Contacts of the helix formed by residues 62 - 70 (chain B) in PDB entry 3TDM
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 62 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ARG* 5.0 5.5 + - - -
17B PHE* 4.3 6.5 - - - -
51B SER* 3.6 32.0 + - - +
53B ASP* 5.8 1.2 - - - +
54B ARG* 4.0 25.1 + - + +
60B GLY 3.9 0.4 + - - -
61B TYR* 1.3 69.8 - - - +
63B THR* 1.3 61.3 + - - +
64B GLU* 3.4 10.4 + - - +
65B MET* 3.1 45.2 + - + +
66B ILE* 3.2 16.7 + - - +
81B GLY 4.3 1.2 + - - -
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Residues in contact with THR 63 (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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54B ARG* 5.3 1.4 - - - +
61B TYR* 3.0 20.0 + - + +
62B ASP* 1.3 71.3 + - - +
64B GLU* 1.3 58.9 + - - +
65B MET 3.4 0.2 - - - -
66B ILE* 3.9 9.0 - - + -
67B ARG* 2.9 32.2 + - - +
88B HIS 5.3 0.4 - - - +
91B GLU* 3.9 41.1 - - + +
92B ALA* 4.1 7.6 - - - +
95B ARG* 3.6 16.9 + - + +
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Residues in contact with GLU 64 (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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12B ARG* 4.4 27.2 + - - +
17B PHE* 4.6 2.5 - - - -
62B ASP* 3.2 8.5 + - - +
63B THR* 1.3 78.2 + - - +
65B MET* 1.3 61.7 + - - +
67B ARG* 2.8 33.2 + - - +
68B PHE* 2.9 31.7 + - - +
95B ARG* 5.4 0.2 + - - -
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Residues in contact with MET 65 (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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10B ALA* 3.0 43.3 - - + +
11B LYS* 4.2 2.0 - - - +
12B ARG 5.3 0.2 - - - +
17B PHE* 3.7 31.1 - - + -
32B LEU* 4.1 12.1 - - + -
49B LEU* 4.0 31.6 - - + -
51B SER* 3.8 21.5 - - - +
62B ASP* 3.1 35.8 + - - +
64B GLU* 1.3 74.8 - - - +
66B ILE* 1.3 59.1 + - - +
68B PHE* 3.0 4.3 - - - +
69B VAL* 3.0 31.8 + - - +
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Residues in contact with ILE 66 (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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49B LEU* 4.3 17.3 - - + -
61B TYR* 4.2 11.2 - - + -
62B ASP 3.2 14.7 + - - +
63B THR* 3.8 9.0 - - - +
64B GLU 3.3 0.2 - - - -
65B MET* 1.3 73.1 - - + +
67B ARG* 1.3 66.6 + - - +
68B PHE 2.9 1.6 - - - -
69B VAL* 3.0 12.8 + - - +
70B ARG* 3.1 14.5 + - + +
77B ILE* 5.1 8.6 - - + +
79B ALA* 3.5 31.4 - - + -
92B ALA* 3.9 21.5 - - + +
95B ARG* 3.6 24.2 - - + +
96B GLY 4.4 0.7 - - - -
97B ALA* 3.8 19.5 - - + +
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Residues in contact with ARG 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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63B THR 2.9 21.7 + - - +
64B GLU* 2.8 34.2 + - - +
66B ILE* 1.3 74.7 - - - +
68B PHE* 1.3 62.8 + - - +
70B ARG* 4.1 1.4 - - - +
71B PRO* 3.3 18.0 - - - +
95B ARG* 2.7 68.2 - - + +
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Residues in contact with PHE 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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16B GLU* 5.4 2.5 - - - -
17B PHE* 3.7 34.1 - + + -
32B LEU* 4.2 3.8 - - + -
33B ARG* 3.7 66.9 - - + -
64B GLU* 2.9 24.0 + - - +
65B MET* 3.0 5.8 - - - +
67B ARG* 1.3 81.1 - - - +
69B VAL* 1.3 70.5 + - + +
71B PRO* 3.1 20.8 - - - +
72B LEU* 4.0 12.4 - - + +
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Residues in contact with VAL 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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32B LEU* 3.4 34.3 - - + -
36B VAL* 4.0 23.8 - - + -
47B ILE* 5.7 3.4 - - + -
49B LEU* 3.8 23.6 - - + -
65B MET 3.0 19.8 + - - +
66B ILE 3.0 3.5 + - - +
68B PHE* 1.3 77.4 - - + +
70B ARG* 1.3 65.8 + - - +
71B PRO 3.4 0.4 - - - -
72B LEU* 3.1 27.6 + - + +
73B THR* 4.0 5.0 - - + +
77B ILE* 3.9 20.6 - - + -
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Residues in contact with ARG 70 (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 ILE* 3.1 16.5 + - + +
67B ARG 4.1 2.2 - - - +
69B VAL* 1.3 78.7 - - - +
71B PRO* 1.3 71.3 - - + +
72B LEU 3.2 0.3 + - - -
73B THR* 2.9 44.1 + - - +
74B THR* 3.8 5.5 + - - +
75B LEU 2.8 23.2 + - - -
77B ILE* 3.5 18.3 - - + +
95B ARG 4.0 13.2 - - - +
96B GLY* 3.0 36.0 + - - -
98B ASP* 3.1 23.6 + - - -
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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