Contacts of the helix formed by residues 293 - 309 (chain C) in PDB entry 1RZR
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 PRO 293 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C ILE* 4.3 8.7 - - + -
291C VAL* 4.0 15.2 - - + +
292C GLN* 1.3 83.6 - - + +
294C MSE 1.3 69.5 + - + +
295C TYR* 3.0 3.8 - - + -
296C ASP* 2.8 41.1 + - + +
297C ILE* 3.1 12.3 + - + +
321C LEU* 4.1 14.1 - - + -
322C PRO 4.1 17.7 - - - +
15T HIS* 5.0 10.5 - - + +
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Residues in contact with MSE 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C PHE* 3.0 53.2 - - + +
77C GLU* 3.8 28.0 - - + +
78C LEU* 3.0 40.5 - - + +
275C ASP* 4.3 11.0 - - - +
276C ASN 4.8 8.1 - - - +
277C THR* 4.4 15.3 - - - +
292C GLN* 2.9 29.5 + - + +
293C PRO* 1.3 73.5 - - + +
295C TYR* 1.3 61.3 + - + +
297C ILE* 3.9 9.9 - - - -
298C GLY 3.2 2.3 + - - -
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Residues in contact with TYR 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C GLU* 4.1 21.4 + - + +
80C ARG* 4.1 9.2 - - + -
81C GLY* 3.6 22.3 - - - -
84C ASP* 2.9 32.7 + - + +
293C PRO 3.0 1.7 - - - -
294C MSE 1.3 79.4 - - + +
296C ASP* 1.3 67.8 + - - +
299C ALA* 2.8 33.6 + - + +
16T ALA* 3.2 41.5 - - + +
17T ARG* 3.4 24.9 - - + -
20T THR* 3.1 28.4 + - + +
51T MET* 4.9 0.2 - - - -
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Residues in contact with ASP 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C PRO* 2.8 19.6 + - + +
295C TYR* 1.3 76.0 - - - +
297C ILE* 1.3 57.5 + - - +
300C VAL* 2.5 40.7 + - - +
321C LEU* 3.6 17.7 - - + -
15T HIS* 2.7 33.4 + - - -
16T ALA 3.2 22.0 + - - -
51T MET* 2.9 37.6 - - + +
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Residues in contact with ILE 297 (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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78C LEU* 3.8 3.6 - - + -
145C ALA* 3.7 9.6 - - + -
146C ALA* 3.3 43.3 - - + +
157C VAL* 3.7 12.4 - - + +
158C THR* 4.3 10.1 - - - -
159C ILE* 4.1 21.5 - - + -
161C TYR* 5.8 0.7 - - - +
292C GLN* 5.2 5.8 - - + +
293C PRO* 3.1 18.0 + - + +
294C MSE 3.6 13.7 - - - +
296C ASP* 1.3 76.1 - - - +
298C GLY* 1.3 53.6 + - - +
300C VAL* 3.5 1.0 - - - +
301C ALA* 2.5 38.7 + - - +
321C LEU* 3.5 24.5 - - + -
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Residues in contact with GLY 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LEU* 3.0 29.6 - - - +
81C GLY 3.7 6.5 - - - -
82C ILE* 3.5 20.9 - - - +
294C MSE 3.2 2.6 + - - -
295C TYR 4.0 0.4 - - - -
297C ILE* 1.3 75.7 - - - +
299C ALA* 1.3 69.7 + - - +
301C ALA* 4.1 3.8 - - - -
302C MSE 3.0 18.9 + - - +
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Residues in contact with ALA 299 (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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81C GLY 3.2 13.2 + - - -
85C ILE* 3.6 25.2 - - + +
295C TYR* 2.8 40.2 + - + +
298C GLY* 1.3 76.1 - - - +
300C VAL* 1.3 57.2 + - - +
302C MSE 3.4 0.7 + - - +
303C ARG* 3.0 23.4 + - - +
47T ILE* 4.2 2.9 - - + -
51T MET* 3.5 22.7 - - + -
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Residues in contact with VAL 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C VAL* 3.7 21.5 - - + -
296C ASP 2.5 30.6 + - - +
297C ILE 3.5 2.0 - - - +
299C ALA* 1.3 68.6 - - - +
301C ALA* 1.3 71.8 + - - +
303C ARG* 2.7 19.4 + - - +
304C LEU* 2.8 10.6 + - - +
319C VAL* 4.3 5.4 - - + -
321C LEU* 4.1 19.5 - - + -
47T ILE 4.2 5.8 - - - +
48T MET* 3.3 38.6 - - + +
51T MET* 3.3 22.9 - - + -
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Residues in contact with ALA 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ILE* 4.5 11.4 - - + -
143C VAL* 4.1 12.0 - - + +
145C ALA* 3.5 28.3 - - + -
157C VAL* 3.6 18.6 - - + +
297C ILE 2.5 21.6 + - - +
298C GLY* 3.6 5.6 - - - +
300C VAL* 1.3 76.1 - - - +
302C MSE 1.3 63.0 + - - +
304C LEU* 3.1 10.9 + - - +
305C LEU* 3.1 12.8 + - - +
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Residues in contact with MSE 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C VAL* 4.0 30.5 - - + -
82C ILE* 3.0 27.1 - - + +
85C ILE* 3.4 20.6 - - + -
86C ALA* 3.5 29.8 - - + +
91C TYR* 5.3 4.0 - - - -
93C ILE* 4.5 1.6 - - + -
121C ILE* 3.0 39.8 - - + +
298C GLY 3.0 16.7 + - - +
299C ALA 3.7 3.1 - - - +
301C ALA* 1.3 75.3 - - - +
303C ARG* 1.3 54.1 + - - +
305C LEU* 3.3 6.2 + - - +
306C THR* 2.5 33.2 + - + +
309C MSE 4.5 7.6 - - - -
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Residues in contact with ARG 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ILE* 3.9 4.7 - - + +
89C TYR* 2.8 47.4 + - - -
299C ALA 3.0 13.2 + - - +
300C VAL* 2.7 16.1 + - - +
302C MSE 1.3 67.1 - - - +
304C LEU* 1.3 58.0 + - - +
306C THR* 2.3 41.2 + - - -
307C LYS* 2.8 37.8 + - - +
312C GLU* 4.4 8.5 + - - -
45T LYS 5.7 0.4 + - - -
46T SEP 2.6 51.1 + - - +
47T ILE* 4.2 17.4 - - + +
48T MET* 3.7 9.0 - - + -
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Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C VAL* 4.9 5.6 - - + -
155C PRO* 4.4 4.5 - - + -
156C SER 4.4 0.7 - - - +
157C VAL* 4.4 13.7 - - + -
300C VAL 2.8 12.7 + - - +
301C ALA* 3.4 10.3 - - - +
303C ARG* 1.3 71.1 - - - +
305C LEU* 1.3 65.7 + - - +
307C LYS* 2.8 26.2 + - + +
308C TYR* 3.2 39.3 + - + +
314C VAL* 4.3 18.4 - - + +
315C ASP 5.4 0.2 - - - +
316C SER 5.1 3.6 - - - +
317C SER* 4.2 19.3 - - - +
319C VAL* 4.2 21.8 - - + -
48T MET* 4.1 23.9 - - + -
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Residues in contact with LEU 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C VAL* 3.7 14.4 - - + -
119C GLY* 4.2 0.4 - - - -
120C ILE 3.7 18.6 - - - +
121C ILE* 3.2 31.6 - - + -
141C PRO* 3.5 41.7 - - + +
142C VAL 4.0 0.2 - - - +
143C VAL* 3.4 24.3 - - + +
301C ALA 3.1 4.5 + - - +
302C MSE 3.3 11.2 - - - +
304C LEU* 1.3 79.6 - - - +
306C THR* 1.3 56.1 + - - +
308C TYR* 4.3 4.3 - - + -
309C MSE 2.9 56.2 + - + +
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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
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89C TYR* 3.5 45.9 - - + -
91C TYR* 4.2 14.6 + - + -
302C MSE 2.5 21.9 + - + +
303C ARG* 2.3 38.8 + - - -
305C LEU* 1.3 73.2 - - - +
307C LYS* 1.3 61.8 + - - +
309C MSE 3.6 9.7 + - + +
310C ASN* 3.2 22.9 + - - +
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Residues in contact with LYS 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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303C ARG* 2.8 31.4 - - - +
304C LEU* 2.8 11.5 + - + +
306C THR* 1.3 73.6 - - - +
308C TYR* 1.3 58.5 + - + +
310C ASN 2.5 27.5 + - - -
311C LYS 2.8 9.7 + - - -
312C GLU* 3.0 43.1 + - + +
314C VAL* 3.1 46.3 - - + +
46T SEP 3.0 34.8 + - - -
48T MET* 3.3 19.1 - - - +
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Residues in contact with TYR 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C PRO* 3.6 31.1 - - + +
142C VAL 5.4 1.6 - - - -
143C VAL* 4.9 3.8 - - + -
155C PRO* 3.1 23.6 - - + +
304C LEU* 3.2 40.3 + - + -
305C LEU* 3.9 9.9 - - + +
307C LYS* 1.3 78.7 - - + +
309C MSE 1.3 54.7 + - - +
311C LYS* 2.7 27.5 + - - +
312C GLU 4.6 9.9 - - - -
313C THR* 6.2 0.7 - - - -
314C VAL 4.3 13.4 + - - -
315C ASP* 5.6 0.6 - - - -
317C SER* 3.0 35.3 - - - -
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Residues in contact with MSE 309 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C LYS* 3.6 22.7 + - - +
63C VAL* 3.6 24.2 - - + -
91C TYR* 3.5 33.2 + - + +
118C ASP* 3.0 39.3 - - - +
119C GLY* 3.9 1.3 - - - -
141C PRO* 4.0 14.6 - - + -
302C MSE 4.5 4.7 - - - -
305C LEU* 2.9 55.4 + - + +
306C THR* 3.8 9.4 - - - +
308C TYR* 1.3 77.9 - - - +
310C ASN* 1.3 56.8 + - - +
311C LYS* 3.3 9.2 + - - +
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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