Contacts of the helix formed by residues 281 - 288 (chain A) in PDB entry 1R37
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 281 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A TYR 3.2 5.8 + - - -
280A HIS* 1.3 70.7 - - - +
282A PRO* 1.3 67.2 - - + +
284A ILE* 3.0 16.9 + - - +
285A THR* 3.0 16.9 + - - -
249B ASN* 4.4 13.7 - - + +
254B LEU* 4.1 14.6 - - + -
269B MET* 3.6 28.1 - - + +
274B GLY 5.9 0.2 - - - +
275B ALA 3.1 20.7 + - - +
277B LEU 4.5 1.3 - - - +
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Residues in contact with PRO 282 (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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280A HIS* 3.5 25.6 - - + +
281A ALA* 1.3 93.8 - - + +
283A LEU* 1.3 56.1 + - - +
285A THR* 3.7 0.3 - - - -
286A LEU* 2.8 37.9 + - + +
49B PHE* 3.9 10.5 - - + +
50B GLY* 4.0 5.8 - - - +
52B LEU* 3.9 17.9 - - + -
272B LEU* 3.9 25.8 - - + +
274B GLY* 3.7 22.4 - - - +
275B ALA 3.5 7.6 - - - +
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TYR* 3.9 34.1 - - + +
280A HIS* 3.0 29.0 + - + +
282A PRO* 1.3 78.4 - - - +
284A ILE* 1.3 63.2 + - - +
286A LEU* 4.8 3.6 - - + -
287A SER* 3.2 36.7 + - - +
289A ILE* 4.5 1.7 - - - +
52B LEU* 4.0 30.8 - - + +
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Residues in contact with ILE 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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279A TYR* 3.8 24.0 - - + -
280A HIS 3.8 4.7 - - - +
281A ALA* 3.0 9.3 + - - +
283A LEU* 1.3 76.7 - - - +
285A THR* 1.3 58.1 + - - +
288A GLU* 2.8 26.7 + - - -
289A ILE* 3.2 37.9 + - + +
291A PHE* 3.6 24.7 - - + -
269B MET* 4.0 22.0 - - + -
277B LEU* 3.8 30.1 - - + -
291B PHE* 4.6 4.3 - - + +
292B VAL 4.5 0.7 - - - -
293B GLY* 3.7 13.1 - - - +
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Residues in contact with THR 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ALA 3.0 12.4 + - - -
282A PRO 3.7 6.5 - - - -
284A ILE* 1.3 77.3 - - - +
286A LEU* 1.3 63.4 + - - +
288A GLU* 3.2 11.8 + - - +
249B ASN* 4.3 0.7 + - - -
269B MET* 3.0 24.5 + - - +
270B VAL 3.7 7.2 - - - +
271B GLY 4.0 8.3 + - - -
272B LEU* 3.8 15.5 - - + -
293B GLY* 4.0 9.0 - - - -
294B SER 3.5 8.6 - - - +
295B LEU* 3.5 17.6 - - + +
403B NAD 3.3 30.5 - - - +
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Residues in contact with LEU 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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263A LYS* 5.2 2.3 - - - +
282A PRO* 2.8 32.9 + - + +
283A LEU* 4.5 4.9 - - + +
285A THR* 1.3 71.7 - - - +
287A SER* 1.3 59.6 + - - +
49B PHE* 4.8 7.2 - - + -
52B LEU* 3.5 27.8 - - + -
58B LEU* 4.8 17.7 - - + -
111B LEU* 4.2 5.4 - - - +
117B TRP* 5.6 1.8 - - + -
272B LEU* 4.2 16.6 - - + -
295B LEU* 3.2 43.1 - - + +
600B ETX 4.2 21.3 - - + -
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Residues in contact with SER 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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262A ALA 5.1 0.7 - - - -
263A LYS* 3.4 22.4 - - - +
264A GLN 2.8 31.4 + - - -
283A LEU* 3.2 28.2 + - - +
285A THR 3.2 0.4 - - - -
286A LEU* 1.3 79.3 - - - +
288A GLU* 1.3 59.9 + - - +
289A ILE* 3.2 18.1 + - - -
111B LEU* 4.9 1.5 - - - +
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Residues in contact with GLU 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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264A GLN* 3.4 25.0 + - + +
284A ILE 2.8 9.7 + - - -
285A THR 3.2 2.1 + - - +
287A SER* 1.3 79.5 - - - +
289A ILE* 1.3 64.7 + - - +
290A GLN* 4.0 9.5 + - - +
110B HIS* 3.4 10.7 + - - -
111B LEU* 3.4 18.6 - - + +
161B ARG* 2.7 45.7 + - - -
165B LYS* 3.8 4.9 + - - +
293B GLY 3.5 18.0 - - - +
294B SER* 3.7 1.9 - - - -
295B LEU* 3.0 36.5 + - + +
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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