Contacts of the helix formed by residues 65 - 70 (chain T) in PDB entry 3MQT
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 ASN 65 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54T SER 2.9 27.4 + - - -
55T GLU* 3.7 4.0 - - - +
56T ILE* 3.0 35.3 + - - +
58T ASN* 2.7 18.4 + - - +
64T ASN* 1.3 73.9 - - - +
66T ILE* 1.3 64.7 + - - +
67T LYS* 2.8 41.8 + - - +
68T GLU* 3.1 34.4 + - + +
69T ALA 4.1 1.7 + - - -
88T THR* 5.1 1.9 + - - -
89T THR* 4.8 0.2 - - - -
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Residues in contact with ILE 66 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12T PHE* 5.0 0.7 - - + -
53T PHE* 4.5 15.8 + - + +
54T SER* 4.2 28.9 - - - -
56T ILE* 5.2 1.8 - - - +
64T ASN 3.3 3.2 + - - -
65T ASN* 1.3 72.4 + - - +
67T LYS* 1.3 66.2 + - + +
69T ALA* 3.2 19.9 + - - +
70T VAL* 4.3 2.6 + - - +
85T MET* 4.1 16.6 - - + +
88T THR* 5.3 0.4 - - - -
89T THR* 4.0 21.3 - - + +
98T GLY 4.6 0.7 - - - +
101T ALA* 3.8 15.7 - - + -
102T ILE* 3.5 44.4 - - + +
105T ILE* 3.9 18.3 - - + +
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Residues in contact with LYS 67 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10T VAL* 2.9 51.3 + - + +
11T GLU* 4.5 5.9 - - - +
12T PHE* 4.9 2.1 - - + +
54T SER* 3.2 35.3 + - - +
55T GLU* 4.3 17.2 + - - +
65T ASN* 2.8 15.4 + - - +
66T ILE* 1.3 81.8 - - + +
68T GLU* 1.3 57.9 + - + +
69T ALA 3.1 0.4 - - - -
70T VAL* 3.0 15.3 + - - +
71T ILE* 3.0 37.8 + - + +
105T ILE* 5.0 2.0 - - - -
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Residues in contact with GLU 68 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58T ASN* 3.0 36.7 + - - +
64T ASN* 5.6 2.5 - - + -
65T ASN* 3.1 27.8 + - + +
67T LYS* 1.3 77.0 - - + +
69T ALA* 1.3 59.5 + - - +
70T VAL 3.3 0.6 + - - -
71T ILE* 4.4 17.9 + - + +
73T ARG* 5.4 3.3 + - - -
84T ARG* 5.3 1.0 - - - -
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Residues in contact with ALA 69 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65T ASN 4.1 1.2 + - - -
66T ILE 3.2 14.1 + - - +
67T LYS 3.1 0.8 - - - -
68T GLU* 1.3 80.2 - - - +
70T VAL* 1.3 60.5 + - - +
73T ARG* 3.6 3.7 - - - +
84T ARG* 2.8 45.7 + - + +
85T MET* 3.6 37.0 - - + +
88T THR* 3.8 13.2 - - + +
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Residues in contact with VAL 70 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7T ILE* 3.3 22.5 - - + +
10T VAL* 3.9 23.8 - - + -
66T ILE 4.5 2.5 - - - +
67T LYS* 3.3 17.3 - - - +
69T ALA* 1.3 85.4 - - - +
71T ILE* 1.3 61.7 + - - +
72T GLY 3.2 0.3 + - - -
73T ARG* 2.9 29.3 + - - +
81T ASN* 4.0 22.9 - - + -
85T MET* 4.0 25.1 - - + -
105T ILE* 4.3 12.1 - - + -
109T LEU* 4.2 10.3 - - + -
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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