Contacts of the helix formed by residues 62 - 76 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ALA* 1.3 75.3 - - - +
63A GLY* 1.3 63.2 + - - -
65A THR* 3.5 1.2 + - - -
66A GLY* 3.1 13.9 + - - -
84A GLU* 5.3 2.2 - - - -
85A ALA 3.5 17.7 - - - -
87A ASP 3.9 11.3 + - - -
88A TRP* 3.5 7.4 - - - -
89A THR* 2.9 28.2 + - - +
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Residues in contact with GLY 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLY* 1.3 73.7 - - - +
64A ALA* 1.3 60.9 + - - -
65A THR 3.2 0.4 - - - -
67A GLU* 3.0 34.4 + - - +
84A GLU* 5.7 3.2 + - - +
85A ALA 4.7 1.6 + - - -
86A LYS 5.7 1.0 + - - -
88A TRP* 4.4 11.4 - - - +
64B ALA* 5.1 9.0 - - - -
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLY* 1.3 70.2 - - - -
65A THR* 1.3 60.2 + - - +
67A GLU* 3.3 16.9 + - - +
68A HIS* 3.0 27.0 + - - +
88A TRP* 5.6 0.4 - - - +
63B GLY* 5.1 8.5 - - - -
64B ALA* 5.5 3.8 - - - +
86B LYS 5.9 2.2 - - - +
88B TRP* 3.9 38.5 - - + +
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Residues in contact with THR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.7 22.5 - - + +
62A GLY 3.5 1.7 + - - -
64A ALA* 1.3 77.7 - - - +
66A GLY* 1.3 58.5 + - - +
68A HIS* 3.3 3.1 + - - +
69A LEU* 3.0 27.9 + - - +
88A TRP* 3.8 12.5 - - + +
89A THR* 2.7 38.8 + - - +
91A GLN* 3.9 15.3 - - + +
65B THR* 5.5 2.2 - - + -
88B TRP* 3.9 33.4 - - + +
91B GLN* 5.1 1.6 - - - +
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Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ALA* 4.1 8.6 - - - +
62A GLY 3.1 23.0 + - - -
63A GLY 3.6 0.9 - - - -
65A THR* 1.3 75.9 + - - +
67A GLU* 1.3 63.1 + - - +
69A LEU* 3.3 6.1 + - - +
70A VAL* 3.0 29.0 + - - +
89A THR* 3.3 22.1 - - - -
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLY 3.0 20.7 + - - +
64A ALA* 3.5 17.8 + - - +
65A THR 3.3 0.2 - - - -
66A GLY* 1.3 75.9 - - - +
68A HIS* 1.3 57.8 + - - +
70A VAL* 3.3 8.5 + - - +
71A SER* 2.9 27.6 + - - -
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Residues in contact with HIS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.9 15.9 - - + -
35A PHE* 3.8 43.6 - + + +
64A ALA 3.0 16.8 + - - +
65A THR 3.7 4.5 - - - +
66A GLY 3.2 0.2 - - - -
67A GLU* 1.3 74.2 - - - +
69A LEU* 1.3 60.3 + - - +
71A SER* 3.2 12.7 + - - -
72A LEU* 2.9 50.3 + - + +
88B TRP* 4.1 15.2 - + + -
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PRO* 3.9 24.0 - - + -
12A SER 3.6 14.8 - - - +
13A LEU* 3.9 12.6 - - + +
37A PRO* 3.5 37.9 - - + -
38A GLY 4.2 0.9 - - - +
42A ILE* 4.1 7.2 - - + -
59A PHE* 3.6 29.2 - - + -
61A ALA* 5.3 0.2 - - + -
65A THR 3.0 14.6 + - - +
66A GLY* 3.3 9.4 + - - +
68A HIS* 1.3 75.7 - - - +
70A VAL* 1.3 62.2 + - - +
72A LEU* 3.3 4.3 + - - +
73A LEU* 3.2 26.1 + - + +
89A THR* 4.1 14.8 - - + +
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 4.1 15.0 - - + -
61A ALA* 4.2 6.7 - - + -
66A GLY 3.0 15.2 + - - +
67A GLU* 3.6 10.1 - - - +
69A LEU* 1.3 76.3 - - - +
71A SER* 1.3 58.3 + - - +
73A LEU* 3.3 5.6 + - - +
74A ALA* 3.0 27.7 + - + +
80A VAL* 4.5 17.4 - - + +
82A THR* 4.0 27.4 - - + +
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Residues in contact with SER 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A GLU 2.9 17.2 + - - -
68A HIS* 3.2 16.6 + - - -
70A VAL* 1.3 76.5 - - - +
72A LEU* 1.3 65.6 + - - +
74A ALA* 3.3 7.7 + - - +
75A ASP* 3.0 34.0 + - - -
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.8 24.0 - - + -
35A PHE 3.6 34.5 - - - +
36A GLU* 3.8 9.0 - - - -
37A PRO* 3.9 15.7 - - + -
68A HIS* 2.9 37.1 + - + +
69A LEU* 3.6 5.2 - - - +
71A SER* 1.3 77.1 - - - +
73A LEU* 1.3 62.7 + - - +
75A ASP* 3.3 13.6 + - + +
76A GLU* 3.1 29.5 + - - +
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PRO* 3.8 24.5 - - + -
42A ILE* 4.0 25.8 - - + -
46A ARG* 4.0 16.6 - - + -
57A ALA* 5.0 2.7 - - + -
59A PHE* 3.7 37.0 - - + -
69A LEU* 3.2 15.1 + - + +
70A VAL* 3.8 7.2 - - - +
71A SER 3.3 0.2 - - - -
72A LEU* 1.3 74.6 - - - +
74A ALA* 1.3 65.2 + - - +
76A GLU* 3.1 7.1 + - - +
77A ASN 3.0 4.0 + - - -
78A VAL* 2.9 43.4 + - + +
80A VAL* 3.9 17.0 - - + -
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A VAL* 3.0 15.4 + - + +
71A SER* 3.5 12.1 - - - +
72A LEU 3.3 0.2 - - - -
73A LEU* 1.3 77.0 - - - +
75A ASP* 1.3 60.8 + - - +
77A ASN* 3.0 26.4 + - - +
78A VAL 4.5 4.2 + - - -
80A VAL* 5.7 0.6 - - - +
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Residues in contact with ASP 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A SER* 3.0 27.1 + - - +
72A LEU* 3.6 17.6 - - + +
73A LEU 3.2 0.2 - - - -
74A ALA* 1.3 79.1 - - - +
76A GLU* 1.3 61.9 + - + +
77A ASN* 3.2 8.5 + - - -
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PRO* 4.2 11.1 - - - +
46A ARG* 2.6 55.4 + - - +
49A ALA* 5.0 6.6 - - - +
50A HIS* 5.6 6.3 - - + -
72A LEU* 3.1 17.0 + - - +
73A LEU* 3.1 10.6 + - - +
75A ASP* 1.3 76.8 - - + +
77A ASN* 1.3 70.8 + - - +
78A VAL* 3.2 12.1 + - + +
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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