Contacts of the helix formed by residues 92 - 103 (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 ASN 92 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B TRP* 2.9 23.9 + - - +
21B GLY 3.9 4.0 + - - -
23B ALA 2.8 24.9 + - - +
25B ALA* 3.5 5.7 - - - +
36B ILE* 3.6 22.0 - - - +
90B GLU* 3.0 16.9 + - - +
91B CYS* 1.3 75.8 - - - +
93B ASP* 1.4 53.2 + - - +
94B GLY* 3.0 11.3 + - - -
95B VAL* 2.9 34.2 + - + +
96B PHE* 2.7 37.0 + - - +
4001B SAH 3.5 11.7 - - - +
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Residues in contact with ASP 93 (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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21B GLY* 3.0 28.9 + - - +
22B ALA* 4.2 8.9 - - - +
91B CYS 3.4 4.1 + - - +
92B ASN* 1.4 69.9 - - - +
94B GLY* 1.3 58.3 + - - +
96B PHE* 3.4 7.4 + - - +
97B GLN* 3.0 28.4 + - - +
114B LYS* 3.5 23.9 - - - +
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Residues in contact with GLY 94 (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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21B GLY 4.8 0.2 + - - -
23B ALA 5.0 2.0 + - - -
24B PRO* 6.0 0.6 - - - +
25B ALA* 4.0 17.5 - - - -
27B TYR* 4.7 0.6 - - - -
92B ASN* 3.0 9.5 + - - -
93B ASP* 1.3 74.4 - - - +
95B VAL* 1.3 64.8 + - - +
97B GLN* 3.4 14.9 + - - +
98B ARG* 3.4 17.2 + - - +
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Residues in contact with VAL 95 (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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25B ALA* 4.0 6.3 - - + -
27B TYR* 3.5 26.2 - - - +
34B LEU* 4.2 5.2 - - + -
36B ILE* 3.9 13.9 - - + -
69B PHE* 3.9 6.7 - - + -
70B GLY 3.6 15.7 - - - +
90B GLU* 3.5 20.6 - - + +
92B ASN* 2.9 22.6 + - + +
94B GLY* 1.3 71.8 - - - +
96B PHE* 1.4 59.5 + - - +
98B ARG* 3.0 5.6 + - - +
99B LEU* 3.0 24.8 + - - +
4001B SAH 3.4 24.5 - - - +
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Residues in contact with PHE 96 (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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90B GLU* 3.8 10.7 - - + +
92B ASN 2.7 21.8 + - - +
93B ASP* 3.6 9.2 - - - +
95B VAL* 1.4 72.2 - - - +
97B GLN* 1.3 58.5 + - - +
99B LEU* 3.2 26.7 + - + +
100B ARG* 2.9 54.2 + - + +
112B PRO* 4.0 18.8 - - + -
113B LEU 3.5 30.5 - - - -
114B LYS* 3.5 42.4 - - + -
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Residues in contact with GLN 97 (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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93B ASP 3.0 13.6 + - - +
94B GLY* 3.6 12.1 - - - +
95B VAL 3.2 0.2 - - - -
96B PHE* 1.3 75.8 - - - +
98B ARG* 1.3 62.3 + - + +
100B ARG* 3.2 15.6 + - - +
101B ASP* 3.1 45.7 + - - +
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Residues in contact with ARG 98 (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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27B TYR* 3.4 65.5 + - + +
31B ASP* 4.3 12.7 + - - -
69B PHE* 4.0 10.9 - - + -
70B GLY 5.5 0.2 - - - +
94B GLY 3.6 13.7 - - - +
95B VAL 3.0 8.6 + - - +
97B GLN* 1.3 75.4 - - + +
99B LEU* 1.4 56.7 + - - +
101B ASP* 3.4 9.2 + - - +
102B TRP* 3.0 29.5 + - - +
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Residues in contact with LEU 99 (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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69B PHE* 3.6 36.3 - - + -
88B ILE* 3.8 41.5 - - + +
90B GLU* 4.4 7.4 - - + -
95B VAL 3.0 11.6 + - - +
96B PHE* 3.2 28.7 + - + +
98B ARG* 1.4 75.1 - - - +
100B ARG* 1.3 56.2 + - - +
102B TRP* 3.3 7.2 + - + +
103B ALA* 2.9 34.0 + - - +
110B VAL* 4.2 11.9 - - + -
112B PRO* 3.8 24.7 - - + -
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Residues in contact with ARG 100 (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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96B PHE* 2.9 49.7 + - + +
97B GLN* 3.2 23.2 + - - +
99B LEU* 1.3 76.4 - - - +
101B ASP* 1.3 56.9 + - - +
103B ALA* 4.4 3.8 - - - +
104B PRO* 3.2 24.3 - - - +
112B PRO* 4.3 16.9 - - - +
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Residues in contact with ASP 101 (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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97B GLN* 3.1 37.5 + - - +
98B ARG* 3.4 10.3 + - - +
99B LEU 3.3 0.2 - - - -
100B ARG* 1.3 78.1 - - - +
102B TRP* 1.4 60.1 + - - +
104B PRO* 3.4 9.9 - - - +
105B ARG* 5.0 4.5 + - - +
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Residues in contact with TRP 102 (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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69B PHE* 3.7 23.6 - + + -
72B ALA* 4.1 12.4 - - + +
75B ALA* 3.8 35.9 - - + -
76B SER* 3.4 19.1 + - - -
79B GLN* 3.7 13.5 - - + -
86B HIS* 3.9 7.0 - + - -
88B ILE* 3.6 20.4 - - + -
98B ARG 3.0 18.2 + - - +
99B LEU* 3.7 7.0 - - + +
101B ASP* 1.4 76.6 - - - +
103B ALA* 1.4 77.5 + - - +
104B PRO 3.4 0.9 - - - -
105B ARG* 3.5 11.1 + - - +
106B GLN* 2.8 67.5 + - + +
110B VAL* 3.7 11.2 - - + -
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Residues in contact with ALA 103 (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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99B LEU* 2.9 21.5 + - + +
100B ARG* 4.4 4.7 - - - +
102B TRP* 1.4 82.4 - - + +
104B PRO* 1.4 66.2 - - + +
106B GLN* 3.3 19.7 + - - +
110B VAL* 3.8 32.9 + - + +
112B PRO* 5.0 9.0 - - + -
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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