Contacts of the helix formed by residues 288 - 293 (chain A) in PDB entry 2J51
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 GLN 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A TRP* 5.6 1.1 - - + -
284A SER 4.1 7.5 - - - +
285A GLN* 3.2 25.0 + - - +
286A LEU 3.1 1.2 - - - -
287A LEU* 1.3 78.7 - - + +
289A HIS* 1.3 62.1 + - - +
290A PRO* 3.8 3.8 - - - +
293A THR* 4.7 6.3 - - - +
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Residues in contact with HIS 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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264A ASN* 3.4 28.7 - - - -
267A ASP* 2.7 30.1 + - + -
268A PHE* 3.5 29.9 + + + -
271A LYS* 4.5 3.1 - - + -
281A TRP* 4.1 28.3 - + + -
285A GLN 3.9 1.6 + - - -
286A LEU* 3.0 18.1 + - - +
288A GLN* 1.3 77.4 - - - +
290A PRO* 1.4 85.2 - - + +
291A PHE* 3.1 24.2 + - - +
292A VAL* 3.1 19.2 + - - +
293A THR* 3.4 7.9 - - - +
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Residues in contact with PRO 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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133A GLN* 4.2 5.4 + - - -
264A ASN* 3.6 33.6 + - - +
288A GLN 3.8 4.7 - - - +
289A HIS* 1.4 98.7 - - + +
291A PHE* 1.3 60.6 + - - +
292A VAL 3.2 0.2 - - - -
293A THR* 2.9 32.0 + - + +
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Residues in contact with PHE 291 (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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129A GLU* 3.6 13.0 - - + -
132A ILE* 3.9 20.9 - - + -
133A GLN* 2.8 62.4 + - + +
136A CYS* 4.1 23.1 - - + -
225A LEU* 4.5 2.5 - - + -
264A ASN* 3.8 18.0 - - + +
265A PHE* 3.4 57.0 - + + -
268A PHE* 3.8 23.3 - + + -
289A HIS* 3.1 19.5 + - - +
290A PRO* 1.3 76.5 - - - +
292A VAL* 1.3 58.3 + - + +
294A VAL* 4.4 0.2 - - - +
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Residues in contact with VAL 292 (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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133A GLN 4.7 0.2 - - - +
136A CYS* 3.8 30.3 - - + -
137A LYS* 3.6 45.3 - - + +
140A LEU* 3.9 8.7 - - + -
268A PHE* 3.9 12.3 - - + -
286A LEU 3.3 26.0 - - - +
287A LEU* 3.8 19.3 - - + +
289A HIS 3.1 9.2 + - - +
291A PHE* 1.3 78.7 - - - +
293A THR* 1.3 60.5 + - - +
294A VAL* 2.9 10.7 + - - +
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Residues in contact with THR 293 (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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287A LEU 5.0 6.3 - - - +
288A GLN* 4.7 5.8 - - - +
289A HIS 3.4 18.2 - - - +
290A PRO* 2.9 27.8 + - + +
291A PHE 3.5 0.4 - - - -
292A VAL* 1.3 75.4 - - - +
294A VAL* 1.3 62.1 + - - +
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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