Contacts of the helix formed by residues 274 - 294 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D GLN* 1.3 68.1 - - - +
275D GLN* 1.3 62.0 + - + +
276D ASN* 2.9 11.8 + - - +
277D LYS* 3.3 17.2 + - - +
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Residues in contact with GLN 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ASN* 4.7 13.2 + - + +
273D GLN* 3.2 10.4 - - + +
274D ALA* 1.3 74.9 - - + +
276D ASN* 1.3 55.8 + - - +
277D LYS* 2.9 11.8 + - - -
278D THR* 2.9 31.6 + - - -
279D ILE* 3.0 33.1 + - + +
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Residues in contact with ASN 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ASP 6.0 1.8 - - - +
99D ARG* 3.8 24.4 - - + +
270D LEU* 4.1 20.8 - - + +
271D THR* 3.0 28.7 + - - +
273D GLN* 3.1 33.0 + - - +
274D ALA 2.9 1.5 + - - +
275D GLN* 1.3 76.2 - - - +
277D LYS* 1.3 61.0 + - - +
278D THR 3.1 0.7 - - - -
279D ILE* 3.9 14.2 - - - +
280D LYS* 3.2 27.4 + - + +
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Residues in contact with LYS 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D ALA 3.3 13.2 + - - +
275D GLN* 2.9 1.5 + - - +
276D ASN* 1.3 80.0 - - - +
278D THR* 1.3 62.0 + - - +
281D PRO* 3.4 17.2 - - - +
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Residues in contact with THR 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 5.7 6.7 - - + +
275D GLN* 2.9 20.5 + - - +
277D LYS* 1.3 82.9 + - - +
279D ILE* 1.3 66.0 + - - +
280D LYS 3.2 2.0 - - - -
281D PRO* 3.0 14.1 - - + +
282D ALA* 3.2 17.3 + - + +
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Residues in contact with ILE 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PHE* 3.6 38.8 - - + +
7C ASN* 3.3 34.5 - - - +
9C ILE 5.8 0.2 - - - -
270D LEU* 4.4 12.3 - - + -
273D GLN* 3.3 13.7 - - - +
275D GLN* 3.0 33.2 + - + +
276D ASN* 4.0 11.9 - - - +
278D THR* 1.3 77.7 - - - +
280D LYS* 1.3 57.4 + - - +
282D ALA* 3.3 5.7 + - + +
283D VAL* 2.9 42.0 + - + +
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Residues in contact with LYS 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ASP* 3.1 51.9 + - - +
99D ARG 5.4 0.2 - - - -
100D VAL 3.2 27.0 + - - -
101D ILE* 4.0 21.1 - - + +
270D LEU* 4.0 17.2 - - + +
276D ASN* 3.2 18.5 + - + +
279D ILE* 1.3 79.2 - - - +
281D PRO* 1.4 67.5 - - + +
284D THR* 2.8 34.1 + - - +
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Residues in contact with PRO 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 3.3 19.2 - - + +
277D LYS 3.4 17.3 - - - +
278D THR* 3.0 24.2 - - + +
280D LYS* 1.4 89.2 - - + +
282D ALA* 1.3 60.3 + - - +
284D THR* 3.7 5.3 + - - -
285D SER* 3.2 22.5 + - - -
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Residues in contact with ALA 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ILE* 3.6 28.0 - - + +
10C GLU 3.7 11.1 - - - +
11C LEU* 4.0 12.5 - - + +
278D THR* 3.2 20.0 + - + +
279D ILE* 3.5 8.1 - - - +
280D LYS 3.1 0.4 - - - -
281D PRO* 1.3 75.5 - - - +
283D VAL* 1.3 65.4 + - - +
285D SER* 2.8 22.2 + - - -
286D GLN* 3.2 14.8 - - - +
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Residues in contact with VAL 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PHE* 3.9 20.0 - - + -
9C ILE* 4.4 16.4 - - + -
101D ILE* 3.7 22.0 - - + -
118D PHE* 4.2 18.2 - - + -
269D LEU* 4.0 20.2 - - - +
270D LEU* 4.6 2.0 - - + -
279D ILE* 2.9 41.8 + - + +
282D ALA* 1.3 72.4 - - - +
284D THR* 1.3 56.6 + - - +
286D GLN* 3.3 5.5 + - - +
287D LEU* 3.0 31.8 + - + +
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Residues in contact with THR 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D THR* 4.7 15.8 - - + +
101D ILE* 3.5 27.7 - - + +
103D VAL* 4.8 5.2 - - + -
280D LYS* 2.8 27.4 + - - +
281D PRO* 4.0 6.1 - - - -
283D VAL* 1.3 75.4 - - - +
285D SER* 1.3 58.8 + - - +
287D LEU* 3.3 10.0 + - - +
288D ALA* 2.9 25.9 + - + +
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Residues in contact with SER 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 3.8 2.4 - - - +
12C LEU* 3.1 47.1 + - - +
13C PRO 5.5 0.9 - - - -
281D PRO 3.2 14.0 + - - -
282D ALA 2.8 19.4 + - - -
284D THR* 1.3 76.5 - - - +
286D GLN* 1.3 60.0 + - - +
288D ALA* 3.6 8.2 - - - +
289D LYS* 2.9 28.8 + - - +
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Residues in contact with GLN 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ILE* 3.5 19.6 - - + +
10C GLU* 2.9 25.8 + - - +
12C LEU* 3.3 34.2 - - + +
118D PHE* 4.7 4.9 - - + -
121D LYS* 4.8 7.4 + - - +
122D PHE* 3.4 35.1 - - + -
282D ALA 3.2 14.6 - - - +
283D VAL* 3.4 9.0 - - - +
284D THR 3.2 0.4 - - - -
285D SER* 1.3 79.3 + - - +
287D LEU* 1.3 64.1 + - - +
289D LYS* 3.4 4.7 + - - +
290D ILE* 3.2 27.6 + - - +
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Residues in contact with LEU 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D THR* 5.8 0.2 - - - -
101D ILE* 3.8 28.7 - - + -
103D VAL* 4.6 15.0 - - + -
114D ILE* 3.8 27.4 - - + +
118D PHE* 4.1 26.7 - - + -
269D PHE* 3.9 28.9 - - - +
283D VAL* 3.0 27.8 + - + +
284D THR* 3.6 7.4 - - - +
285D SER 3.2 0.2 - - - -
286D GLN* 1.3 74.5 - - - +
288D ALA* 1.3 64.4 + - - +
290D ILE* 3.1 18.1 + - + +
291D ILE* 3.2 18.9 + - + +
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Residues in contact with ALA 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D ILE* 3.3 19.3 - - + +
74D THR* 3.9 23.5 - - + +
284D THR* 2.9 18.7 + - + +
285D SER* 3.6 9.6 - - - +
287D LEU* 1.3 75.6 - - - +
289D LYS* 1.3 57.5 + - - +
291D ILE* 3.5 2.8 + - - +
292D ARG* 3.0 30.5 + - - +
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Residues in contact with LYS 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.7 22.9 - - + -
15C ASP* 5.8 1.8 + - - -
142C ASN* 5.0 3.4 - - - +
145C ALA* 3.4 33.0 - - + +
149C ASN* 6.1 0.2 - - - +
121D LYS* 5.4 7.9 - - - +
285D SER 2.9 17.9 + - - +
286D GLN* 3.5 7.6 - - - +
287D LEU 3.1 0.2 - - - -
288D ALA* 1.3 75.4 - - - +
290D ILE* 1.3 55.1 + - + +
292D ARG* 4.4 8.6 - - + +
293D SER* 2.7 37.6 + - - +
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Residues in contact with ILE 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ASN* 4.9 2.0 - - - +
114D ILE* 4.4 22.9 - - + +
117D LYS* 3.9 31.2 - - + -
118D PHE* 4.2 26.0 - - + +
121D LYS* 3.5 25.4 - - + +
122D PHE* 5.6 0.9 - - + -
286D GLN 3.4 15.5 - - - +
287D LEU* 3.1 17.1 + - + +
289D LYS* 1.3 78.1 - - - +
291D ILE* 1.3 63.2 + - - +
293D SER* 3.0 16.3 + - - -
294D GLU* 3.1 32.6 + - - +
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Residues in contact with ILE 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D ILE* 3.4 31.0 - - + +
74D THR* 4.6 3.4 - - + -
103D VAL* 4.3 18.2 - - + -
104D GLN 3.7 21.8 - - - +
114D ILE* 4.2 25.1 - - + -
287D LEU 3.2 14.9 + - - +
288D ALA* 3.9 7.9 - - - +
290D ILE* 1.3 76.9 - - + +
292D ARG* 1.3 52.3 + - - +
294D GLU* 4.9 1.6 - - - -
295D VAL* 2.9 32.2 + - + +
296D SER 2.8 33.9 + - - +
297D ASN* 4.5 2.7 - - - -
298D PRO* 4.8 3.6 - - + -
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Residues in contact with ARG 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ASP* 3.2 34.4 + - + +
17C LEU* 3.8 9.9 - - - +
18C PHE* 3.5 13.2 - - - -
109C THR* 3.8 1.6 - - - +
140C TRP* 4.1 3.0 - - - -
141C ALA* 5.8 0.4 - - - +
142C ASN* 3.1 50.9 + - - +
903C MAE 3.0 34.8 + - - -
73D ILE* 3.6 23.3 - - + +
288D ALA 3.0 19.3 + - - +
289D LYS* 3.9 12.6 - - + +
291D ILE* 1.3 78.8 - - - +
293D SER* 1.3 59.5 + - - +
296D SER* 2.5 59.6 + - - +
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Residues in contact with SER 293 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C THR* 4.5 0.7 - - - -
113C HIS* 4.1 4.9 - - - +
142C ASN* 4.3 7.4 - - - +
145C ALA* 3.6 32.5 - - - -
146C ILE* 3.8 29.2 - - - +
149C ASN* 3.4 22.3 + - - -
289D LYS* 2.7 26.5 + - - +
290D ILE* 3.0 8.8 + - - -
292D ARG* 1.3 75.4 - - - +
294D GLU* 1.3 59.9 + - - +
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Residues in contact with GLU 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C THR* 3.5 10.8 - - - +
110C GLY* 3.8 4.2 - - - -
113C HIS* 3.4 45.5 + - + +
149C ASN* 3.2 28.8 + - - +
150C GLN* 4.3 1.0 + - - -
294C GLU* 4.9 0.2 - - - +
113D HIS* 2.8 38.8 + - - -
114D ILE* 5.9 0.5 - - - +
117D LYS* 4.2 8.7 - - - +
150D GLN* 5.2 0.5 + - - -
290D ILE* 3.1 33.0 + - - +
291D ILE* 4.2 1.9 - - - +
293D SER* 1.3 78.6 - - - +
295D VAL* 1.3 72.4 + - + +
296D SER 3.7 0.4 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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