Contacts of the helix formed by residues 282 - 290 (chain A) in PDB entry 1R60
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 SER 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A VAL* 3.5 16.8 - - - +
194A GLY 3.4 18.6 - - - -
195A GLY* 3.3 6.2 - - - -
259A ALA* 4.0 2.7 - - - +
260A LEU 2.8 21.2 + - - -
261A SER* 3.2 8.8 - - - -
279A THR* 2.9 26.0 + - - -
280A SER 3.4 0.2 - - - -
281A ALA* 1.3 78.0 - - - +
283A THR* 1.3 68.6 + - - +
284A PRO* 3.3 1.1 - - - +
285A VAL* 2.9 15.8 + - - +
286A PHE 3.2 9.2 + - - -
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Residues in contact with THR 283 (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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127A THR* 3.7 17.3 - - + +
128A VAL 3.7 7.9 - - - +
129A SER* 4.7 3.4 - - - -
160A LEU* 3.1 37.3 - - + +
161A PHE 2.8 27.4 + - - +
162A ALA* 3.3 14.7 - - - +
193A VAL* 3.4 12.9 + - + +
279A THR 3.5 2.0 + - - -
282A SER* 1.3 77.6 - - - +
284A PRO* 1.4 62.4 - - - +
286A PHE* 3.3 2.9 + - - +
287A GLY* 2.9 24.9 + - - -
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Residues in contact with PRO 284 (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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80A LEU* 4.3 0.4 - - + -
81A ASP* 3.5 32.1 - - - +
84A TYR* 3.3 33.6 - - + +
85A LEU* 3.5 16.3 - - + +
127A THR* 3.8 5.4 - - + -
129A SER* 3.7 8.3 - - - +
280A SER 3.2 28.0 - - - +
281A ALA* 4.1 0.4 - - - -
282A SER 3.4 4.0 - - - +
283A THR* 1.4 91.4 - - - +
285A VAL* 1.3 59.9 + - - +
288A GLY 2.9 20.0 + - - -
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Residues in contact with VAL 285 (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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10A ILE* 5.1 2.7 - - + -
14A TYR* 4.7 4.3 - - + +
84A TYR* 3.4 24.0 - - + -
259A ALA* 4.6 6.1 - - + -
260A LEU* 3.9 25.8 - - + +
264A TYR* 3.4 22.9 - - + +
281A ALA 3.1 26.2 - - - +
282A SER 2.9 7.5 + - - +
284A PRO* 1.3 75.4 - - - +
286A PHE* 1.3 71.4 + - - +
288A GLY* 3.1 0.7 + - - -
289A ILE* 3.1 40.3 + - + +
358A PHE* 5.5 0.7 - - + -
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Residues in contact with PHE 286 (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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124A HIS* 4.7 1.8 - - - -
160A LEU* 3.7 34.3 - - + -
191A THR* 5.6 0.9 - - + -
193A VAL* 3.8 22.7 - - + -
257A VAL* 3.9 28.3 - - + -
259A ALA* 4.7 5.3 - - + +
282A SER 3.2 2.4 + - - -
283A THR 3.5 6.7 - - - +
285A VAL* 1.3 79.6 - - - +
287A GLY* 1.3 64.5 + - - +
289A ILE 3.0 11.6 + - - -
290A LEU* 3.2 35.1 + - + +
308A LEU* 3.9 28.0 - - + -
312A LEU* 5.3 0.7 - - + -
355A THR* 5.9 0.2 - - - -
356A PRO* 4.0 22.7 - - + -
358A PHE* 3.3 30.9 - + - -
361A LEU* 4.7 4.7 - - + -
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Residues in contact with GLY 287 (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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30A GLN* 2.8 24.7 + - - -
85A LEU* 3.6 10.3 - - - -
87A SER* 4.8 1.6 - - - -
127A THR* 4.2 9.4 - - - -
160A LEU* 4.5 2.0 - - - +
283A THR 2.9 16.2 + - - -
286A PHE* 1.3 77.9 - - - +
288A GLY* 1.3 60.3 + - - +
289A ILE 3.4 0.3 + - - -
290A LEU* 3.5 27.7 + - - +
291A SER 5.1 0.2 + - - -
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Residues in contact with GLY 288 (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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84A TYR 3.4 24.2 - - - -
85A LEU* 3.6 8.7 - - - +
86A MET 4.4 0.2 - - - -
87A SER* 3.1 9.0 - - - -
88A ALA 2.9 28.2 + - - -
284A PRO 2.9 12.4 + - - -
285A VAL 3.1 1.5 + - - -
287A GLY* 1.3 77.8 - - - +
289A ILE* 1.3 66.1 + - - +
290A LEU 3.4 0.4 - - - -
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Residues in contact with ILE 289 (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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10A ILE* 3.8 32.3 - - + +
11A ARG* 4.5 12.8 - - + +
14A TYR* 3.5 34.3 - - + -
88A ALA* 4.8 1.3 - - + +
285A VAL* 3.1 16.8 + - + +
286A PHE 3.0 3.8 + - - -
288A GLY* 1.3 80.8 - - - +
290A LEU* 1.3 66.1 + - - +
291A SER 3.0 5.1 + - - -
292A LEU* 3.2 36.0 + - + +
358A PHE* 3.5 39.6 - - + -
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Residues in contact with LEU 290 (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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124A HIS* 3.2 45.1 - - + +
125A VAL* 4.1 10.5 - - + -
160A LEU* 3.8 10.5 - - + -
286A PHE* 3.2 36.8 - - + +
287A GLY* 3.5 22.6 + - - +
288A GLY 3.4 2.6 - - - -
289A ILE* 1.3 77.9 - - - +
291A SER* 1.3 56.2 + - - +
292A LEU 3.0 4.2 + - - -
293A ILE* 3.0 15.5 + - + +
294A ASN* 2.8 39.4 + - + +
358A PHE* 3.8 12.3 - - + -
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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