Contacts of the helix formed by residues 65 - 78 (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 ASP 65 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B HIS* 3.7 6.7 + - - +
60B PRO* 3.8 23.1 - - + +
61B PRO* 5.5 2.4 - - - +
62B GLY* 5.9 1.8 - - - +
64B ASN* 1.3 79.0 + - - +
66B VAL* 1.3 63.5 + - - +
67B PRO* 3.2 23.9 - - - +
68B LYS* 3.1 30.8 + - - +
69B GLN* 3.1 9.9 + - - +
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B HIS* 5.1 1.3 - - + -
64B ASN* 3.7 26.4 + - - +
65B ASP* 1.3 74.0 - - - +
67B PRO* 1.3 71.9 - - + +
69B GLN* 3.0 10.1 + - - +
70B VAL* 3.0 22.8 + - + +
89B PRO* 4.4 17.9 - - + -
90B SER* 4.7 6.1 - - - -
93B ALA* 3.5 31.4 - - + -
94B PHE* 3.6 16.4 - - + -
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Residues in contact with PRO 67 (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 ASP* 3.2 17.5 - - - +
66B VAL* 1.3 95.7 - - + +
68B LYS* 1.3 58.4 + - - +
70B VAL* 3.5 10.5 + - + +
71B GLN* 3.3 23.6 + - - +
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Residues in contact with LYS 68 (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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60B PRO* 4.0 9.2 - - + -
61B PRO* 5.4 5.4 - - + -
65B ASP* 3.1 34.4 + - - +
66B VAL 3.1 0.6 - - - -
67B PRO* 1.3 75.0 - - - +
69B GLN* 1.3 65.8 + - - +
71B GLN* 3.1 22.0 + - + +
72B PHE* 3.1 64.2 + - + -
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Residues in contact with GLN 69 (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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28B ILE* 3.7 10.1 + - + -
29B THR 3.6 25.8 - - - +
30B HIS* 3.1 22.0 - - - +
60B PRO* 4.2 3.3 - - + +
65B ASP 3.1 10.8 + - - +
66B VAL* 3.0 9.6 + - - +
68B LYS* 1.3 74.9 - - - +
70B VAL* 1.3 64.1 + - - +
72B PHE* 3.1 12.7 + - - +
73B ILE* 3.0 23.5 + - + +
86B THR* 3.1 13.9 + - - -
87B THR* 2.9 37.4 + - - -
89B PRO* 3.9 0.9 - - - +
94B PHE* 3.3 25.9 - - + -
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 3.0 25.3 + - + +
67B PRO* 3.7 11.0 - - + +
69B GLN* 1.3 75.6 - - - +
71B GLN* 1.3 62.0 + - + +
73B ILE* 3.4 5.9 + - - +
74B GLU* 3.0 28.5 + - + +
93B ALA* 3.5 25.1 - - + +
94B PHE* 3.7 20.9 - - + -
97B SER* 3.4 20.0 - - - +
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Residues in contact with GLN 71 (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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67B PRO 3.3 14.0 + - - +
68B LYS* 3.1 31.5 + - + +
69B GLN 3.0 0.2 - - - -
70B VAL* 1.3 78.2 - - - +
72B PHE* 1.3 66.8 + - - +
74B GLU* 3.3 11.0 + - - +
75B SER* 2.9 32.5 + - - -
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Residues in contact with PHE 72 (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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28B ILE* 3.7 11.4 - - + -
58B LEU* 3.7 47.5 - - + +
59B ALA 3.6 15.3 - - - -
60B PRO* 3.5 35.0 - - + -
61B PRO* 5.6 2.0 - - + -
68B LYS* 3.1 48.3 + - + -
69B GLN* 3.1 14.8 + - - +
71B GLN* 1.3 78.1 - - - +
73B ILE* 1.3 56.9 + - - +
75B SER* 3.2 7.6 + - - -
76B ALA* 2.8 31.4 + - - +
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Residues in contact with ILE 73 (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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28B ILE* 3.7 24.5 - - + -
69B GLN* 3.0 15.2 + - + +
70B VAL* 3.7 7.4 - - - +
72B PHE* 1.3 75.7 - - - +
74B GLU* 1.3 62.3 + - - +
76B ALA* 3.4 1.4 + - - +
77B LEU* 3.0 41.4 + - + +
84B ILE* 4.8 7.1 - - + +
86B THR* 3.5 32.3 - - + +
94B PHE* 3.9 31.4 - - + -
97B SER* 3.8 23.6 - - - -
98B LEU* 5.7 7.9 - - + -
101B ALA* 5.9 1.1 - - + -
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Residues in contact with GLU 74 (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* 3.0 25.6 + - + +
71B GLN* 3.7 13.2 - - - +
73B ILE* 1.3 75.6 - - - +
75B SER* 1.3 63.6 + - - +
77B LEU* 3.5 5.9 + - - +
78B ALA* 3.3 20.4 + - - +
96B LYS* 3.4 23.8 + - - +
97B SER* 3.0 32.0 + - - +
100B ARG* 3.3 30.9 + - - -
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Residues in contact with SER 75 (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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58B LEU* 5.7 2.2 - - - -
71B GLN* 2.9 23.8 + - - -
72B PHE* 3.6 9.1 - - - -
74B GLU* 1.3 75.2 - - - +
76B ALA* 1.3 66.4 + - - +
78B ALA* 3.3 18.6 + - - +
79B THR* 3.6 10.6 - - - +
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Residues in contact with ALA 76 (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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26B TYR* 3.7 45.3 - - + -
28B ILE* 4.1 11.7 - - + -
58B LEU* 4.4 1.5 - - + +
72B PHE 2.8 21.4 + - - +
73B ILE 3.8 3.6 - - - +
75B SER* 1.3 73.6 - - - +
77B LEU* 1.3 61.5 + - - +
79B THR* 2.6 26.1 + - - -
81B PRO* 3.2 7.4 - - - +
84B ILE* 4.1 5.8 - - + -
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Residues in contact with LEU 77 (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* 3.0 32.4 + - + +
74B GLU* 3.7 21.8 - - - +
76B ALA* 1.3 75.9 - - - +
78B ALA* 1.3 57.1 + - - +
80B TYR* 3.0 29.3 + - - -
81B PRO* 3.8 4.6 - - - +
84B ILE* 3.6 21.8 - - + -
97B SER 3.6 24.0 - - - +
100B ARG* 4.0 18.8 - - + +
101B ALA* 3.4 32.5 - - + +
104B LEU* 4.9 7.5 - - + +
106B ILE* 4.3 15.0 - - + +
108B VAL* 5.4 0.2 - - + -
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Residues in contact with ALA 78 (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 9.4 + - - +
75B SER* 3.3 14.7 + - - +
76B ALA 3.1 0.8 + - - -
77B LEU* 1.3 77.4 - - - +
79B THR* 1.3 59.3 + - + +
80B TYR* 3.3 20.9 + - - -
100B ARG* 4.7 13.2 - - - +
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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