Contacts of the strand formed by residues 83 - 90 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B SER* 4.0 18.2 - - - -
61B GLY* 3.9 14.4 - - - -
62B GLY 3.5 9.6 - - - +
64B VAL* 3.8 22.2 - - + -
78B VAL* 3.8 21.3 - - + +
79B GLN* 4.3 3.4 - - - +
81B ALA* 2.8 22.3 + - + +
82B PRO* 1.3 76.6 - - - +
84B ASP* 1.3 63.5 + - - +
85B GLU 3.7 9.9 - - - +
86B HIS* 3.7 30.3 - - + -
108B HIS* 2.8 42.4 + - + -
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Residues in contact with ASP 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLY* 2.8 32.6 + - - +
63B ARG* 5.2 2.7 - - + -
82B PRO 4.9 2.4 - - - +
83B ILE* 1.3 78.2 - - - +
85B GLU* 1.3 68.8 + - + +
108B HIS* 4.5 4.5 + - - +
109B LYS* 4.1 17.3 + - - +
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B GLY 3.4 5.3 + - - +
63B ARG* 3.4 37.3 + - + +
64B VAL 3.0 24.6 + - - -
83B ILE* 3.7 7.5 - - - +
84B ASP* 1.3 86.6 - - + +
86B HIS* 1.3 61.4 + - - +
87B TRP* 2.8 36.3 + - + +
109B LYS* 3.6 12.8 - - + +
111B ILE* 3.8 16.7 - - + +
128B HIS* 4.6 0.9 + - - -
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Residues in contact with HIS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B VAL* 3.5 12.1 - - + -
66B GLU* 3.0 29.5 + - + +
75B ALA* 3.5 26.0 - - - -
78B VAL* 3.6 23.9 - - + +
79B GLN* 3.0 34.4 + - - +
83B ILE* 3.7 4.7 - - + -
85B GLU* 1.3 74.9 - - - +
87B TRP* 1.3 60.0 + - - +
88B ILE* 3.6 25.9 - - + +
102B TRP* 3.9 5.0 - + - -
109B LYS 2.9 11.0 + - - +
110B VAL* 3.2 9.1 - - + +
111B ILE 2.8 27.8 + - - -
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Residues in contact with TRP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ARG* 4.5 3.3 - - + +
64B VAL 2.8 11.2 + - - +
65B LEU* 3.4 15.9 - - + -
66B GLU* 2.8 32.1 + - - +
85B GLU* 2.8 31.5 + - + +
86B HIS* 1.3 72.7 - - - +
88B ILE* 1.3 56.2 + - - +
111B ILE* 3.4 43.2 - - + +
113B LEU* 4.2 13.7 - - + -
124B LEU* 3.9 27.4 - - + -
125B PRO* 4.2 18.2 - - + -
128B HIS* 3.9 18.8 - + - -
129B PHE* 3.5 27.8 - + + -
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B GLU* 3.3 15.5 - - + +
69B PHE* 4.0 29.2 - - + +
75B ALA* 4.4 2.7 - - + -
86B HIS* 3.6 33.0 - - + +
87B TRP* 1.3 79.1 - - - +
89B ILE* 1.4 68.6 + - - +
99B LEU* 3.8 31.4 - - + +
102B TRP* 3.6 31.9 - - + -
110B VAL* 4.0 6.3 - - + -
111B ILE 2.9 11.0 + - - +
112B PRO* 3.6 1.9 - - - +
113B LEU* 2.9 28.2 + - - +
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Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B LEU* 3.8 16.8 - - + -
66B GLU 2.9 9.6 + - - +
67B VAL* 4.3 15.0 - - + -
68B GLY* 2.8 31.5 + - - -
69B PHE 4.2 0.2 + - - -
88B ILE* 1.4 73.7 - - - +
90B GLU* 1.3 65.0 + - - +
113B LEU* 3.4 11.9 - - + +
115B GLY 3.5 18.4 - - - +
117B TRP* 4.1 19.1 - - + +
120B VAL* 3.8 39.9 - - + -
121B ALA* 4.4 9.9 - - + +
124B LEU* 3.8 23.8 - - + -
151B PHE* 5.8 0.2 - - + -
4001B SAH 4.4 3.3 + - + -
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Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B GLY* 3.7 0.2 - - - -
69B PHE* 2.8 31.9 + - + -
89B ILE* 1.3 75.7 - - - +
91B CYS* 1.3 62.4 + - - +
92B ASN* 3.0 29.6 + - - +
95B VAL* 3.5 18.5 - - + +
96B PHE* 3.8 19.9 - - + +
99B LEU* 4.4 4.7 - - + -
113B LEU 3.1 6.9 + - - -
114B LYS* 3.3 11.4 - - - +
115B GLY 2.9 21.7 + - - -
4001B SAH 2.6 54.5 + - - -
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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