Contacts of the strand formed by residues 83 - 88 (chain D) in PDB entry 4OA5
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 HIS 83 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58D HIS 3.0 7.8 + - - +
59D SER* 3.4 3.8 - - - -
60D ILE 2.9 25.3 + - - +
78D LEU* 3.7 2.3 - - - +
81D LYS 4.6 0.7 - - - +
82D GLY* 1.3 74.2 + - - -
84D ILE* 1.3 87.5 + - - +
85D TYR* 3.4 39.4 - + + +
107D GLU 5.1 0.7 - - - -
108D ASP* 3.2 30.2 + - - -
109D LYS* 3.3 15.9 + - - -
110D ILE 3.9 0.7 - - - -
111D THR* 2.7 29.4 + - - -
312D IOD 4.2 10.9 - - + +
127E MET 6.0 2.2 + - - -
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Residues in contact with ILE 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D ILE* 3.3 25.6 - - + +
62D GLU* 4.5 4.9 - - + -
71D ALA* 3.3 37.0 - - + +
74D MET* 3.7 14.8 - - + -
75D ALA* 3.5 26.5 - - + +
78D LEU* 3.6 12.3 - - + -
83D HIS* 1.3 80.7 - - - +
85D TYR* 1.3 72.7 + - - +
86D THR* 4.3 12.6 - - - -
109D LYS 2.7 12.6 + - - +
110D ILE* 3.3 7.7 - - + +
111D THR 2.9 27.9 + - - +
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Residues in contact with TYR 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D SER* 4.7 5.9 - - - -
60D ILE 2.8 17.5 + - - +
61D VAL* 3.3 6.0 - - + +
62D GLU 2.8 25.7 + - - +
83D HIS* 3.4 46.8 - + + +
84D ILE* 1.3 71.4 - - - +
86D THR* 1.3 59.8 + - - +
87D ILE* 4.9 2.4 - - - +
111D THR* 3.5 11.0 - - + +
113D LEU* 4.8 4.5 - - + -
124D LEU* 3.9 36.1 - - + +
127D MET* 5.5 3.5 - - + +
130D PHE* 3.5 32.3 - + - -
126E GLU 4.7 8.3 + - - -
127E MET* 5.5 3.0 - - - -
128E ALA 3.7 23.2 + - - -
129E PRO* 4.1 9.9 - - + -
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Residues in contact with THR 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D GLU* 2.5 39.8 + - - +
65D THR* 2.6 36.9 + - + +
71D ALA* 4.4 2.2 - - + -
84D ILE* 4.3 4.7 - - - -
85D TYR* 1.3 74.8 - - - +
87D ILE* 1.3 55.8 + - - +
110D ILE* 3.8 22.9 - - + -
111D THR 2.9 15.9 + - - +
112D VAL* 3.3 8.3 - - + +
113D LEU* 2.7 33.1 + - - +
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Residues in contact with ILE 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D VAL* 4.5 1.6 - - + -
62D GLU 2.9 16.3 + - - +
63D VAL* 4.6 8.7 - - + -
64D GLY* 2.9 25.6 + - - -
65D THR* 3.0 9.5 + - - -
86D THR* 1.3 79.2 + - - +
88D GLU* 1.3 61.3 + - - +
113D LEU* 3.4 15.5 - - + +
115D GLY 3.6 18.4 - - - +
117D ALA* 3.7 14.6 - - - +
120D GLN* 3.7 30.7 - - + -
121D LEU* 3.7 38.4 - - + +
124D LEU* 4.3 10.8 - - + -
301D SAH 4.1 3.9 + - + -
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Residues in contact with GLU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D THR* 3.4 16.0 + - - +
66D CYS 2.9 19.1 + - - +
87D ILE* 1.3 74.6 - - - +
89D LYS* 1.3 61.2 + - - +
90D ASP* 3.0 36.2 + - - +
93D ASN* 3.3 15.1 + - + -
94D VAL* 3.7 14.8 - - + +
112D VAL* 4.6 2.2 - - + -
113D LEU 3.0 7.0 + - - +
114D HIS* 3.3 11.3 - - - -
115D GLY 2.9 20.2 + - - -
301D SAH 2.6 52.7 + - - -
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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