Contacts of the helix formed by residues 73 - 83 (chain E) in PDB entry 3IYD
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 73 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1356D LEU* 4.2 11.8 - - - +
1367D GLN* 2.8 56.0 + - - +
25E ARG* 3.4 27.0 + - - +
71E GLU* 3.1 4.6 + - - -
72E GLN* 1.3 81.5 - - + +
74E GLU* 1.3 62.5 + - - +
75E GLN 3.5 1.3 - - - -
76E GLU* 3.1 28.5 - - - +
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Residues in contact with GLU 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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15D GLU* 3.9 20.6 - - - +
72E GLN* 3.8 7.9 - - + +
73E GLN* 1.3 78.8 - - - +
75E GLN* 1.3 61.6 + - - +
76E GLU 3.3 2.6 + - - -
77E ALA* 4.0 4.8 + - - +
78E ALA* 3.4 17.9 + - + +
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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
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1372D ARG* 2.8 37.4 + - - +
1378D ALA* 5.1 1.2 - - - +
1381D ALA* 3.8 29.3 - - + +
1382D PRO* 5.6 0.9 - - + -
71E GLU* 3.0 13.8 + - - +
72E GLN* 3.3 18.9 - - - +
74E GLU* 1.3 75.1 - - - +
76E GLU* 1.3 65.7 + - - +
77E ALA 3.1 3.4 - - - -
78E ALA* 3.0 18.9 + - + -
79E GLU* 3.2 45.1 + - + +
80E LEU 4.3 0.9 + - - +
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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
----------------------------------------------------------
1285C TYR* 4.9 3.3 + - - -
1372D ARG* 4.0 23.5 + - - +
25E ARG* 2.8 48.1 + - - +
28E ARG* 3.9 22.8 + - - -
29E GLN* 3.4 16.4 + - - +
71E GLU* 3.3 7.1 + - - +
73E GLN* 3.1 25.6 - - - +
74E GLU 4.6 0.7 - - - -
75E GLN* 1.3 82.0 - - - +
77E ALA* 1.3 66.9 + - + +
80E LEU* 3.2 19.6 - - - +
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Residues in contact with ALA 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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1316C GLU* 6.5 0.9 - - + -
28E ARG* 5.8 7.0 - - - +
74E GLU 4.0 4.1 + - - +
75E GLN 3.1 0.2 - - - -
76E GLU* 1.3 87.5 - - + +
78E ALA* 1.3 59.9 + - - +
79E GLU 3.9 0.4 - - - -
80E LEU* 4.1 11.2 - - + -
81E GLN* 4.2 31.1 - - + +
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Residues in contact with ALA 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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74E GLU* 3.4 21.3 + - + +
75E GLN* 3.0 12.7 + - + -
77E ALA* 1.3 79.4 - - - +
79E GLU* 1.3 69.3 + - + +
80E LEU 3.3 0.9 - - - -
81E GLN* 4.3 1.6 + - - +
82E ALA* 3.5 18.0 + - - +
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Residues in contact with GLU 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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1381D ALA* 5.6 4.7 - - + +
75E GLN* 3.2 40.0 + - + +
78E ALA* 1.3 82.8 - - + +
80E LEU* 1.3 63.9 + - - +
81E GLN 3.5 0.2 - - - -
82E ALA* 3.5 15.3 - - - +
83E VAL* 3.2 26.2 + - - +
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Residues in contact with LEU 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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1372D ARG* 6.2 0.4 - - - +
1374D ALA* 6.4 2.2 - - + -
29E GLN* 3.4 31.9 - - + +
32E VAL* 3.7 38.8 - - + +
33E GLY* 4.3 13.0 - - - -
37E PRO* 5.4 9.2 - - + -
75E GLN* 4.3 2.0 + - - +
76E GLU 3.2 20.4 - - - +
77E ALA* 4.1 5.6 - - + -
78E ALA 3.3 0.8 - - - +
79E GLU* 1.3 74.7 - - - +
81E GLN* 1.3 70.2 + - + +
82E ALA 3.0 7.9 + - - -
83E VAL* 3.3 22.7 - - + +
84E THR* 3.4 9.9 + - - +
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Residues in contact with GLN 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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1315C MET* 3.5 30.7 - - - +
32E VAL* 5.4 10.4 - - + +
77E ALA* 4.2 28.4 + - - +
78E ALA 4.3 3.4 + - - +
80E LEU* 1.3 88.6 - - + +
82E ALA* 1.3 58.1 + - - +
84E THR 3.2 20.2 - - - +
85E ALA* 4.2 7.9 - - - +
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Residues in contact with ALA 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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78E ALA 3.5 19.1 + - - +
79E GLU* 3.5 22.0 - - - +
80E LEU 3.0 0.8 - - - -
81E GLN* 1.3 79.2 - - - +
83E VAL* 1.3 65.2 + - - +
84E THR* 3.3 1.8 + - - -
85E ALA* 5.0 1.2 + - - +
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Residues in contact with VAL 83 (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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79E GLU 3.2 16.5 + - - +
80E LEU* 3.3 15.9 - - + +
82E ALA* 1.3 80.5 - - - +
84E THR* 1.3 70.7 + - - +
85E ALA 4.3 0.4 + - - -
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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