Contacts of the strand formed by residues 83 - 90 (chain D) in PDB entry 3ORH
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 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 SER* 4.0 17.0 - - - -
61D GLY* 3.9 14.1 - - - -
62D GLY 3.4 10.1 - - - +
64D VAL* 3.8 23.3 - - + -
78D VAL* 3.8 21.5 - - + +
79D GLN* 4.3 3.6 - - - +
81D ALA* 2.8 21.7 + - + +
82D PRO* 1.4 74.7 - - - +
84D ASP* 1.3 64.1 + - - +
85D GLU 3.7 18.8 - - - +
86D HIS* 3.8 21.5 - - + -
108D HIS* 2.8 44.6 + - + -
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Residues in contact with ASP 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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62D GLY* 2.8 31.6 + - - +
63D ARG* 5.2 2.9 - - + +
82D PRO 4.8 2.8 - - - +
83D ILE* 1.3 77.9 - - - +
85D GLU* 1.3 68.6 + - + +
108D HIS* 4.5 5.0 + - - +
109D LYS* 4.1 17.5 + - - +
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Residues in contact with GLU 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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62D GLY 3.3 4.2 + - - +
63D ARG* 3.4 38.1 + - + +
64D VAL 3.0 25.0 + - - -
83D ILE* 3.7 8.2 - - - +
84D ASP* 1.3 85.7 - - + +
86D HIS* 1.3 59.4 + - - +
87D TRP* 2.8 41.5 + - + +
108D HIS* 5.5 0.2 - - - -
109D LYS* 3.6 19.5 - - + +
111D ILE* 4.7 8.1 - - + +
128D HIS* 4.6 0.7 + - - -
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Residues in contact with HIS 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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64D VAL* 3.5 11.2 - - + +
66D GLU* 2.9 29.9 + - + +
75D ALA* 3.4 26.5 - - + -
78D VAL* 3.5 25.0 - - + +
79D GLN* 3.1 33.3 + - - +
83D ILE* 3.8 4.7 - - + -
85D GLU* 1.3 73.7 - - - +
87D TRP* 1.3 62.3 - - - +
88D ILE* 3.6 25.2 - - + +
102D TRP* 4.0 4.5 - + - -
109D LYS 2.8 11.1 + - - +
110D VAL* 3.3 8.0 - - + +
111D ILE* 2.7 29.4 + - - +
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Residues in contact with TRP 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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63D ARG* 4.5 2.7 - - + +
64D VAL 2.9 11.7 + - - +
65D LEU* 3.4 16.1 - - + -
66D GLU* 2.7 32.2 + - - +
85D GLU* 2.8 37.4 + - + +
86D HIS* 1.3 75.7 - - - +
88D ILE* 1.3 57.0 + - - +
111D ILE* 3.4 35.8 - - + +
113D LEU* 4.2 14.4 - - + -
124D LEU* 4.0 27.8 - - + -
125D PRO* 4.1 18.6 - - + -
128D HIS* 3.9 19.7 - + - -
129D PHE* 3.5 29.1 - + + -
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Residues in contact with ILE 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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66D GLU* 3.3 13.5 - - + +
69D PHE* 4.0 31.0 - - + +
75D ALA* 4.4 2.0 - - + -
86D HIS* 3.6 32.3 - - + +
87D TRP* 1.3 78.5 - - - +
89D ILE* 1.3 69.1 + - - +
99D LEU* 3.8 30.2 - - + +
102D TRP* 3.6 32.5 - - + -
110D VAL* 4.0 5.8 - - + -
111D ILE 2.9 12.1 + - - +
112D PRO* 3.6 2.4 - - - +
113D LEU* 2.9 28.2 + - - +
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Residues in contact with ILE 89 (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 LEU* 3.8 25.4 - - + -
66D GLU 3.0 10.2 + - - +
67D VAL* 4.4 15.0 - - + -
68D GLY* 2.8 31.7 + - - -
69D PHE 4.2 0.2 + - - -
87D TRP 5.6 0.2 - - - -
88D ILE* 1.3 74.2 - - - +
90D GLU* 1.3 64.2 + - - +
113D LEU* 3.5 12.6 - - + +
115D GLY 3.5 18.8 - - - +
117D TRP* 4.1 16.8 - - + +
120D VAL* 3.8 38.8 - - + -
121D ALA* 4.4 9.9 - - + +
124D LEU* 3.8 14.1 - - + -
151D PHE* 5.8 0.2 - - + -
4003D SAH 4.3 5.6 + - + -
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Residues in contact with GLU 90 (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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69D PHE* 2.8 30.6 + - + -
89D ILE* 1.3 75.5 - - - +
91D CYS* 1.3 61.2 + - - +
92D ASN* 3.0 30.2 + - - +
95D VAL* 3.5 19.7 - - + +
96D PHE* 3.8 20.7 - - + +
99D LEU* 4.4 4.7 - - + -
113D LEU 3.1 6.9 + - - -
114D LYS* 3.3 11.3 - - - +
115D GLY 2.9 19.9 + - - -
4003D SAH 2.5 55.5 + - - -
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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