Contacts of the helix formed by residues 69 - 80 (chain B) in PDB entry 4U2M
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 GLY 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ALA 3.1 1.2 + - - -
68B ALA* 1.3 76.8 - - - +
70B LEU* 1.3 61.5 + - - +
71B GLY 3.4 2.2 - - - -
72B GLN* 3.4 9.2 + - - +
73B VAL* 3.2 25.8 + - - +
88B ASN* 6.1 1.8 - - - -
91B ASP* 3.7 30.2 + - - +
92B VAL* 4.2 9.5 - - - +
95B VAL* 4.1 7.7 - - - +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B PHE* 4.0 29.8 - - + -
30B VAL* 3.6 27.4 - - + -
35B PHE* 4.6 3.6 - - + -
49B PHE* 5.0 10.3 - - + -
64B ILE* 4.4 7.0 - - + -
67B ALA* 3.0 24.8 + - + +
68B ALA 3.5 0.2 - - - -
69B GLY* 1.3 73.8 - - - +
71B GLY* 1.3 64.9 + - - +
73B VAL* 3.1 5.0 + - + +
74B LEU* 2.9 44.5 + - + +
95B VAL* 4.0 22.9 - - + +
99B LEU* 4.8 10.8 - - + -
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Residues in contact with GLY 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ARG* 5.3 0.9 + - - -
35B PHE* 3.7 37.5 - - - -
67B ALA 4.7 0.6 + - - -
68B ALA 4.6 4.7 + - - -
69B GLY 3.4 0.4 - - - -
70B LEU* 1.3 79.2 - - - +
72B GLN* 1.3 60.4 + - - +
74B LEU* 3.5 3.0 + - - +
75B GLU* 3.0 23.7 + - - +
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Residues in contact with GLN 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ALA 5.4 0.4 + - - -
69B GLY* 3.4 11.4 + - - +
70B LEU 3.2 0.6 - - - -
71B GLY* 1.3 76.6 - - - +
73B VAL* 1.3 59.8 + - - +
75B GLU* 3.5 14.0 - - - +
76B PHE* 2.9 26.0 + - - +
81B LYS 4.3 2.9 - - - +
82B LEU* 4.0 11.7 - - + +
83B SER* 3.1 52.2 + - - +
88B ASN* 3.7 15.2 - - - +
92B VAL* 3.8 15.5 - - + -
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLY 3.2 14.9 + - - +
70B LEU* 3.1 10.6 + - + +
72B GLN* 1.3 72.3 - - - +
74B LEU* 1.3 68.4 + - - +
76B PHE* 3.2 8.4 + - - +
77B MET* 3.0 31.4 + - + +
82B LEU* 5.1 0.7 - - - -
92B VAL* 4.4 16.8 - - + +
95B VAL* 3.8 21.8 - - + -
96B ALA* 4.8 2.9 - - - +
99B LEU* 4.2 9.9 - - + -
101B MET* 3.8 29.6 - - + -
104B ILE* 4.0 15.5 - - + -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ARG* 4.0 16.2 - - - +
28B PHE* 4.3 15.7 - - + -
35B PHE* 3.6 38.6 - - + -
36B LYS 5.1 5.6 - - - +
37B ALA* 4.7 3.4 - - + -
42B LEU* 3.9 30.1 - - + -
49B PHE* 5.5 1.6 - - + -
70B LEU* 2.9 38.7 + - + +
71B GLY 3.8 3.8 - - - +
73B VAL* 1.3 77.3 - - - +
75B GLU* 1.3 63.5 + - - +
77B MET* 3.0 23.5 + - + +
78B TYR* 3.1 22.1 + - + -
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASN* 5.1 1.7 + - - -
18B ARG* 3.0 30.3 + - - +
71B GLY 3.0 18.8 + - - +
72B GLN* 3.5 21.1 - - - +
73B VAL 3.2 0.2 - - - -
74B LEU* 1.3 77.8 - - - +
76B PHE* 1.3 60.7 + - - +
78B TYR 3.4 0.2 + - - -
79B THR* 2.7 51.7 + - - +
81B LYS* 4.0 5.2 - - + +
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Residues in contact with PHE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B GLN 2.9 14.6 + - - +
73B VAL* 3.5 7.2 - - - +
74B LEU 3.2 0.2 - - - -
75B GLU* 1.3 77.9 - - - +
77B MET* 1.3 63.3 + - - +
79B THR* 4.1 0.2 - - - -
80B ALA* 2.8 40.0 + - - -
81B LYS 3.3 15.3 + - - +
82B LEU* 4.0 18.4 - - + -
101B MET* 3.7 23.8 - - + -
103B ASP* 4.9 9.6 - - + -
104B ILE* 3.5 26.0 - - + -
134B PHE* 3.5 39.5 - + + -
137B HIS* 3.4 33.8 + + - -
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Residues in contact with MET 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.5 12.1 - - - +
41B VAL* 4.8 2.9 - - + +
42B LEU* 3.7 28.0 - - - +
45B CYS* 3.7 35.1 - - + -
46B SER* 4.3 2.2 - - - -
49B PHE* 4.1 26.0 - - + -
73B VAL* 3.0 23.6 + - + +
74B LEU* 3.0 17.4 + - + +
76B PHE* 1.3 76.0 - - - +
78B TYR* 1.3 67.9 + - + +
101B MET* 3.6 35.9 - - + -
137B HIS* 2.9 24.4 + - - -
141B VAL* 4.4 0.2 - - - +
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Residues in contact with TYR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.4 20.8 - - - +
12B GLU* 5.2 0.3 - - - -
14B LEU* 3.5 36.3 - - + -
15B ASN* 3.5 38.0 - - - +
18B ARG* 3.5 33.2 - - + +
37B ALA* 3.7 4.4 - - + +
38B HIS* 2.7 48.5 + - - +
41B VAL* 3.6 24.3 - - + +
42B LEU* 4.2 15.9 - - + -
74B LEU* 3.1 23.3 + - + +
75B GLU 4.2 0.2 - - - +
77B MET* 1.3 84.2 - - + +
79B THR* 1.3 58.2 + - - +
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLN* 5.1 6.2 + - - -
11B LEU* 3.9 8.7 - - - +
15B ASN* 3.7 19.7 - - - +
75B GLU* 2.7 45.7 + - - +
78B TYR* 1.3 84.7 - - + +
80B ALA* 1.3 65.0 + - - +
81B LYS* 3.0 29.9 + - - +
133B GLN* 5.7 1.0 - - - +
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Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLN* 5.3 4.9 - - - +
11B LEU* 4.3 6.1 - - + -
76B PHE* 2.8 27.9 + - - -
79B THR* 1.3 73.6 - - - +
81B LYS* 1.3 58.4 + - - +
132B ILE 3.5 1.6 - - - +
133B GLN* 3.5 7.9 - - + -
134B PHE* 2.9 48.8 + - - +
137B HIS* 3.7 23.7 - - + -
138B ALA 4.9 2.0 - - - +
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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