Contacts of the helix formed by residues 66 - 74 (chain U) in PDB entry 7K60
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 LEU 66 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100J C 4.8 3.6 - - - -
64U SER 4.2 0.4 + - - -
65U SER* 1.3 77.5 + - - +
67U ALA* 1.3 63.4 + - - +
69U ILE* 3.1 16.1 - - + +
70U TYR* 2.9 29.1 + - + +
85U ARG* 3.5 28.9 - - + +
88U LEU* 4.4 24.0 - - + -
89U LYS* 3.8 16.4 - - + -
92U ILE* 4.5 16.4 - - + -
109U ALA* 3.6 41.3 - - + +
111U GLY 4.2 0.4 + - - -
113U PHE* 4.2 13.3 - - + -
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Residues in contact with ALA 67 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I G 6.0 0.9 - - - +
102I T 4.0 24.5 - - - +
65U SER* 3.2 7.5 + - - +
66U LEU* 1.3 79.6 - - - +
68U LYS* 1.3 59.5 + - - +
70U TYR* 3.3 3.3 + - - +
71U THR* 2.9 34.3 + - + +
85U ARG* 4.4 14.3 - - - +
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Residues in contact with LYS 68 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102I T 3.6 32.3 + - - +
103I C 3.8 29.9 + - - +
58U LEU* 4.3 17.9 - - + -
60U GLU* 3.5 27.4 - - + +
64U SER* 5.6 1.3 - - - +
65U SER 3.5 8.6 + - - +
67U ALA* 1.3 76.6 - - - +
69U ILE* 1.3 61.5 + - - +
71U THR* 2.6 26.4 + - - +
72U GLU* 2.9 23.5 + - + +
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Residues in contact with ILE 69 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51U VAL* 3.6 35.7 - - + +
54U THR* 3.7 18.8 - - + +
55U ILE* 3.5 33.9 - - + -
58U LEU* 4.1 12.8 - - + +
64U SER* 5.1 3.3 - - - -
65U SER 3.2 16.1 + - - +
66U LEU* 3.1 29.4 - - + +
68U LYS* 1.3 76.6 - - - +
70U TYR* 1.3 61.8 + - - +
72U GLU* 3.4 1.0 + - - +
73U ALA* 2.9 34.7 + - + +
88U LEU* 4.8 3.4 - - + -
92U ILE* 4.9 7.2 - - + -
113U PHE* 6.2 1.1 - - + -
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Residues in contact with TYR 70 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66U LEU* 2.9 22.8 + - + +
67U ALA 3.5 3.8 - - - +
69U ILE* 1.3 78.4 - - - +
71U THR* 1.3 64.6 + - + +
73U ALA 3.3 0.7 + - - -
74U LYS* 2.9 47.2 + - + +
79U PHE* 3.4 34.5 - + - -
81U GLN* 4.5 12.5 + - - -
85U ARG* 3.4 61.7 + - + +
88U LEU* 3.9 13.7 - - + -
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Residues in contact with THR 71 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103I C 5.6 5.3 + - - +
67U ALA* 2.9 20.4 + - + +
68U LYS* 2.6 32.0 + - - +
70U TYR* 1.3 84.9 - - + +
72U GLU* 1.3 64.4 + - - +
74U LYS* 3.5 24.2 + - - +
75U LYS* 4.4 8.7 + - - -
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Residues in contact with GLU 72 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U THR* 4.4 4.5 - - + -
57U ARG* 2.7 42.8 + - - +
58U LEU* 3.8 26.2 - - + -
68U LYS* 2.9 26.7 + - + +
69U ILE 4.0 2.7 - - - +
71U THR* 1.3 82.5 + - - +
73U ALA* 1.3 58.0 + - - +
74U LYS 3.3 0.2 - - - -
75U LYS* 3.2 40.0 + - - +
76U VAL* 4.6 2.8 - - - +
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Residues in contact with ALA 73 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50U LEU* 3.8 28.5 - - + -
51U VAL* 5.8 0.7 - - + -
54U THR* 4.7 7.6 - - + +
69U ILE* 2.9 21.2 + - + +
70U TYR 4.1 0.9 - - - +
72U GLU* 1.3 73.5 - - - +
74U LYS* 1.3 65.3 + - - +
75U LYS 3.1 2.9 - - - -
76U VAL* 3.0 24.3 + - - +
79U PHE* 3.2 22.4 - - + -
88U LEU* 4.5 6.7 - - + -
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Residues in contact with LYS 74 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70U TYR* 2.9 34.9 + - + +
71U THR* 3.7 15.3 - - - +
72U GLU 3.3 0.8 - - - -
73U ALA* 1.3 78.0 - - - +
75U LYS* 1.3 59.3 + - - +
76U VAL 3.2 7.4 + - - +
79U PHE* 4.1 16.2 - - + +
81U GLN* 3.9 32.8 + - - +
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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