Contacts of the helix formed by residues 277 - 290 (chain D) in PDB entry 2AC0
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 CYS 277 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120D LYS* 3.2 24.2 - - + +
121D SER* 3.7 15.7 - - - -
275D CYS* 3.4 3.8 - - - +
276D ALA* 1.3 80.8 - - - +
278D PRO* 1.4 65.3 - - - +
279D GLY 3.3 0.3 + - - -
280D ARG* 3.4 31.0 + - + +
281D ASP* 3.1 23.5 + - - -
8H G 4.5 1.0 + - - -
9H C 3.5 35.4 - - - -
10H C 5.4 0.9 - - - -
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Residues in contact with PRO 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LYS 4.1 1.8 - - - +
121D SER* 4.2 1.8 - - - -
122D VAL 3.2 27.6 - - - +
125D THR* 3.8 7.4 - - + +
134D PHE* 3.6 29.5 - - + +
135D CYS* 3.5 31.2 - - - +
136D GLN* 3.6 7.0 - - + -
275D CYS* 3.6 13.2 - - - +
276D ALA 3.3 8.7 - - - +
277D CYS* 1.4 86.8 - - - +
279D GLY* 1.3 55.8 + - - +
282D ARG* 2.9 30.5 + - - +
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Residues in contact with GLY 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D THR* 3.4 25.0 - - - -
119D ALA 3.3 21.4 + - - -
120D LYS 3.0 5.5 + - - -
122D VAL* 4.0 4.7 - - - +
125D THR* 4.6 1.8 - - - -
278D PRO* 1.3 76.3 - - - +
280D ARG* 1.3 65.3 + - - +
282D ARG* 3.5 0.4 + - - -
283D ARG* 3.1 27.6 + - - +
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Residues in contact with ARG 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LYS* 3.2 28.9 + - + +
277D CYS* 3.7 33.5 - - + +
279D GLY* 1.3 73.1 - - - +
281D ASP* 1.3 77.1 + - - +
283D ARG* 3.2 9.9 + - - +
284D THR* 3.0 37.0 + - - +
4G G 3.8 12.3 + - - -
5G C 4.5 2.2 - - - +
7H T 3.7 35.7 + - - +
8H G 2.9 50.7 + - - -
9H C 3.8 1.4 - - - +
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Residues in contact with ASP 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D PHE* 3.7 6.1 - - + -
273D ARG* 2.9 48.4 + - - +
275D CYS* 3.4 15.0 - - - +
277D CYS 3.1 13.9 + - - +
278D PRO 4.2 0.7 - - - +
280D ARG* 1.3 107.3 + - - +
282D ARG* 1.3 67.8 + - - +
284D THR* 3.4 6.9 + - - -
285D GLU* 2.9 30.0 + - + +
7H T 5.2 3.5 - - - +
8H G 4.5 2.8 + - - -
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Residues in contact with ARG 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D SER 3.3 18.6 + - - -
117D GLY 3.5 4.6 + - - -
118D THR* 3.6 18.4 - - + +
125D THR* 2.7 39.7 + - + -
126D TYR 3.2 20.8 + - - -
127D SER* 3.6 9.6 - - - +
128D PRO* 3.7 12.9 - - - +
134D PHE* 3.6 29.7 - - + -
278D PRO 2.9 19.3 + - - +
279D GLY 3.8 3.8 - - - +
281D ASP* 1.3 76.1 - - - +
283D ARG* 1.3 53.4 + - - +
285D GLU* 3.2 1.9 + - - +
286D GLU* 2.8 65.9 + - - +
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Residues in contact with ARG 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D THR* 3.7 31.8 + - + +
279D GLY 3.1 14.2 + - - +
280D ARG* 3.2 12.6 - - - +
282D ARG* 1.3 78.5 - - - +
284D THR* 1.3 55.7 - - - +
286D GLU* 3.3 8.8 + - - +
287D GLU* 2.8 52.8 + - - +
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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
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280D ARG* 3.0 22.2 + - - +
281D ASP* 3.6 10.9 + - - -
282D ARG 3.4 0.2 - - - -
283D ARG* 1.3 75.0 - - - +
285D GLU* 1.3 60.4 + - + +
287D GLU* 3.0 14.7 + - - +
288D ASN* 2.8 50.3 + - - +
6H A 4.7 19.7 - - - +
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Residues in contact with GLU 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D LEU* 3.6 22.6 - - + +
132D LYS* 2.8 40.4 + - - +
134D PHE* 3.6 9.9 - - + -
273D ARG* 3.7 25.6 + - - -
281D ASP* 2.9 24.7 + - + +
282D ARG 4.0 0.2 - - - +
284D THR* 1.3 75.6 - - + +
286D GLU* 1.3 58.8 + - - +
288D ASN* 3.4 12.5 + - - +
289D LEU* 3.0 26.5 + - - +
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Residues in contact with GLU 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D THR* 4.7 4.3 - - - +
127D SER* 2.6 29.5 + - - +
128D PRO* 4.8 0.7 - - - +
129D ALA* 4.6 12.5 - - + +
130D LEU* 4.0 9.6 - - + -
282D ARG* 2.8 54.2 + - - +
283D ARG* 3.6 7.3 - - - +
285D GLU* 1.3 77.5 - - - +
287D GLU* 1.3 60.6 + - + +
289D LEU* 3.3 23.6 - - + +
290D ARG* 3.4 10.7 + - - +
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Residues in contact with GLU 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D ARG* 2.8 48.5 + - - +
284D THR* 3.0 15.3 + - - +
286D GLU* 1.3 75.9 - - + +
288D ASN* 1.3 66.4 + - - +
289D LEU 3.4 0.3 + - - -
290D ARG* 3.5 12.9 + - - +
291D LYS* 3.4 32.5 + - - +
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Residues in contact with ASN 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D THR* 2.8 36.6 + - - +
285D GLU* 3.6 11.4 - - - +
287D GLU* 1.3 76.6 - - - +
289D LEU* 1.3 66.2 + - - +
291D LYS* 3.1 29.8 + - - +
292D LYS* 3.7 11.0 - - - +
6H A 5.3 4.6 + - - -
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Residues in contact with LEU 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ALA* 3.9 33.4 - - + +
130D LEU* 4.1 21.1 - - + -
285D GLU 3.0 14.8 + - - +
286D GLU* 3.3 16.4 - - + +
288D ASN* 1.3 75.9 - - - +
290D ARG* 1.3 57.8 + - + +
291D LYS 2.8 11.6 + - - -
292D LYS* 3.2 31.9 + - + +
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Residues in contact with ARG 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286D GLU 3.4 8.1 + - - +
287D GLU* 3.7 11.2 - - - +
288D ASN 3.5 0.2 - - - -
289D LEU* 1.3 80.0 - - + +
291D LYS* 1.3 67.8 + - - +
292D LYS 3.4 4.3 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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