Contacts of the helix formed by residues 94 - 104 (chain B) in PDB entry 3ROT
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 PHE 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B VAL* 3.6 17.9 - - + -
69B GLN* 3.3 42.8 - - + -
70B VAL* 3.7 22.2 - - + -
73B ILE* 3.9 19.3 - - + -
87B THR 4.5 2.0 - - - -
88B ILE* 3.7 19.7 - - + -
89B PRO* 3.5 23.6 - - + -
90B SER* 3.7 25.8 - - - -
92B THR 3.2 0.6 - - - -
93B ALA* 1.3 75.7 - - - +
95B SER* 1.3 66.2 + - - +
96B LYS 3.3 2.7 - - - -
97B SER* 2.9 10.3 + - - +
98B LEU* 2.8 42.6 + - + +
121B ASN* 3.7 3.7 - - - +
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASP 3.7 1.4 + - - -
92B THR* 3.4 22.9 + - - -
94B PHE* 1.3 74.5 - - - +
96B LYS* 1.3 57.8 + - - +
98B LEU* 3.5 1.5 + - - +
99B GLN* 2.9 42.2 + - - +
120B LYS* 3.6 19.5 + - - +
121B ASN* 2.8 32.1 + - - +
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Residues in contact with LYS 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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74B GLU* 3.4 23.1 + - - +
92B THR 4.9 0.8 + - - -
93B ALA 5.1 2.2 + - - +
94B PHE 3.3 0.8 - - - -
95B SER* 1.3 78.5 - - - +
97B SER* 1.3 59.8 + - - +
99B GLN* 3.4 8.9 + - - +
100B ARG* 3.0 40.3 + - + +
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Residues in contact with SER 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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70B VAL* 3.4 26.5 + - - +
73B ILE* 3.8 26.9 - - - -
74B GLU* 3.0 26.9 + - - +
77B LEU* 3.6 4.2 - - - +
93B ALA 5.1 0.6 + - - -
94B PHE* 2.9 13.4 + - - -
96B LYS* 1.3 77.9 - - - +
98B LEU* 1.3 60.2 + - - +
100B ARG* 3.3 4.6 + - - +
101B ALA* 3.0 28.2 + - - +
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Residues in contact with LEU 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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73B ILE* 5.7 7.4 - - + -
86B THR* 4.9 6.3 - - + -
88B ILE* 3.6 26.9 - - + -
94B PHE* 2.8 33.0 + - + +
95B SER 3.9 3.1 - - - +
97B SER* 1.3 73.6 - - - +
99B GLN* 1.3 66.3 + - - +
101B ALA* 3.3 5.8 + - + +
102B ASN* 3.0 18.4 + - - +
108B VAL* 4.0 26.6 - - + +
121B ASN* 3.5 33.0 - - + +
122B PRO* 3.4 35.2 - - + +
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Residues in contact with GLN 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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95B SER* 2.9 23.5 + - - +
96B LYS* 3.7 7.6 - - - +
98B LEU* 1.3 76.6 - - - +
100B ARG* 1.3 64.0 + - - +
102B ASN* 3.2 3.2 + - - +
103B LYS* 3.0 47.2 + - - +
119B THR 4.2 5.1 + - - +
120B LYS* 2.9 35.1 + - - +
122B PRO* 3.8 14.4 - - + -
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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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74B GLU* 3.3 31.2 + - - -
77B LEU* 4.0 11.0 - - + +
78B ALA* 4.7 21.8 - - - +
80B TYR* 5.7 3.2 + - - -
96B LYS* 3.0 25.1 + - + +
97B SER* 3.4 9.2 - - - +
98B LEU 3.2 0.2 - - - -
99B GLN* 1.3 76.7 - - - +
101B ALA* 1.3 63.7 + - - +
103B LYS* 3.1 19.8 + - - +
104B LEU* 3.1 43.8 + - + +
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Residues in contact with ALA 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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73B ILE* 5.9 1.3 - - + -
77B LEU* 3.4 32.1 - - + -
97B SER 3.0 15.3 + - - +
98B LEU* 3.6 7.4 - - + +
100B ARG* 1.3 75.5 - - - +
102B ASN* 1.3 62.2 + - - +
104B LEU* 3.4 4.2 + - - +
105B ASN 3.2 3.8 + - - -
106B ILE* 3.0 32.5 + - + +
108B VAL* 3.8 25.4 - - + -
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Residues in contact with ASN 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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98B LEU 3.0 13.8 + - - +
99B GLN* 3.5 8.3 - - - +
100B ARG 3.2 0.2 - - - -
101B ALA* 1.3 77.9 - - - +
103B LYS* 1.3 67.9 + - + +
105B ASN* 3.2 18.7 + - - +
106B ILE 5.0 2.2 - - - -
108B VAL* 6.2 0.2 - - - -
122B PRO* 3.8 28.7 - - + +
123B TYR 5.7 0.2 - - - +
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Residues in contact with LYS 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 GLN* 3.0 42.1 + - - +
100B ARG* 3.1 9.9 + - - +
102B ASN* 1.3 82.1 - - + +
104B LEU* 1.3 65.2 + - + +
105B ASN* 3.1 5.7 + - - +
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Residues in contact with LEU 104 (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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77B LEU* 4.9 11.9 - - + +
80B TYR* 4.7 22.8 - - + +
100B ARG* 3.1 57.6 + - + +
101B ALA* 4.1 4.0 - - - +
102B ASN 3.3 0.4 - - - -
103B LYS* 1.3 81.0 - - + +
105B ASN* 1.3 69.7 + - - +
106B ILE* 3.3 20.6 + - + +
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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