Contacts of the helix formed by residues 62 - 76 (chain B) in PDB entry 3UMO
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 62 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ALA* 1.3 76.6 - - - +
63B GLY* 1.3 61.7 + - - -
65B THR* 3.5 1.6 + - - -
66B GLY* 3.1 15.2 + - - -
84B GLU* 5.6 1.1 - - - -
85B ALA 3.5 17.5 - - - -
87B ASP 3.8 12.2 + - - -
88B TRP* 3.8 4.0 - - - -
89B THR* 3.0 29.7 + - - +
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Residues in contact with GLY 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ALA* 5.1 8.3 - - - -
62B GLY* 1.3 72.7 - - - +
64B ALA* 1.3 65.6 + - - -
65B THR 3.2 0.4 - - - -
67B GLU* 3.1 33.1 + - - +
84B GLU* 6.1 1.2 - - - +
85B ALA 4.6 2.4 + - - -
86B LYS 5.4 1.6 + - - -
88B TRP* 4.4 11.1 - - - +
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLY* 5.1 8.9 - - - -
64A ALA* 5.5 4.2 - - - +
86A LYS 5.9 2.0 - - - +
88A TRP* 3.8 39.2 - - + +
63B GLY* 1.3 69.4 - - - -
65B THR* 1.3 66.0 + - - +
67B GLU* 3.3 16.6 + - - +
68B HIS* 3.0 23.6 + - - +
88B TRP* 5.7 0.2 - - - +
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Residues in contact with THR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR* 5.5 2.2 - - + -
88A TRP* 3.8 33.2 - - + +
13B LEU* 3.7 25.6 - - + +
62B GLY 3.5 1.7 + - - -
64B ALA* 1.3 77.3 - - - +
66B GLY* 1.3 58.5 + - - +
68B HIS* 3.2 4.0 + - - +
69B LEU* 2.9 27.4 + - - +
88B TRP* 3.9 11.5 - - + +
89B THR* 2.7 37.9 + - - +
91B GLN* 4.1 15.7 - - - +
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Residues in contact with GLY 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ALA* 4.0 10.1 - - - +
62B GLY 3.1 22.9 + - - -
63B GLY 3.6 0.7 - - - -
65B THR* 1.3 78.0 + - - +
67B GLU* 1.3 61.2 + - - +
69B LEU* 3.2 8.1 + - - +
70B VAL* 3.0 26.7 + - - +
89B THR* 3.3 22.6 - - - -
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Residues in contact with GLU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLY* 3.1 22.1 + - - +
64B ALA* 3.6 15.8 + - - +
66B GLY* 1.3 75.3 - - - +
68B HIS* 1.3 58.7 + - - +
70B VAL* 3.4 7.9 + - - +
71B SER* 2.9 28.1 + - - -
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Residues in contact with HIS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TRP* 4.2 18.8 - + + -
13B LEU* 4.0 6.1 - - + -
35B PHE* 3.8 43.9 - + + +
64B ALA 3.0 16.3 + - - +
65B THR 3.2 4.2 + - - +
67B GLU* 1.3 73.6 - - - +
69B LEU* 1.3 61.4 + - - +
71B SER* 3.2 11.8 + - - -
72B LEU* 2.8 54.1 + - + +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PRO* 4.0 19.1 - - + -
12B SER 3.6 18.2 - - - +
13B LEU* 4.0 13.8 - - + +
37B PRO* 3.5 36.6 - - + -
38B GLY 4.2 0.9 - - - +
42B ILE* 4.1 7.9 - - + -
59B PHE* 3.7 28.0 - - + -
60B PRO 5.2 0.2 - - - +
61B ALA* 5.4 0.2 - - + -
65B THR 2.9 13.4 + - - +
66B GLY* 3.2 8.9 + - - +
68B HIS* 1.3 77.5 - - - +
70B VAL* 1.3 61.9 + - - +
72B LEU* 3.3 4.5 + - - +
73B LEU* 3.2 26.2 + - + +
89B THR* 4.0 15.9 - - + +
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Residues in contact with VAL 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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59B PHE* 4.0 12.6 - - + -
61B ALA* 4.2 7.0 - - + -
66B GLY 3.0 13.6 + - - +
67B GLU* 3.7 9.9 - - - +
68B HIS 3.3 0.2 - - - -
69B LEU* 1.3 75.7 - - - +
71B SER* 1.3 64.2 + - - +
73B LEU* 3.3 7.3 + - - +
74B ALA* 3.0 23.6 + - + +
80B VAL* 4.5 17.5 - - + +
82B THR* 3.8 28.9 - - + +
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Residues in contact with SER 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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67B GLU 2.9 17.2 + - - -
68B HIS* 3.2 19.4 + - - -
70B VAL* 1.3 79.5 - - - +
72B LEU* 1.3 61.7 + - - +
74B ALA* 3.3 7.0 + - - +
75B ASP* 3.2 32.5 + - - +
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Residues in contact with LEU 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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13B LEU* 3.7 30.1 - - + -
35B PHE 3.6 29.8 - - - +
36B GLU* 3.9 10.1 - - - +
37B PRO* 4.0 14.1 - - + -
68B HIS* 2.8 36.6 + - + +
69B LEU* 3.6 5.4 - - - +
70B VAL 3.3 0.2 - - - -
71B SER* 1.3 76.2 - - - +
73B LEU* 1.3 61.3 + - - +
75B ASP* 3.3 14.2 + - + +
76B GLU* 3.2 30.0 + - - +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PRO* 3.7 26.9 - - + -
42B ILE* 4.1 18.6 - - + -
46B ARG* 4.0 22.0 - - + -
57B ALA* 5.0 3.1 - - + -
59B PHE* 3.8 36.1 - - + -
69B LEU* 3.2 15.0 + - + +
70B VAL 3.3 6.5 + - - +
72B LEU* 1.3 75.0 - - - +
74B ALA* 1.3 63.4 + - - +
76B GLU* 3.2 8.0 + - - +
77B ASN 3.1 4.2 + - - -
78B VAL* 2.9 50.2 + - + +
80B VAL* 3.8 10.8 - - + -
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B VAL* 3.0 14.6 + - + +
71B SER* 3.5 12.3 - - - +
73B LEU* 1.3 78.7 - - - +
75B ASP* 1.3 61.8 + - - +
77B ASN* 3.1 26.6 + - - +
78B VAL 4.5 3.8 + - - +
80B VAL* 5.7 0.2 - - - +
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Residues in contact with ASP 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B SER* 3.2 22.8 + - - +
72B LEU* 3.6 15.7 - - + +
73B LEU 3.3 0.2 - - - -
74B ALA* 1.3 79.5 - - - +
76B GLU* 1.3 61.3 + - + +
77B ASN* 3.2 9.7 + - - +
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PRO* 3.9 14.4 - - - +
46B ARG* 2.8 52.8 + - - +
49B ALA* 4.8 6.6 - - - +
50B HIS* 5.3 5.2 + - - +
72B LEU* 3.2 16.8 + - - +
73B LEU* 3.2 11.6 + - - +
75B ASP* 1.3 79.7 - - + +
77B ASN* 1.3 71.7 + - - +
78B VAL* 3.3 11.5 + - + +
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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