Contacts of the helix formed by residues 65 - 79 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A HIS* 3.6 9.6 + - - +
60A PRO* 3.5 26.4 - - + +
61A PRO* 5.9 1.0 - - - +
62A GLY* 5.9 1.3 - - - +
64A ASN* 1.3 77.9 + - - +
66A VAL* 1.3 62.0 + - - +
67A PRO* 3.4 12.1 - - - +
68A LYS* 2.8 37.9 + - - +
69A GLN* 3.1 17.0 + - - +
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A HIS* 5.7 1.1 - - + -
64A ASN* 4.0 15.7 + - - +
65A ASP* 1.3 68.3 - - - +
67A PRO* 1.3 79.1 - - + +
69A GLN* 2.8 10.9 + - - +
70A VAL* 2.8 22.9 + - + +
89A PRO* 4.9 16.2 - - + +
90A SER* 4.8 5.8 - - - -
93A ALA* 3.3 33.9 - - + -
94A PHE* 3.7 13.9 - - + -
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Residues in contact with PRO 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP* 3.4 10.1 - - - +
66A VAL* 1.3 96.9 - - + +
68A LYS* 1.3 62.5 + - - +
70A VAL* 3.2 10.7 + - + +
71A GLN* 3.0 23.0 + - - +
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PRO* 4.0 8.5 - - + -
61A PRO* 4.1 20.0 - - - +
65A ASP* 2.8 35.6 + - + +
67A PRO* 1.3 76.0 - - - +
69A GLN* 1.3 58.6 + - - +
71A GLN* 3.1 14.6 + - + +
72A PHE* 2.9 63.6 + - + -
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Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 3.8 6.9 + - + -
29A THR* 3.6 26.6 - - - +
30A HIS* 3.2 20.7 - - - +
60A PRO* 4.3 2.2 - - + +
65A ASP 3.1 9.8 + - - +
66A VAL* 2.8 9.4 + - - +
68A LYS* 1.3 79.4 - - - +
70A VAL* 1.3 63.2 + - - +
72A PHE* 3.1 14.5 + - - +
73A ILE* 3.0 23.0 + - + +
86A THR* 3.2 13.7 + - - -
87A THR* 3.1 35.1 + - - -
89A PRO* 3.9 1.6 - - - +
94A PHE* 3.2 29.9 - - + -
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A VAL* 2.8 23.3 + - + +
67A PRO* 3.4 12.1 - - + +
68A LYS 3.2 0.2 - - - -
69A GLN* 1.3 75.6 - - - +
71A GLN* 1.3 62.8 + - - +
73A ILE* 3.3 7.5 + - - +
74A GLU* 3.0 27.0 + - + +
93A ALA* 3.5 26.2 - - + +
94A PHE* 3.6 22.0 - - + -
97A SER* 3.7 18.6 + - - +
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Residues in contact with GLN 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PRO 3.0 12.3 + - - +
68A LYS* 3.1 17.5 + - + +
70A VAL* 1.3 78.7 - - - +
72A PHE* 1.3 57.6 + - + +
74A GLU* 3.1 12.1 + - - +
75A SER* 2.8 49.4 + - - +
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Residues in contact with PHE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 4.0 11.9 - - + -
58A LEU* 3.8 44.0 - - + +
59A ALA 3.8 13.7 - - - -
60A PRO* 3.7 23.8 - - + -
61A PRO* 5.5 1.1 - - + -
68A LYS* 2.9 58.7 + - + -
69A GLN* 3.3 15.9 - - + +
71A GLN* 1.3 76.3 - - + +
73A ILE* 1.3 57.8 + - - +
75A SER* 3.0 9.3 + - - -
76A ALA* 2.9 30.3 + - - +
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Residues in contact with ILE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 3.7 27.8 - - + -
69A GLN* 3.0 18.6 + - + +
70A VAL* 3.6 7.2 - - - +
72A PHE* 1.3 74.3 - - - +
74A GLU* 1.3 58.2 + - - +
76A ALA* 3.3 2.6 + - - +
77A LEU* 3.0 46.9 + - + +
84A ILE* 4.6 6.2 - - + +
86A THR* 3.8 26.7 - - + +
94A PHE* 3.5 34.5 - - + -
97A SER* 3.9 23.6 - - - +
98A LEU* 5.8 6.5 - - + -
101A ALA* 5.9 1.1 - - + -
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A VAL* 3.0 20.3 + - + +
71A GLN* 3.1 19.3 + - - +
73A ILE* 1.3 77.2 - - - +
75A SER* 1.3 61.8 + - - +
77A LEU* 3.3 18.6 + - - +
78A ALA* 3.3 10.2 + - - +
96A LYS* 5.1 2.6 - - - +
97A SER* 2.7 31.3 + - - -
100A ARG* 2.5 56.5 + - - +
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Residues in contact with SER 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 4.9 3.1 - - - +
71A GLN* 2.8 31.7 + - - +
72A PHE* 3.0 23.4 + - - -
74A GLU* 1.3 74.0 - - - +
76A ALA* 1.3 61.1 + - - +
78A ALA* 3.4 18.5 + - - +
79A THR* 3.7 12.0 - - - +
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Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 3.9 38.1 - - + -
28A ILE* 4.0 10.1 - - + -
58A LEU* 4.7 1.6 - - + -
72A PHE 2.9 17.7 + - - +
73A ILE 3.4 5.4 - - - +
74A GLU 3.2 0.2 - - - -
75A SER* 1.3 78.7 + - - +
77A LEU* 1.3 59.7 + - - +
79A THR* 2.5 24.8 + - - -
81A PRO* 3.2 9.8 - - - +
84A ILE* 3.9 12.1 - - + -
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ILE* 3.0 27.7 + - + +
74A GLU* 3.3 30.7 + - - +
76A ALA* 1.3 75.9 - - - +
78A ALA* 1.3 57.7 + - - +
80A TYR* 2.9 25.1 + - - -
81A PRO* 4.3 0.2 - - - -
84A ILE* 4.0 18.2 - - + -
97A SER 3.6 18.2 - - - +
100A ARG* 3.5 28.9 - - + +
101A ALA* 3.5 25.4 - - + +
104A LEU* 4.3 7.7 - - + +
106A ILE* 3.7 26.1 - - + +
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLU 3.3 8.8 + - - +
75A SER* 3.6 13.9 - - - +
76A ALA 3.2 0.6 - - - -
77A LEU* 1.3 78.7 - - - +
79A THR* 1.3 61.5 + - + +
80A TYR* 3.2 19.9 - - - -
100A ARG* 3.8 13.0 - - - +
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Residues in contact with THR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LYS* 5.5 1.6 - - - +
26A TYR* 3.2 32.5 + - - +
75A SER 3.7 13.5 - - - +
76A ALA 2.5 17.8 + - - -
78A ALA* 1.3 77.1 - - + +
80A TYR* 1.3 71.2 + - - +
81A PRO* 3.5 3.7 - - - +
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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