Contacts of the helix formed by residues 65 - 77 (chain G) in PDB entry 3KTM
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 THR 65 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G ILE* 3.6 3.2 - - - +
64G ASP* 1.3 97.3 - - - +
66G LYS* 1.3 62.9 + - - +
67G GLU* 4.2 6.6 - - - +
68G GLY* 2.9 22.4 + - - -
69G ILE* 2.8 31.6 + - - +
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Residues in contact with LYS 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G ASP 5.2 3.1 - - - +
65G THR* 1.3 75.7 - - - +
67G GLU* 1.3 58.3 + - + +
69G ILE* 3.3 11.8 + - + +
70G LEU 2.9 24.4 + - - -
85G VAL* 4.3 3.8 - - + +
87G GLU* 3.6 11.5 + - - -
115G TYR* 3.8 24.7 - - - -
146G THR* 5.4 9.9 - - - +
176G ILE* 3.4 34.6 - - + +
177G ASP* 3.2 38.1 + - + +
178G LYS* 5.3 8.7 - - - +
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Residues in contact with GLU 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G THR* 3.2 6.2 - - - +
66G LYS* 1.3 76.9 - - + +
68G GLY* 1.3 58.7 + - - +
70G LEU* 3.5 4.9 + - - +
71G GLN* 3.0 30.1 + - - +
176G ILE* 4.1 27.1 - - + +
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Residues in contact with GLY 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G ILE* 3.6 16.9 - - - +
65G THR* 2.9 21.8 + - - -
67G GLU* 1.3 76.1 - - - +
69G ILE* 1.3 58.6 + - - +
71G GLN* 3.2 11.0 + - - +
72G TYR* 3.0 27.7 + - - +
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Residues in contact with ILE 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G ILE* 4.0 16.6 - - + -
36G MET* 3.6 20.6 - - + -
63G ILE* 4.0 14.8 - - + +
64G ASP 5.6 0.9 - - - -
65G THR 2.8 21.0 + - - +
66G LYS* 3.3 16.6 + - - +
68G GLY* 1.3 72.6 - - - +
70G LEU* 1.3 67.0 + - - +
72G TYR* 3.1 6.8 + - - +
73G CYS* 2.9 23.0 + - - +
85G VAL* 4.4 9.6 - - + -
115G TYR* 3.5 61.5 - - + +
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Residues in contact with LEU 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G BU4 5.9 3.1 - - + -
66G LYS 2.9 8.4 + - - +
67G GLU* 3.8 6.1 - - - +
69G ILE* 1.3 75.3 - - - +
71G GLN* 1.3 59.0 + - - +
73G CYS* 3.3 1.2 - - - +
74G GLN* 2.9 59.9 + - - +
82G ILE* 3.4 25.8 - - + +
83G THR 4.3 14.6 - - - +
84G ASN* 4.1 7.6 - - - +
85G VAL* 3.6 12.0 - - + +
176G ILE* 3.3 36.3 - - + -
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Residues in contact with GLN 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G GLU* 3.0 16.7 + - - +
68G GLY* 3.3 14.1 - - - +
70G LEU* 1.3 74.8 - - - +
72G TYR* 1.3 54.5 + - - +
74G GLN* 3.1 19.2 + - + +
75G GLU* 2.8 34.7 + - - +
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Residues in contact with TYR 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G ILE* 4.0 30.1 - - + -
42G ASN* 3.5 35.3 + - + +
43G MET 4.8 3.4 - - - -
44G HIS* 5.0 2.8 + - + -
55G ASP* 2.9 37.5 + - - +
56G PRO* 4.0 0.2 - - - +
60G LYS* 3.4 32.8 - - + -
63G ILE* 4.6 11.4 - - + -
68G GLY 3.0 13.3 + - - +
69G ILE* 3.1 11.4 + - - +
71G GLN* 1.3 71.8 - - - +
73G CYS* 1.3 65.8 + - - +
75G GLU* 3.1 15.4 + - - +
76G VAL* 2.9 46.9 + - + +
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Residues in contact with CYS 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G ILE* 3.8 14.1 - - - -
69G ILE* 2.9 11.8 + - - +
70G LEU 3.3 10.8 - - - +
72G TYR* 1.3 78.1 - - - +
74G GLN* 1.3 62.1 + - - +
76G VAL* 3.3 8.5 - - - +
77G TYR* 3.0 26.8 + - - +
82G ILE* 3.8 13.9 - - + -
85G VAL* 3.7 18.4 - - - -
115G TYR 4.9 0.4 - - - -
116G ARG 4.8 0.7 - - - -
117G CYS* 2.0 53.2 - - - -
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Residues in contact with GLN 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G LEU* 2.9 45.6 + - + +
71G GLN* 3.1 16.7 + - - +
73G CYS* 1.3 74.8 - - - +
75G GLU* 1.3 65.4 + - - +
77G TYR 3.6 4.1 - - - +
78G PRO* 3.5 20.4 - - - +
80G LEU 5.7 1.8 - - - +
82G ILE* 3.2 33.4 + - + +
83G THR* 5.2 0.6 - - - +
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Residues in contact with GLU 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E PRO* 4.0 19.4 - - + +
79E GLU* 3.1 40.4 - - + +
55G ASP* 5.6 1.1 - - - +
57G SER* 5.5 0.9 + - - -
60G LYS* 3.6 18.3 + - - +
71G GLN 2.8 12.9 + - - +
72G TYR* 3.1 20.8 + - - +
74G GLN* 1.3 79.1 - - - +
76G VAL* 1.3 64.4 + - + +
78G PRO* 3.3 15.5 - - - +
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Residues in contact with VAL 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G ILE* 4.3 3.6 - - + -
44G HIS* 4.3 24.8 + - + +
56G PRO* 4.3 20.7 - - + +
72G TYR* 2.9 52.5 + - + +
73G CYS* 3.3 16.4 - - - +
75G GLU* 1.3 77.8 - - + +
77G TYR* 1.3 89.2 + - + +
78G PRO* 3.2 7.6 - - - +
79G GLU* 4.5 0.5 - - - +
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Residues in contact with TYR 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G PRO* 3.3 30.7 - - + -
33G GLN 3.1 30.0 + - - -
44G HIS* 3.8 10.5 - + - +
45G MET 2.5 32.1 + - - -
47G VAL* 4.0 14.6 - - + -
73G CYS 3.0 23.6 + - - +
74G GLN* 3.6 6.3 - - - +
76G VAL* 1.3 97.5 - - + +
78G PRO* 1.3 63.0 - - - +
79G GLU* 3.0 14.8 - - - +
80G LEU* 3.0 37.1 + - + +
82G ILE* 3.9 7.6 - - + +
117G CYS* 3.8 16.4 - - + -
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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