Contacts of the strand formed by residues 259 - 264 (chain A) in PDB entry 1J71
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 ASP 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A ASN 3.5 2.6 - - - +
205A ASP* 2.9 27.3 + - - +
206A GLY 4.6 0.9 + - - -
258A GLY* 1.3 81.3 - - - +
260A ALA* 1.3 61.6 + - - +
261A VAL* 3.9 7.5 + - + +
271A THR* 3.5 31.8 - - + +
272A VAL 3.5 6.3 - - - +
273A PRO* 3.5 17.8 - - - +
274A LEU* 3.9 5.8 - - - +
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Residues in contact with ALA 260 (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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202A ILE* 4.4 1.8 - - + -
203A ASN 3.1 8.5 - - - +
204A PHE* 4.1 11.2 - - + +
259A ASP* 1.3 73.2 - - - +
261A VAL* 1.3 61.5 + - - +
262A PHE* 3.9 20.6 - - + -
270A ILE 3.8 1.4 - - - +
271A THR* 3.6 1.2 - - - -
272A VAL* 2.8 38.4 + - - +
274A LEU* 3.7 19.5 - - + +
277A LEU* 4.0 10.8 - - + -
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Residues in contact with VAL 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ILE* 3.2 6.8 - - - +
203A ASN* 2.8 51.0 + - + +
259A ASP* 4.5 8.1 - - + +
260A ALA* 1.3 75.2 - - - +
262A PHE* 1.3 62.1 + - - +
263A ASN* 3.3 23.4 + - - +
269A LYS* 4.1 22.9 - - + -
270A ILE 3.6 3.1 - - - +
271A THR* 3.9 27.6 - - + +
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Residues in contact with PHE 262 (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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199A LEU* 4.0 13.7 - - + -
201A SER 4.0 3.1 - - - -
202A ILE* 3.7 30.1 - - + -
224A THR* 5.3 3.6 - - + -
226A PHE* 5.1 2.0 - + - -
260A ALA* 3.9 22.4 - - + -
261A VAL* 1.3 73.4 - - - +
263A ASN* 1.3 61.5 + - - +
264A PHE* 3.7 21.2 - - + -
269A LYS* 3.2 7.8 - - - -
270A ILE 2.9 39.6 + - - +
272A VAL* 3.9 22.0 - - + -
277A LEU* 5.0 12.1 - - + -
291A ILE* 5.2 7.2 - - + -
299A LEU* 3.9 23.6 - - + -
303A PHE* 3.7 27.8 - + + -
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Residues in contact with ASN 263 (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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199A LEU* 3.6 3.1 - - - +
200A GLY* 2.9 25.5 + - - -
201A SER* 2.8 40.7 + - - +
203A ASN* 2.9 27.4 + - - +
261A VAL* 3.3 19.4 + - - +
262A PHE* 1.3 71.4 - - - +
264A PHE* 1.3 64.3 + - - +
268A VAL 3.8 3.6 - - - +
269A LYS* 3.2 37.9 - - + +
574A EOH 3.6 10.2 + - - +
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Residues in contact with PHE 264 (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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187A LEU* 3.8 17.7 - - + -
197A VAL* 3.7 27.6 - - + -
198A HIS 3.6 19.3 - - - +
199A LEU* 3.8 18.2 - - + -
215A VAL* 4.4 0.4 - - + -
217A LEU* 5.0 0.9 - - + -
262A PHE* 3.7 26.7 - - + -
263A ASN* 1.3 74.3 - - - +
265A ASP* 1.3 71.4 + - - +
267A GLY* 4.2 3.3 + - - -
268A VAL* 2.8 27.9 + - + +
269A LYS* 6.0 0.2 + - - -
270A ILE* 4.1 6.5 - - + -
299A LEU* 3.9 17.5 - - + -
303A PHE* 3.6 29.8 - + - -
320A LEU* 3.9 19.7 - - + -
574A EOH 3.1 16.1 + - - -
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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