Contacts of the helix formed by residues 281 - 288 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A ASN* 4.3 13.7 - - + +
254A LEU* 4.0 13.9 - - + -
269A MET* 3.5 29.5 - - + +
275A ALA 3.0 22.1 + - - +
277A LEU 4.5 1.1 - - - +
279B TYR 3.1 5.8 + - - -
280B HIS* 1.3 71.0 - - - +
282B PRO* 1.3 66.0 - - + +
284B ILE* 2.9 16.4 + - - +
285B THR* 3.0 16.1 + - - -
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Residues in contact with PRO 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 3.7 18.6 - - + +
50A GLY* 4.0 5.6 - - - +
52A LEU* 4.1 6.3 - - + -
272A LEU* 3.9 26.7 - - + +
274A GLY* 3.6 23.6 - - - +
275A ALA 3.5 8.5 - - - +
280B HIS* 3.5 24.9 - - + +
281B ALA* 1.3 94.6 - - + +
283B LEU* 1.3 55.1 - - - +
285B THR 3.4 0.2 + - - -
286B LEU* 2.9 36.8 + - + +
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Residues in contact with LEU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 4.1 27.0 - - + +
279B TYR* 3.7 33.7 - - + +
280B HIS* 3.0 26.7 + - + +
282B PRO* 1.3 76.6 - - - +
284B ILE* 1.3 57.1 + - - +
286B LEU* 4.9 2.5 - - + -
287B SER* 2.5 44.0 + - - +
289B ILE* 4.9 1.1 - - + -
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Residues in contact with ILE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A MET* 4.1 24.7 - - + -
277A LEU* 3.9 29.4 - - + -
291A PHE 4.8 3.8 - - - +
292A VAL 4.5 0.2 - - - -
293A GLY* 3.7 13.4 - - - +
279B TYR* 3.7 24.9 - - + +
280B HIS 3.3 3.1 + - - +
281B ALA* 2.9 11.7 + - - +
283B LEU* 1.3 78.2 - - - +
285B THR* 1.3 57.2 + - - +
288B GLU* 2.9 26.3 + - - -
289B ILE* 3.2 37.7 + - + +
291B PHE* 3.7 24.0 - - + -
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Residues in contact with THR 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ASN* 4.2 0.5 + - - -
269A MET* 2.9 26.3 + - - +
270A VAL 3.7 7.2 - - - +
271A GLY 4.0 7.8 + - - -
272A LEU* 3.8 14.9 - - + +
293A GLY* 4.0 7.6 - - - -
294A SER 3.4 9.7 - - - +
295A LEU* 3.6 13.4 - - + +
403A NAD 3.3 29.8 - - - +
281B ALA 3.0 12.4 + - - -
282B PRO 3.8 6.5 - - - -
284B ILE* 1.3 78.1 - - - +
286B LEU* 1.3 67.0 + - + +
288B GLU* 3.2 12.6 + - - +
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 4.7 13.5 - - + -
52A LEU* 3.3 31.9 - - + -
58A LEU* 4.8 17.5 - - + -
111A LEU* 4.2 5.4 - - - +
117A TRP* 5.5 2.0 - - + -
272A LEU* 4.1 15.5 - - + -
295A LEU* 3.2 42.3 - - + +
600A ETX 3.9 21.3 - - + -
263B LYS* 5.2 2.4 - - - +
282B PRO 2.9 16.4 + - - +
283B LEU* 4.5 5.2 - - + +
285B THR* 1.3 72.6 - - + +
287B SER* 1.3 58.6 + - - +
288B GLU 3.4 0.2 - - - -
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Residues in contact with SER 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 4.9 1.3 - - - -
262B ALA 5.2 0.7 - - - -
263B LYS* 3.4 24.3 - - - +
264B GLN 2.8 31.0 + - - -
283B LEU* 2.5 32.9 + - - +
284B ILE 3.9 0.5 + - - -
285B THR 3.2 0.4 - - - -
286B LEU* 1.3 77.3 - - - +
288B GLU* 1.3 60.6 + - - +
289B ILE* 3.1 22.3 + - - +
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Residues in contact with GLU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A HIS* 3.3 10.3 + - - -
111A LEU* 3.4 18.5 - - + +
161A ARG* 2.7 46.1 + - - -
165A LYS* 4.2 6.0 + - - +
293A GLY 3.5 19.6 - - - +
294A SER* 3.8 1.6 - - - -
295A LEU* 3.0 37.1 + - + +
264B GLN* 3.4 25.3 + - + -
284B ILE 2.9 9.6 + - - -
285B THR 3.2 2.7 + - - +
287B SER* 1.3 79.5 - - - +
289B ILE* 1.3 65.6 + - - +
290B GLN* 4.0 9.2 + - - +
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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