Contacts of the helix formed by residues 74 - 82 (chain E) in PDB entry 3PHW
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 GLN 74 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E ARG 5.1 7.2 - - - +
71E LYS 6.0 1.1 - - - +
72E TYR* 2.9 2.0 + - - +
73E TYR* 1.3 98.1 - - + +
75E GLU* 1.3 66.9 + - + +
76E GLU 3.6 2.8 + - - +
79E ALA* 5.5 0.5 - - - +
80E ARG* 5.7 2.4 + - - -
86E LEU* 3.5 33.5 - - + +
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Residues in contact with GLU 75 (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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71E LYS 6.1 0.7 - - - +
72E TYR* 2.8 15.8 + - + +
74E GLN* 1.3 82.8 - - + +
76E GLU* 1.3 60.1 + - - +
77E PRO* 3.3 12.1 - - - +
80E ARG* 5.6 5.2 + - - +
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Residues in contact with GLU 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E GLN* 4.4 3.1 + - - -
72E TYR* 3.2 18.7 + - - +
73E TYR* 3.9 6.4 - - - +
74E GLN 3.4 4.6 - - - +
75E GLU* 1.3 78.1 - - - +
77E PRO* 1.3 76.3 - - - +
78E GLU* 4.5 2.5 + - - +
79E ALA* 3.0 16.5 + - + +
80E ARG* 4.0 5.6 + - - +
103E LEU* 3.9 19.1 - - + +
106E SER* 2.7 26.5 + - - -
107E MET* 3.7 27.5 - - + +
110E LYS* 2.6 36.7 + - - -
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Residues in contact with PRO 77 (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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13E ILE* 3.9 20.0 - - + -
16E GLN* 5.6 4.3 - - - +
75E GLU 3.3 9.8 - - - +
76E GLU* 1.3 92.5 - - + +
78E GLU* 1.3 63.0 + - - +
80E ARG* 3.1 33.4 + - - +
42F ARG* 4.0 6.5 - - - +
49F GLN* 2.8 47.1 - - + +
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Residues in contact with GLU 78 (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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16E GLN* 5.2 3.4 + - - +
76E GLU* 3.2 3.2 - - + +
77E PRO* 1.3 75.3 - - - +
79E ALA* 1.3 60.5 + - - +
80E ARG 3.0 2.7 - - - -
81E LEU* 2.8 27.5 + - + +
82E VAL* 3.9 3.1 + - - +
102E THR* 2.6 34.4 + - - +
103E LEU* 3.3 25.7 + - + -
106E SER* 5.8 1.1 - - - -
133E PHE* 5.1 1.6 - - - -
42F ARG* 3.2 46.8 + - - +
49F GLN* 3.8 1.8 - - - +
72F ARG* 3.0 39.8 + - - +
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Residues in contact with ALA 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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73E TYR* 3.4 47.1 + - + +
74E GLN 5.5 0.7 - - - +
76E GLU* 3.0 20.0 + - + +
78E GLU* 1.3 77.8 - - - +
80E ARG* 1.3 55.4 + - + +
82E VAL* 2.9 33.7 + - - +
83E GLY* 3.4 4.9 + - - -
84E LEU 5.3 0.2 - - - +
103E LEU* 3.8 7.0 - - + +
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Residues in contact with ARG 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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74E GLN 5.7 2.4 + - - -
75E GLU* 5.6 4.9 + - - +
76E GLU 4.5 4.5 - - - +
77E PRO* 3.3 45.4 + - - +
78E GLU 3.0 1.0 - - - -
79E ALA* 1.3 76.6 - - + +
81E LEU* 1.3 62.4 + - + +
82E VAL 3.3 0.6 + - - -
83E GLY* 3.8 10.7 + - - +
49F GLN* 4.2 22.6 + - - +
51F GLU* 3.5 42.2 + - + -
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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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97C ASN* 5.5 1.6 + - - -
78E GLU* 2.8 17.4 + - - +
80E ARG* 1.3 79.5 - - + +
82E VAL* 1.3 62.4 + - - +
83E GLY 3.5 0.2 - - - -
27F LYS* 4.1 14.8 - - - +
38F PRO 4.9 0.7 - - - +
39F ASP* 3.8 23.3 - - - +
41F GLN 3.9 13.7 - - - +
42F ARG* 3.8 20.9 - - + -
49F GLN* 3.6 24.2 - - - +
52F ASP* 5.6 0.7 - - - +
72F ARG* 3.9 24.5 + - + -
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Residues in contact with VAL 82 (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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97C ASN* 3.7 20.0 + - - +
73E TYR* 3.8 14.1 - - + +
78E GLU 4.3 2.7 - - - +
79E ALA* 2.9 13.4 + - - +
81E LEU* 1.3 81.1 - - - +
83E GLY* 1.3 56.4 + - - +
84E LEU* 3.0 37.1 + - + +
89E TYR* 4.2 10.5 - - + -
92E ARG* 6.0 0.2 - - - +
103E LEU* 3.5 31.4 - - + -
72F ARG* 4.2 19.1 - - - +
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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