Contacts of the strand formed by residues 259 - 264 (chain A) in PDB entry 4DHJ
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 ILE 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ALA 4.7 2.9 - - - +
93A ILE* 4.0 13.5 - - + +
96A GLY* 4.0 19.3 - - - -
97A LEU* 3.9 27.8 - - + +
100A ILE* 4.1 5.8 - - + -
227A THR* 3.4 31.9 - - + +
228A ARG 3.2 2.2 + - - +
229A VAL* 3.3 15.7 - - + +
230A ARG 3.1 22.0 + - - -
257A PRO* 3.4 2.7 - - - +
258A GLU* 1.3 85.8 - - + +
260A THR* 1.3 68.2 + - - +
261A LEU* 3.9 26.2 - - + -
270A VAL* 5.0 4.7 - - + -
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Residues in contact with THR 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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76A TYR* 3.3 32.4 + - + +
230A ARG* 3.3 19.4 - - + +
232A GLU* 4.2 4.0 - - + -
257A PRO* 4.6 6.8 + - - +
259A ILE* 1.3 79.9 + - - +
261A LEU* 1.3 71.4 - - - +
270A VAL* 3.9 3.0 - - - +
271A ILE* 3.1 54.7 + - + +
272A TYR* 5.7 0.2 - - - -
273A LYS* 5.3 6.0 - - - +
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Residues in contact with LEU 261 (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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89A PHE* 3.7 37.2 - - + -
92A ALA* 3.7 24.5 - - + +
93A ILE* 4.0 11.4 - - + -
229A VAL* 4.2 15.0 - - + -
230A ARG 2.8 11.7 + - - +
231A ILE* 3.5 6.4 - - + -
232A GLU* 2.8 36.9 + - - +
259A ILE* 3.9 15.9 - - + -
260A THR* 1.3 81.1 - - - +
262A LEU* 1.3 55.3 + - - +
263A TYR 3.9 0.4 - - - -
268A TYR* 3.8 19.7 - - + -
269A ASP 3.3 14.1 - - - +
270A VAL* 4.1 7.2 - - + -
271A ILE* 4.1 3.8 - - - -
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Residues in contact with LEU 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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50A PHE* 4.8 0.9 - - + -
53A LEU* 3.7 38.4 - - + -
72A LEU* 3.7 29.6 - - + -
79A ILE* 3.9 13.5 - - + -
232A GLU* 4.0 9.0 - - + +
234A MET* 4.0 17.5 - - + -
261A LEU* 1.3 71.5 - - - +
263A TYR* 1.3 58.5 + - - +
264A ARG* 3.8 19.1 + - + +
267A HIS 3.6 1.4 - - - +
268A TYR* 3.4 7.8 - - - -
269A ASP* 2.9 38.1 + - + +
271A ILE* 3.9 24.4 - - + +
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Residues in contact with TYR 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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231A ILE* 3.6 22.7 - - + -
232A GLU 2.8 11.3 + - - +
233A TYR* 3.5 43.7 - + - -
234A MET* 2.8 33.7 + - - +
261A LEU 3.9 1.6 + - - -
262A LEU* 1.3 73.6 - - - +
264A ARG* 1.3 71.3 + - - +
265A PRO* 4.2 5.9 - - + +
266A GLY 3.3 14.1 + - - -
267A HIS 3.4 13.7 - - - -
268A TYR* 3.3 25.4 - + + -
572B ARG 4.0 4.5 + - - -
573B LEU* 3.6 15.2 - - + -
574B ARG* 2.7 35.1 + - - +
551D GLU* 5.4 3.5 + - - -
554D ARG* 4.5 6.9 + - - -
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Residues in contact with ARG 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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53A LEU* 3.5 21.4 - - - +
56A GLU* 2.9 23.0 + - - -
57A TYR* 2.7 38.5 + - - -
65A PHE* 5.2 3.4 - - + -
81A TYR* 3.9 12.1 - - - -
234A MET* 3.8 32.3 - - + +
262A LEU* 3.8 12.3 + - + +
263A TYR* 1.3 84.5 - - - +
265A PRO* 1.4 78.8 - - + +
266A GLY 2.9 1.2 + - - -
267A HIS* 2.8 36.5 + - + +
269A ASP* 3.1 25.3 + - - -
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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