Contacts of the helix formed by residues 274 - 294 (chain C) in PDB entry 1YAA
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 ALA 274 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C GLN* 1.3 70.1 - - - +
275C GLN* 1.3 58.0 + - - +
276C ASN* 3.1 9.3 + - - +
277C LYS* 3.8 13.0 + - - +
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Residues in contact with GLN 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C GLN* 4.2 5.6 - - - +
274C ALA* 1.3 75.0 - - - +
276C ASN* 1.3 60.1 + - - +
277C LYS* 3.1 3.6 - - - -
278C THR* 2.9 46.8 - - + +
279C ILE* 3.0 30.7 + - + -
7D ASN* 3.9 29.2 + - + +
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Residues in contact with ASN 276 (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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98C ASP 6.1 0.7 - - - +
99C ARG* 3.9 16.8 - - + +
270C LEU* 3.7 27.5 - - + +
271C THR* 2.8 27.7 + - - +
273C GLN* 3.3 24.1 + - - +
274C ALA 3.1 1.8 - - - -
275C GLN* 1.3 77.3 - - - +
277C LYS* 1.3 62.6 + - - +
278C THR 3.0 0.2 - - - -
279C ILE* 3.6 21.3 - - - +
280C LYS* 3.0 27.9 + - + +
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Residues in contact with LYS 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C ALA 3.8 10.7 + - - +
275C GLN 3.0 1.6 + - - +
276C ASN* 1.3 76.8 - - - +
278C THR* 1.3 56.6 + - + +
281C PRO* 3.2 18.8 - - - +
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Residues in contact with THR 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C GLN* 2.9 49.8 - - + +
277C LYS* 1.3 80.5 - - + +
279C ILE* 1.3 62.6 + - + +
280C LYS 3.4 0.7 - - - -
281C PRO* 3.3 8.0 - - - +
282C ALA* 3.2 25.7 + - - +
11D LEU* 4.9 4.3 - - - +
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Residues in contact with ILE 279 (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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270C LEU* 4.2 11.2 - - + -
273C GLN* 3.2 25.8 - - - +
275C GLN* 3.0 31.8 + - + +
276C ASN* 3.3 22.9 + - - +
278C THR* 1.3 76.5 - - + +
280C LYS* 1.3 66.0 + - - +
282C ALA* 3.6 4.2 - - - +
283C VAL* 3.0 28.8 + - + +
6D PHE* 3.7 35.0 - - + +
7D ASN* 3.7 23.6 - - - +
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Residues in contact with LYS 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ASP* 3.2 36.8 - - - +
99C ARG 4.9 0.2 - - - -
100C VAL 4.3 8.5 - - - +
101C ILE* 3.5 33.7 - - + +
270C LEU* 4.0 12.3 - - + +
276C ASN* 3.0 15.5 + - + +
279C ILE* 1.3 78.0 - - - +
281C PRO* 1.3 72.4 - - + +
284C THR* 2.8 34.2 + - - +
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Residues in contact with PRO 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C LYS 3.2 28.0 - - - +
278C THR* 3.3 15.3 - - - +
280C LYS* 1.3 100.5 - - + +
282C ALA* 1.3 56.1 + - - -
284C THR* 3.6 7.9 + - - +
285C SER* 2.8 26.2 + - - -
11D LEU* 3.8 19.5 - - + +
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Residues in contact with ALA 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C THR* 3.2 21.5 + - - +
279C ILE* 3.6 6.7 - - - +
280C LYS 3.2 0.8 - - - -
281C PRO* 1.3 75.4 - - - +
283C VAL* 1.3 65.4 + - + +
285C SER* 3.1 21.6 + - - -
286C GLN* 3.3 12.9 + - - +
6D PHE 5.9 0.2 - - - +
9D ILE* 3.8 24.7 - - + +
10D GLU 3.8 2.6 - - - +
11D LEU* 3.9 23.3 - - + +
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Residues in contact with VAL 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ILE* 3.9 14.4 - - + -
118C PHE* 4.2 12.8 - - + -
269C LEU* 3.9 26.9 - - + -
279C ILE* 3.0 23.6 + - + +
282C ALA* 1.3 73.1 - - + +
284C THR* 1.3 65.8 + - - +
286C GLN* 3.1 9.5 + - - +
287C LEU* 3.0 31.4 + - + +
6D PHE* 4.0 35.0 - - + +
9D ILE* 4.6 12.6 - - + -
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Residues in contact with THR 284 (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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74C THR* 4.7 18.1 - - + +
101C ILE* 3.6 26.0 - - + +
103C VAL* 5.3 3.6 - - + -
280C LYS* 2.8 27.3 + - - +
281C PRO* 3.7 8.5 - - - +
283C VAL* 1.3 77.5 - - - +
285C SER* 1.3 55.9 + - - +
287C LEU* 3.3 6.9 + - - +
288C ALA* 2.9 30.3 + - + +
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Residues in contact with SER 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C PRO 2.8 18.8 + - - -
282C ALA 3.1 9.6 + - - -
283C VAL 3.1 0.2 - - - -
284C THR* 1.3 80.2 - - - +
286C GLN* 1.3 57.9 - - - +
288C ALA* 3.5 5.5 + - - +
289C LYS* 3.0 30.0 + - - +
11D LEU* 3.4 17.0 - - - +
12D LEU* 3.3 38.4 + - - +
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Residues in contact with GLN 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C PHE* 4.3 11.0 - - + -
121C LYS* 4.0 14.2 + - - +
122C PHE* 3.4 30.3 - - + -
282C ALA 3.4 12.8 - - - +
283C VAL* 3.1 8.0 + - - +
285C SER* 1.3 76.3 - - - +
287C LEU* 1.3 61.0 + - - +
289C LYS* 3.6 2.6 + - - +
290C ILE* 3.2 30.7 + - + +
9D ILE* 3.5 20.4 - - + +
10D GLU* 2.7 32.1 + - - +
12D LEU* 3.5 29.8 - - - +
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C ILE* 4.0 24.5 - - + -
103C VAL* 4.7 15.5 - - + -
114C ILE* 3.8 26.5 - - + +
118C PHE* 3.9 27.1 - - + -
269C PHE* 3.5 34.3 - - + +
283C VAL* 3.0 27.8 + - + +
284C THR* 3.7 6.1 - - - +
286C GLN* 1.3 74.5 - - - +
288C ALA* 1.3 64.8 + - - +
290C ILE* 3.2 9.6 + - + +
291C ILE* 3.1 27.0 + - + +
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Residues in contact with ALA 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ILE* 3.3 22.5 - - + +
74C THR* 4.0 21.0 - - + +
284C THR* 2.9 19.0 + - + +
285C SER* 3.9 5.6 - - - +
287C LEU* 1.3 75.3 - - - +
289C LYS* 1.3 57.8 + - - +
291C ILE* 3.2 7.1 + - - -
292C ARG* 2.8 28.6 + - - +
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Residues in contact with LYS 289 (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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121C LYS* 4.7 15.5 - - - +
285C SER 3.0 18.5 + - - +
286C GLN* 3.6 6.7 - - - +
288C ALA* 1.3 76.1 - - - +
290C ILE* 1.3 60.2 + - + +
292C ARG* 4.0 7.3 - - - +
293C SER* 2.7 46.4 + - - +
12D LEU* 3.6 24.7 - - + -
142D ASN* 5.5 0.2 + - - -
145D ALA* 3.4 30.1 - - - +
149D ASN* 5.5 3.8 - - - +
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Residues in contact with ILE 290 (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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114C ILE* 4.8 18.6 - - + +
117C LYS* 3.7 38.4 - - + -
118C PHE* 4.4 27.1 - - + +
121C LYS* 5.0 17.7 - - + +
122C PHE* 5.5 0.2 - - + -
286C GLN* 3.2 21.3 - - + +
287C LEU* 3.2 13.3 + - + +
289C LYS* 1.3 77.5 - - + +
291C ILE* 1.3 62.5 + - - +
293C SER* 3.6 3.9 + - - -
294C GLU* 3.2 40.1 + - - +
149D ASN* 4.6 8.1 - - - +
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Residues in contact with ILE 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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73C ILE* 3.6 27.6 - - + +
74C THR* 4.7 2.0 - - - -
103C VAL* 4.3 20.0 - - + -
104C GLN 4.0 18.4 - - - +
106C LEU* 6.5 0.7 - - + -
114C ILE* 4.3 22.2 - - + -
287C LEU* 3.1 19.6 + - + +
288C ALA* 3.2 9.8 + - - +
290C ILE* 1.3 74.8 - - - +
292C ARG* 1.3 56.1 + - - +
294C GLU* 3.2 1.3 + - - -
295C VAL* 2.8 21.9 + - + +
296C SER 2.7 40.0 + - - +
297C ASN* 4.6 4.0 - - - +
298C PRO* 4.9 3.6 - - + -
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Residues in contact with ARG 292 (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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73C ILE* 3.4 22.4 - - + -
288C ALA 2.8 21.3 + - - +
289C LYS* 4.0 7.9 - - - +
291C ILE* 1.3 73.0 - - - +
293C SER* 1.3 61.2 + - - +
296C SER* 2.7 43.4 + - - -
15D ASP* 3.1 40.3 + - + +
17D LEU* 3.7 11.3 - - - +
18D PHE* 3.6 12.0 - - - -
109D THR* 3.8 1.0 - - - +
140D TRP* 3.8 8.3 - - - -
141D ALA* 5.8 0.4 - - - +
142D ASN* 3.0 48.7 + - - +
904D MAE 2.7 43.4 + - - -
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Residues in contact with SER 293 (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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289C LYS* 2.7 34.0 + - - +
290C ILE 3.9 3.8 - - - -
291C ILE 3.2 0.2 - - - -
292C ARG* 1.3 77.3 - - - +
294C GLU* 1.3 58.7 + - - +
109D THR* 4.6 0.4 - - - -
113D HIS* 4.4 3.1 - - - +
142D ASN* 4.3 7.4 + - - +
145D ALA* 3.5 23.9 + - - +
146D ILE* 3.4 32.1 - - - +
149D ASN* 3.9 26.1 - - - +
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Residues in contact with GLU 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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113C HIS* 2.8 38.4 + - - -
114C ILE* 6.0 0.3 - - - +
117C LYS* 4.1 10.7 - - - +
150C GLN* 5.4 0.3 + - - +
290C ILE* 3.2 27.7 + - - +
291C ILE* 3.2 3.2 + - - +
293C SER* 1.3 79.2 - - - +
295C VAL* 1.3 69.0 + - + +
296C SER 3.7 0.4 - - - -
109D THR* 3.5 11.6 - - - +
110D GLY* 3.7 6.6 - - - -
113D HIS* 3.4 49.4 + - + +
149D ASN* 3.2 26.1 + - - +
150D GLN* 3.9 2.6 + - - -
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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