Contacts of the helix formed by residues 270 - 280 (chain A) in PDB entry 2RD0
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 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A PRO* 3.7 22.9 - - + -
170A ASN* 3.4 22.0 - - + +
171A VAL* 3.6 5.8 - - + -
217A PRO* 4.3 8.3 - - + -
259A GLU* 5.3 3.1 - - - +
260A TYR 4.5 0.9 - - - -
261A PHE* 3.2 54.8 - + + +
262A LEU 3.5 4.5 + - - -
263A GLU* 2.8 41.5 + - - +
265A TYR* 3.7 23.3 - + + -
266A PRO 3.9 6.7 - - - -
267A LEU* 3.3 17.8 + - - +
268A SER 3.5 4.9 - - - +
269A GLN* 1.3 79.2 - - - +
271A LYS* 1.3 64.9 + - - +
272A TYR* 4.3 3.8 - - + +
273A ILE* 3.3 2.8 + - + -
274A ARG* 3.3 17.7 + - - +
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Residues in contact with LYS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-26A TYR* 4.0 6.0 - - + +
170A ASN* 3.0 45.9 + - - +
171A VAL 3.6 13.3 + - - +
172A GLU* 3.7 45.0 + - + +
269A GLN 3.6 0.8 + - - -
270A TYR* 1.3 69.4 - - - +
272A TYR* 1.3 66.1 + - - +
274A ARG* 3.5 3.2 + - - +
275A SER* 3.1 25.3 + - - -
626A ASP* 3.2 28.7 + - - -
630A GLN* 5.7 1.6 + - - -
822A ASN* 6.1 1.4 - - - +
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Residues in contact with TYR 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-26A TYR* 3.4 46.3 + + + +
-25A TYR* 2.7 30.6 + + - -
254A VAL* 3.8 27.0 - - + +
259A GLU* 3.9 11.9 + - - +
261A PHE* 4.6 3.1 - - + -
270A TYR* 3.2 1.2 - - - +
271A LYS* 1.3 79.7 - - - +
273A ILE* 1.3 78.0 + - + +
275A SER* 3.4 1.6 + - - -
276A CYS* 3.0 43.4 + - - -
283A PRO* 3.7 8.7 - - + -
284A ASN* 3.2 21.7 + - - +
285A LEU* 3.5 27.8 - - + -
794A PHE* 5.4 3.6 - + - -
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Residues in contact with ILE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ILE* 4.2 18.2 - - + -
261A PHE* 3.3 39.7 - - + -
267A LEU* 3.2 45.8 - - + +
268A SER* 3.6 25.1 - - - -
270A TYR 3.3 2.5 + - - +
271A LYS 3.3 0.2 - - - -
272A TYR* 1.3 88.9 - - + +
274A ARG* 1.3 60.9 + - - +
276A CYS* 3.0 8.5 + - - +
277A ILE* 2.9 30.0 + - + +
283A PRO* 4.4 11.0 - - + -
285A LEU* 4.5 4.3 - - + -
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Residues in contact with ARG 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLU* 4.2 31.6 + - + +
174A SER* 3.0 28.4 + - - -
175A PRO 3.9 6.3 + - - -
176A GLU 3.6 10.9 + - - -
177A LEU* 3.7 25.8 - - + +
178A PRO* 3.6 23.2 - - - +
181A ILE* 4.1 18.8 - - + -
268A SER* 2.6 21.3 + - - +
269A GLN* 3.3 24.2 - - - +
270A TYR 3.3 9.0 + - - +
271A LYS* 4.1 5.8 - - - +
273A ILE* 1.3 79.0 - - - +
275A SER* 1.3 61.4 + - - +
277A ILE* 3.5 9.6 + - + +
278A MET* 3.2 29.7 + - + +
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Residues in contact with SER 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-26A TYR* 3.6 25.2 - - - +
-25A TYR* 4.7 1.7 - - - -
271A LYS 3.1 18.1 + - - -
272A TYR 3.7 4.3 + - - -
274A ARG* 1.3 75.1 - - - +
276A CYS* 1.3 60.6 + - - +
278A MET* 3.5 5.7 + - - +
279A LEU* 2.9 55.2 + - - +
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Residues in contact with CYS 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-25A TYR* 3.3 17.7 - - - -
190A ILE* 5.6 0.2 - - + -
272A TYR* 3.0 56.1 + - - +
273A ILE 3.0 10.0 + - - +
275A SER* 1.3 77.0 + - - +
277A ILE* 1.3 60.5 + - + +
279A LEU* 3.6 1.3 + - - -
280A GLY 3.1 2.4 + - - -
281A ARG* 2.8 47.7 + - - +
283A PRO* 3.7 20.2 - - + -
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Residues in contact with ILE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LEU* 4.8 1.8 - - + -
181A ILE* 3.5 39.5 - - + +
184A LYS* 4.2 19.5 - - + +
185A LEU* 4.3 28.0 - - + +
190A ILE* 4.4 13.5 - - + -
268A SER* 4.5 12.6 - - - -
273A ILE* 2.9 35.0 + - + +
274A ARG* 3.6 10.5 - - - +
275A SER 3.2 0.2 - - - -
276A CYS* 1.3 71.0 - - - +
278A MET* 1.3 58.2 - - - +
280A GLY* 2.6 29.6 + - - -
281A ARG 5.0 0.9 - - - -
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Residues in contact with MET 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-21A HIS* 3.9 11.4 + - + -
180A HIS* 3.7 21.1 - - + +
181A ILE* 3.4 52.3 - - + -
184A LYS* 3.6 39.7 + - + +
274A ARG* 3.2 17.8 + - + +
275A SER* 3.9 5.2 - - - +
277A ILE* 1.3 78.8 - - - +
279A LEU* 1.3 61.8 + - + +
280A GLY* 3.5 0.7 + - - -
825A GLN* 4.5 8.1 - - - -
830A ASP* 4.4 5.2 - - - +
832A ARG* 4.1 17.6 + - - +
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-26A TYR* 5.7 0.4 - - + -
-25A TYR* 3.8 21.3 - - + +
-23A HIS* 3.6 29.6 - - + +
-22A HIS 3.5 30.7 - - - +
-21A HIS* 3.2 22.9 - - + +
-20A HIS 3.0 25.9 + - - -
275A SER* 2.9 39.0 + - - +
276A CYS 4.1 0.2 - - - +
277A ILE 2.7 4.6 + - - -
278A MET* 1.3 78.4 - - + +
280A GLY* 1.3 57.9 + - - -
281A ARG* 3.8 13.9 - - + +
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Residues in contact with GLY 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-20A HIS* 3.4 34.8 - - - +
-17A TYR* 3.7 30.4 - - - +
184A LYS* 6.3 1.1 - - - -
276A CYS 3.1 0.2 + - - -
277A ILE 2.6 21.6 + - - -
278A MET 3.3 1.8 + - - -
279A LEU* 1.3 71.2 - - - +
281A ARG* 1.3 58.3 + - - +
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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