Contacts of the helix formed by residues 73 - 81 (chain E) in PDB entry 6AHU
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 PHE 73 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E PHE* 4.2 11.2 - + - -
48E ALA* 3.7 29.8 - - + +
49E CYS* 3.4 27.4 - - - -
51E ILE* 5.9 2.0 - - + -
69E CYS* 4.1 7.8 - - - +
70E ARG* 3.8 18.4 + - + +
71E LYS 3.4 0.4 - - - -
72E GLU* 1.3 92.6 - - + +
74E TYR* 1.3 60.0 + - - +
75E GLN 3.4 3.6 - - - +
76E LEU* 3.8 22.2 + - + +
77E VAL* 4.2 1.7 - - - +
174J LEU* 3.7 31.9 - - + -
178J GLN* 4.1 17.0 - - - -
3L THR* 3.3 30.7 - - + -
4L LEU* 4.1 18.2 - - + -
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Residues in contact with TYR 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ARG* 4.1 19.0 + - + -
69E CYS* 3.7 21.7 - - - -
70E ARG 3.5 13.8 + - - +
71E LYS* 3.2 30.3 - - + -
72E GLU 3.8 0.6 - - - -
73E PHE* 1.3 78.4 - - - +
75E GLN* 1.3 92.5 + - + +
76E LEU 3.2 0.9 - - - -
77E VAL* 3.6 2.8 + - - +
78E TRP* 3.2 46.1 + + - +
102E HIS* 3.6 33.0 - + + -
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Residues in contact with GLN 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E PHE* 3.4 1.0 - - - +
74E TYR* 1.3 116.8 + - + +
76E LEU* 1.3 61.6 + - + +
78E TRP* 4.8 3.4 - - + -
79E SER* 3.3 23.2 - - - -
205I ASN* 3.5 13.2 + - - +
208I LEU* 4.2 33.5 - - + +
4L LEU* 4.2 25.3 - - + +
8L ARG* 5.0 5.5 + - - -
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Residues in contact with LEU 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ILE* 4.9 4.6 - - + +
41E HIS* 3.6 40.8 + - + +
44E PHE* 4.7 6.3 - - + -
45E GLY* 4.1 21.8 - - - -
49E CYS* 3.7 19.1 - - - -
73E PHE* 3.8 30.4 + - + +
74E TYR 3.2 0.8 - - - -
75E GLN* 1.3 82.2 - - + +
77E VAL* 1.3 64.9 + - - +
79E SER* 3.7 1.8 + - - -
80E ALA* 3.3 23.2 + - - +
4L LEU* 4.3 24.5 - - + -
8L ARG* 5.8 3.8 - - - +
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Residues in contact with VAL 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E LEU* 3.8 22.7 - - + -
33E VAL* 4.8 11.4 - - + -
37E ILE* 4.3 10.1 - - + -
49E CYS* 3.7 32.5 - - + -
53E PHE* 5.0 11.9 - - + -
67E LEU* 4.6 19.1 - - + -
69E CYS* 4.4 13.2 - - + -
73E PHE 4.2 4.9 - - - +
74E TYR 3.6 5.5 + - - +
76E LEU* 1.3 78.2 - - - +
78E TRP* 1.3 58.1 + - - +
80E ALA* 3.1 19.4 + - - +
81E LEU* 3.4 16.8 + - + +
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Residues in contact with TRP 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E LEU* 4.4 12.8 - - + +
74E TYR* 3.2 38.6 + + - +
75E GLN* 5.2 3.1 - - + -
77E VAL* 1.3 78.2 - - - +
79E SER* 1.3 57.2 + - - +
80E ALA 3.5 0.2 - - - -
81E LEU* 3.9 31.0 - - + +
82E PRO* 4.3 4.0 - - - +
99E ASN* 3.0 25.2 - - + +
102E HIS* 4.8 33.3 - + + +
201I TYR* 3.4 29.4 - - + -
202I ASP* 4.4 3.3 - - - +
204I ALA* 4.4 9.4 - - + -
205I ASN* 3.1 47.4 - - + +
208I LEU* 6.2 3.1 - - + -
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Residues in contact with SER 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E VAL* 5.6 1.6 - - - +
41E HIS* 5.1 6.6 + - - -
75E GLN 3.3 20.6 + - - -
76E LEU* 4.2 4.0 - - - -
77E VAL 3.2 0.4 - - - -
78E TRP* 1.3 75.8 - - - +
80E ALA* 1.3 59.8 + - - +
81E LEU 3.3 2.0 - - - -
82E PRO* 3.4 19.1 - - - +
83E PHE* 4.9 4.0 - - - -
205I ASN* 3.1 21.7 + - - -
206I LEU* 5.4 0.4 - - - +
209I LEU* 3.4 42.8 - - - +
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Residues in contact with ALA 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E VAL* 6.3 1.1 - - + -
36E THR* 4.6 9.4 + - + +
37E ILE* 4.0 28.3 - - + -
40E VAL* 5.2 8.3 - - + -
41E HIS* 5.2 5.6 - - + -
76E LEU 3.3 17.7 + - - +
77E VAL* 3.1 7.2 + - - +
79E SER* 1.3 75.8 - - - +
81E LEU* 1.3 63.2 + - - +
82E PRO 3.5 0.9 - - - -
83E PHE* 3.4 15.3 + - - +
84E ILE* 3.3 19.6 - - + +
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Residues in contact with LEU 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E LEU* 3.9 15.0 - - + -
11E CYS* 3.7 33.2 - - - -
33E VAL* 5.9 2.2 - - + -
67E LEU* 4.9 9.2 - - + -
77E VAL* 3.4 15.4 + - + +
78E TRP* 3.9 31.9 - - + +
80E ALA* 1.3 78.2 - - - +
82E PRO* 1.4 67.0 - - + +
83E PHE 3.4 0.3 + - - -
84E ILE* 3.6 32.8 + - + +
97E PHE* 4.4 25.0 + - + +
99E ASN* 4.8 11.9 - - + +
202I ASP* 4.1 8.5 - - - +
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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