Contacts of the helix formed by residues 285 - 304 (chain C) in PDB entry 8ATC
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 TYR 285 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C VAL* 3.3 36.3 + - + -
265C HIS* 3.9 31.1 - - + +
267C LEU* 4.2 14.9 - - + +
269C ARG* 4.0 7.9 - - - -
273C ILE* 3.3 33.6 - - + +
277C VAL* 3.3 21.5 - - + +
278C ASP* 2.8 32.4 + - - -
283C ALA* 3.8 18.1 - - + -
284C TRP* 1.3 74.3 - - - +
286C PHE* 1.3 92.9 + + - +
288C GLN* 3.4 9.7 - - - +
289C ALA* 2.9 27.4 + - - +
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Residues in contact with PHE 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ARG* 6.0 0.7 - - - -
267C LEU* 3.7 27.8 - - + -
269C ARG* 3.9 20.0 - - - -
278C ASP* 4.2 16.8 - - + -
284C TRP 3.4 0.4 - - - -
285C TYR* 1.3 96.8 - + - +
287C GLN* 1.3 72.6 + - - +
289C ALA* 3.3 8.8 + - + +
290C GLY* 3.1 18.9 + - - -
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Residues in contact with GLN 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C GLN* 5.1 2.0 - - - +
283C ALA 3.8 8.1 + - - +
284C TRP* 3.3 71.1 - - + +
286C PHE* 1.3 82.0 - - - +
288C GLN* 1.3 68.9 + - - +
290C GLY* 3.1 11.8 + - - -
291C ASN* 3.2 20.4 + - - -
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Residues in contact with GLN 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C GLN* 4.1 4.0 + - - +
140C LEU* 3.1 33.1 - - + +
141C ASP* 2.3 35.6 + - - -
144C THR* 3.9 22.4 - - + +
226C TYR* 3.9 8.9 - - - -
264C LEU* 3.2 22.7 - - + +
265C HIS 2.8 40.3 + - - +
266C PRO* 4.9 0.9 - - - -
284C TRP* 2.6 20.6 + - - +
285C TYR* 3.4 6.0 - - - +
287C GLN* 1.3 76.1 - - - +
289C ALA* 1.3 62.9 + - - +
291C ASN* 3.3 8.7 + - - +
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Residues in contact with ALA 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ARG* 4.9 18.4 - - + +
58C SER* 5.4 4.7 - - - -
140C LEU* 4.9 4.5 - - - +
267C LEU* 4.9 11.2 - - + -
285C TYR 2.9 13.2 + - - +
286C PHE* 3.4 14.6 - - + +
287C GLN 3.2 0.2 - - - -
288C GLN* 1.3 77.9 - - - +
290C GLY* 1.3 56.9 + - - +
292C GLY* 2.9 23.6 + - - -
293C ILE* 4.3 1.7 + - - +
296C ARG* 5.5 0.7 + - - -
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Residues in contact with GLY 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C PHE 3.1 11.1 + - - -
287C GLN* 3.1 5.1 + - - -
289C ALA* 1.3 77.9 - - - +
291C ASN* 1.3 61.3 + - - +
292C GLY 3.1 1.1 + - - -
293C ILE* 3.4 23.7 + - - +
294C PHE* 3.9 9.3 - - - -
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Residues in contact with ASN 291 (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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31C LYS* 4.0 10.3 - - - +
140C LEU* 4.3 5.2 - - + +
143C PHE* 3.7 22.7 - - + -
144C THR* 3.2 23.3 + - - +
147C GLN* 3.5 23.4 + - - +
287C GLN* 3.2 11.6 + - - +
288C GLN 3.5 10.3 - - - +
289C ALA 3.1 0.4 + - - -
290C GLY* 1.3 72.5 - - - +
292C GLY* 1.3 60.4 - - - +
293C ILE 2.9 6.7 - - - -
294C PHE* 3.1 38.6 + - - +
295C ALA* 3.2 15.4 + - - +
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Residues in contact with GLY 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C SER* 4.4 5.1 + - - -
62C SER* 4.4 0.2 + - - -
140C LEU* 3.6 27.8 - - - +
288C GLN 3.8 2.2 + - - -
289C ALA 2.9 15.3 + - - -
291C ASN* 1.3 77.9 - - - +
293C ILE* 1.3 57.6 + - - +
296C ARG* 2.9 46.6 + - - +
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Residues in contact with ILE 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C SER* 3.5 23.6 - - - +
61C THR* 3.3 42.2 - - + -
62C SER* 3.2 9.6 + - - +
65C ARG* 5.3 5.8 - - + +
289C ALA 4.3 1.1 + - - +
290C GLY* 3.4 17.7 + - - +
292C GLY* 1.3 80.9 - - - +
294C PHE* 1.3 70.3 + - + +
297C GLN* 3.0 45.2 + - - +
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Residues in contact with PHE 294 (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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27C ALA* 3.7 20.2 - - + +
30C LEU* 4.9 3.6 - - - +
31C LYS* 3.6 55.6 - - + -
143C PHE* 4.5 10.5 - - + -
290C GLY 3.9 10.1 - - - -
291C ASN* 3.1 35.5 + - - +
293C ILE* 1.3 89.5 - - + +
295C ALA* 1.3 58.6 + - - +
297C GLN* 3.4 12.1 + - - +
298C ALA* 2.9 29.8 + - - +
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Residues in contact with ALA 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C VAL* 4.2 7.3 - - + +
24C LEU* 5.5 0.7 - - + -
27C ALA* 4.2 10.5 - - + +
136C THR 5.3 0.4 - - - +
139C LEU* 4.1 15.2 - - + +
140C LEU* 3.8 32.3 - - + +
143C PHE* 4.7 8.0 - - + -
291C ASN 3.2 12.5 + - - +
292C GLY 4.5 0.2 - - - +
294C PHE* 1.3 77.8 - - - +
296C ARG* 1.3 61.1 + - + +
298C ALA* 3.6 2.3 + - - +
299C LEU* 3.1 27.5 + - - +
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Residues in contact with ARG 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ARG* 4.5 4.4 + - - +
55C THR* 3.7 29.2 + - - +
58C SER* 3.0 34.8 + - - -
59C PHE* 3.6 40.0 - - + +
62C SER* 4.0 12.6 - - - +
134C HIS* 4.0 3.4 - - - -
136C THR* 3.2 45.8 + - - +
137C GLN* 3.9 8.9 - - - +
140C LEU* 3.3 28.3 - - - +
289C ALA 5.5 0.6 + - - -
292C GLY* 2.9 22.4 + - - +
295C ALA* 1.3 77.4 - - + +
297C GLN* 1.3 62.9 + - - +
299C LEU* 3.8 5.2 - - - +
300C LEU* 3.4 28.1 + - - +
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Residues in contact with GLN 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 3.8 23.7 + - + +
34C PRO* 5.4 4.6 - - - +
35C GLN 5.2 3.6 - - - +
62C SER* 3.7 18.6 + - - -
65C ARG* 4.2 19.1 + - - +
66C LEU* 3.1 44.6 - - + +
293C ILE* 3.0 41.2 + - - +
294C PHE* 3.6 13.3 - - - +
296C ARG* 1.3 73.2 - - - +
298C ALA* 1.3 66.4 + - - +
299C LEU 3.1 0.3 + - - -
300C LEU* 3.3 2.3 + - - -
301C ALA* 3.1 23.9 + - - +
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Residues in contact with ALA 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C VAL* 3.4 15.5 - - + +
26C THR* 3.8 7.2 - - - -
27C ALA* 3.4 33.7 - - + +
30C LEU* 3.6 13.1 - - - +
294C PHE 2.9 18.1 + - - +
295C ALA 3.8 4.3 - - - +
297C GLN* 1.3 70.8 - - - +
299C LEU* 1.3 62.5 + - - +
301C ALA* 3.5 1.4 + - - +
302C LEU* 3.1 30.9 + - - +
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Residues in contact with LEU 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 5.0 2.7 - - + -
9C ILE* 4.0 29.2 - - + -
15C LEU* 6.0 0.2 - - + -
23C VAL* 4.4 13.9 - - + +
59C PHE* 4.2 7.6 - - + -
125C LEU* 3.5 28.9 - - + -
136C THR* 3.7 28.9 - - + -
139C LEU* 3.9 22.2 - - + -
295C ALA 3.1 18.0 + - - +
296C ARG* 3.8 5.2 - - - +
297C GLN 3.2 0.2 - - - -
298C ALA* 1.3 77.4 - - - +
300C LEU* 1.3 56.6 + - - +
302C LEU* 3.2 6.4 + - - +
303C VAL* 3.0 37.9 + - + +
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Residues in contact with LEU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 4.1 15.0 - - + -
44C ILE* 3.7 34.1 - - + -
59C PHE* 4.2 21.3 - - + -
62C SER* 4.4 6.5 - - - +
63C MET* 3.9 35.0 - - + +
66C LEU* 4.5 1.6 - - + -
101C ALA* 5.3 0.4 - - + -
103C VAL* 5.0 2.2 - - + -
125C LEU* 4.4 19.3 - - + -
296C ARG 3.4 17.2 + - - +
297C GLN 3.3 3.9 + - - +
299C LEU* 1.3 75.9 - - - +
301C ALA* 1.3 60.6 + - - +
303C VAL* 4.6 4.7 - - + +
304C LEU* 2.8 42.8 + - + +
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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
----------------------------------------------------------
26C THR* 5.0 0.9 - - + -
30C LEU* 4.3 11.4 - - + -
38C LEU* 3.7 28.7 - - + -
39C LEU* 4.6 8.1 - - - -
66C LEU* 4.4 4.6 - - + +
297C GLN 3.1 17.0 + - - +
298C ALA* 3.6 5.4 - - - +
300C LEU* 1.3 78.3 - - - +
302C LEU* 1.3 64.6 + - + +
305C ASN* 3.0 31.4 + - - +
307C ASP 5.4 0.3 - - - +
309C VAL* 4.6 9.4 - - + +
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Residues in contact with LEU 302 (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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2C ASN* 2.8 42.6 + - - +
4C LEU* 3.7 30.7 - - + -
5C TYR* 3.4 11.1 - - - -
22C LEU* 4.1 12.1 - - + -
23C VAL* 3.9 21.1 - - + -
26C THR* 3.7 32.8 - - + +
298C ALA 3.1 19.0 + - - +
299C LEU* 3.7 3.8 - - - +
301C ALA* 1.3 80.0 - - + +
303C VAL* 1.3 59.9 + - - +
305C ASN 3.5 3.1 - - - +
307C ASP 6.0 0.2 - - - +
308C LEU* 4.6 13.7 - - + -
309C VAL* 5.6 2.9 - - + +
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Residues in contact with VAL 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 3.5 20.6 - - + +
5C TYR* 4.0 0.7 - - - -
6C GLN* 3.0 30.2 + - - +
7C LYS 3.7 22.2 - - - +
9C ILE* 4.3 21.1 - - + -
123C PRO* 3.8 22.4 - - + -
125C LEU* 4.4 13.0 - - + -
299C LEU* 3.0 24.7 + - + +
300C LEU* 4.0 4.5 - - - +
302C LEU* 1.3 75.9 - - - +
304C LEU* 1.3 68.4 + - + +
305C ASN 3.6 0.2 - - - -
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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
----------------------------------------------------------
5C TYR* 4.0 8.9 + - - -
6C GLN* 4.9 8.5 - - - +
39C LEU* 3.7 19.2 - - + +
42C LYS* 4.0 33.0 + - + +
44C ILE* 3.2 35.0 - - + -
100C ASP* 3.5 29.2 - - + +
101C ALA* 4.1 12.1 - - + -
123C PRO* 4.5 4.0 - - + -
300C LEU* 2.8 25.4 + - + +
303C VAL* 1.3 94.7 - - + +
305C ASN* 1.3 63.5 + - - +
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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