4 + - - +
309C VAL* 3.2 8.8 + - + +
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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