Contacts of the helix formed by residues 59 - 75 (chain G) in PDB entry 4UIS
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 THR 59 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52G ARG* 3.4 10.9 - - - +
58G ILE* 1.3 76.2 - - - +
60G LYS* 1.3 58.8 + - - +
61G ASP* 4.3 7.5 + - - +
62G GLU* 2.8 52.8 + - - +
63G ALA 3.2 3.8 + - - -
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Residues in contact with LYS 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G ARG* 3.9 10.9 - - - +
13G LEU* 3.7 30.3 - - - +
15G LEU* 3.7 33.8 - - + +
58G ILE 3.6 1.6 + - - -
59G THR* 1.3 73.1 - - - +
61G ASP* 1.3 60.4 + - - +
63G ALA* 2.9 5.6 + - + +
64G GLU* 2.9 49.5 + - + +
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Residues in contact with ASP 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G THR* 3.1 8.2 - - - +
60G LYS* 1.3 82.5 - - - +
62G GLU* 1.3 57.1 + - - +
64G GLU* 3.4 21.1 + - - +
65G LYS* 2.9 27.9 + - - +
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Residues in contact with GLU 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G ILE* 3.3 29.5 - - + +
52G ARG* 2.6 50.2 + - - -
58G ILE* 3.3 14.6 - - + +
59G THR* 2.8 21.2 + - - +
61G ASP* 1.3 78.0 - - + +
63G ALA* 1.3 58.4 + - - +
65G LYS* 3.7 11.5 - - + +
66G LEU* 2.9 31.2 + - - +
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Residues in contact with ALA 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LEU* 5.2 11.0 - - + -
14G ARG 5.8 0.2 - - - +
15G LEU* 3.5 29.6 - - + -
28G GLY* 5.7 7.2 - - - -
58G ILE* 3.5 15.1 - - + +
59G THR 3.2 4.2 + - - -
60G LYS* 2.9 11.2 + - + +
62G GLU* 1.3 76.0 - - - +
64G GLU* 1.3 60.2 + - + +
66G LEU* 3.9 3.4 - - - +
67G PHE* 2.9 30.9 + - - +
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Residues in contact with GLU 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G ARG* 5.5 5.5 + - - +
60G LYS* 2.9 39.5 + - + +
61G ASP* 3.7 23.8 - - - +
63G ALA* 1.3 76.7 - - + +
65G LYS* 1.3 58.4 + - - +
67G PHE* 3.5 8.6 - - - +
68G ASN* 2.9 39.6 + - - +
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Residues in contact with LYS 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G ASP 2.9 18.4 + - - +
62G GLU* 3.7 12.1 - - + +
63G ALA 3.2 0.2 - - - -
64G GLU* 1.3 76.0 - - - +
66G LEU* 1.3 60.4 + - - +
68G ASN* 3.2 10.2 + - + +
69G GLN* 2.9 55.9 + - + +
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Residues in contact with LEU 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G ILE* 4.3 5.2 - - + +
28G GLY* 5.9 2.7 - - - -
31G HIS* 3.4 49.8 - - + +
46G LEU* 4.3 13.2 - - + -
49G ALA* 4.0 16.2 - - + -
50G ILE* 4.1 19.0 - - + +
58G ILE* 5.3 5.6 - - + -
62G GLU 2.9 17.1 + - - +
63G ALA* 4.1 2.7 - - - +
65G LYS* 1.3 74.4 - - - +
67G PHE* 1.3 59.9 + - - +
69G GLN* 3.1 25.1 + - + +
70G ASP* 2.9 39.4 + - - +
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Residues in contact with PHE 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G PHE* 3.5 60.1 - + + -
7G LEU* 4.1 18.4 - - + -
8G ARG* 5.5 0.7 - - + -
29G ILE* 3.5 60.6 - - + +
31G HIS* 6.3 0.7 - - - -
63G ALA 2.9 20.0 + - - +
64G GLU* 3.5 9.0 - - - +
66G LEU* 1.3 78.6 - - - +
68G ASN* 1.3 59.6 + - - +
70G ASP* 3.3 8.6 + - + +
71G VAL* 2.9 41.6 + - + +
104G PHE* 5.8 1.1 - + - -
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Residues in contact with ASN 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G PHE* 3.1 32.4 - - + -
64G GLU* 2.9 26.1 + - - +
65G LYS* 3.2 9.5 + - + +
67G PHE* 1.3 78.0 - - - +
69G GLN* 1.3 59.4 + - + +
71G VAL* 4.1 4.2 - - - +
72G ASP* 2.9 43.1 + - - +
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Residues in contact with GLN 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G ALA* 3.7 17.1 + - - +
50G ILE* 5.4 0.3 - - - +
65G LYS* 2.9 46.2 + - + +
66G LEU* 3.1 34.1 + - + +
68G ASN* 1.3 76.1 - - + +
70G ASP* 1.3 61.3 + - - +
72G ASP* 3.8 6.0 - - - +
73G ALA* 2.9 25.6 + - - +
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Residues in contact with ASP 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G ILE 5.4 0.2 - - - +
31G HIS* 2.4 53.4 + - - +
66G LEU* 2.9 24.0 + - - +
67G PHE* 3.7 6.6 - - + +
69G GLN* 1.3 78.6 - - - +
71G VAL* 1.3 60.9 + - + +
73G ALA* 3.0 10.9 + - - +
74G ALA* 2.9 25.6 + - - +
104G PHE* 3.8 26.1 - - + -
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Residues in contact with VAL 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G ILE* 4.3 27.4 - - + -
4G PHE* 4.5 14.1 - - + -
7G LEU* 4.1 25.6 - - + -
67G PHE* 2.9 41.1 + - + +
68G ASN* 4.1 5.2 - - - +
70G ASP* 1.3 77.0 - - + +
72G ASP* 1.3 62.1 + - - +
74G ALA* 3.1 9.0 + - - +
75G VAL* 2.9 34.8 + - + +
100G ILE* 4.7 5.2 - - + -
104G PHE* 5.4 2.0 - - + -
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Residues in contact with ASP 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G PHE* 6.1 0.5 - - - -
68G ASN* 2.9 31.5 + - - +
69G GLN* 3.9 6.5 - - - +
71G VAL* 1.3 77.9 - - - +
73G ALA* 1.3 66.3 + - - +
74G ALA 3.1 0.4 - - - -
75G VAL* 3.3 25.8 + - - +
76G ARG* 4.7 9.5 + - - +
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Residues in contact with ALA 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G GLN 2.9 16.6 + - - +
70G ASP* 3.0 17.0 + - - +
72G ASP* 1.3 77.1 - - - +
74G ALA* 1.3 56.0 + - - +
76G ARG* 5.3 9.4 - - - +
77G GLY* 2.9 23.2 + - - -
80G ARG* 5.1 2.3 + - - -
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Residues in contact with ALA 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G ASP 2.9 11.4 + - - +
71G VAL* 3.1 12.5 + - - +
73G ALA* 1.3 73.6 - - - +
75G VAL* 1.3 54.2 + - - +
77G GLY* 2.6 22.6 + - - +
78G ILE* 2.9 28.1 + - + +
100G ILE* 3.9 30.5 - - + +
103G VAL* 5.1 5.6 - - + -
104G PHE* 4.7 14.6 - - + +
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Residues in contact with VAL 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G VAL* 2.9 25.3 + - + +
72G ASP* 3.3 20.3 + - - +
74G ALA* 1.3 75.3 - - - +
76G ARG 2.9 27.8 + - - -
77G GLY 3.0 18.8 + - - -
78G ILE* 4.4 3.3 + - + +
79G LEU* 3.6 26.6 - - + +
88G TYR* 5.4 9.0 - - + +
100G ILE* 4.2 24.9 - - + -
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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