Contacts of the helix formed by residues 68 - 79 (chain G) in PDB entry 1GUM
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 68 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15G ARG* 3.7 37.7 - - + +
18G SER* 5.0 3.6 - - - +
19G VAL* 4.3 15.5 - - + -
56G PRO* 3.6 21.1 - - + +
67G GLN* 1.3 73.1 + - - +
69G ARG* 1.3 73.8 + - + +
71G ILE* 3.1 11.4 + - - +
72G LEU* 2.8 38.5 + - + +
100G LEU* 6.1 2.2 - - + -
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Residues in contact with ARG 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G ARG* 5.2 10.3 - - - +
67G GLN* 3.3 0.8 - - - +
68G THR* 1.3 82.4 - - - +
70G SER* 1.3 57.1 + - - +
72G LEU* 3.3 9.0 + - - +
73G HIS* 2.9 52.4 + - + +
97G GLU* 3.0 32.5 + - - +
100G LEU* 3.9 33.6 - - + +
101G ASP* 4.8 9.3 + - - -
104G GLU* 5.7 3.2 + - - -
69H ARG* 3.2 40.2 - - - +
97H GLU* 4.0 13.0 - - + +
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Residues in contact with SER 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G LEU* 5.4 1.7 - - - +
66G VAL 3.5 7.2 - - - -
67G GLN* 2.7 23.3 + - - +
69G ARG* 1.3 79.0 - - - +
71G ILE* 1.3 61.1 + - - +
73G HIS 3.4 0.2 + - - -
74G TYR* 3.1 19.9 + - - +
90H THR* 5.6 4.1 - - - +
93H ASP* 3.0 36.0 + - - +
94H MET* 3.8 13.0 - - - -
97H GLU* 3.0 25.1 - - - +
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Residues in contact with ILE 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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19G VAL* 4.2 19.5 - - + -
56G PRO* 4.0 19.3 - - + -
58G VAL* 4.7 15.5 - - + -
60G ILE* 6.4 0.4 - - + -
65G LEU* 3.8 37.9 - - + +
66G VAL 3.9 8.7 - - - -
67G GLN 2.7 28.1 + - - +
68G THR* 3.4 10.8 - - - +
70G SER* 1.3 75.6 - - - +
72G LEU* 1.3 69.0 + - - +
74G TYR* 2.8 16.8 + - - +
75G ILE* 3.0 33.5 + - + +
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Residues in contact with LEU 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G SER* 3.6 40.8 - - - +
19G VAL* 4.1 15.0 - - + -
22G VAL* 3.9 17.2 - - + +
68G THR* 2.8 33.7 + - + +
69G ARG* 3.8 7.6 - - - +
71G ILE* 1.3 77.3 - - - +
73G HIS* 1.3 66.0 + - + +
75G ILE* 3.8 5.3 - - + +
76G ALA* 2.9 25.7 + - - +
96G VAL* 5.4 2.9 - - + -
100G LEU* 4.6 15.5 - - + -
155G LEU* 4.2 19.4 - - + +
159G ILE* 4.5 11.2 - - + -
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Residues in contact with HIS 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G ARG* 2.9 37.7 + - + +
70G SER 3.7 4.3 - - - +
72G LEU* 1.3 81.0 - - + +
74G TYR* 1.3 62.6 + - - +
76G ALA* 3.6 1.8 - - - +
77G ASP* 2.9 27.7 + - - +
82G PHE* 3.7 33.0 - + + -
89G ARG* 5.1 5.5 + - - +
93G ASP* 4.3 7.0 + - - -
96G VAL* 5.8 3.7 - - + +
97G GLU* 3.8 15.7 + - - -
155G LEU* 4.4 9.2 - - + -
73H HIS* 3.6 30.9 - + - -
93H ASP* 3.3 23.7 + - - +
97H GLU* 4.9 0.9 - - - -
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Residues in contact with TYR 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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60G ILE* 3.0 39.9 - - + -
61G ASP* 2.5 27.5 + - + +
63G MET* 4.5 6.1 - - - -
65G LEU* 3.8 22.9 - - + -
70G SER 3.1 12.7 + - - +
71G ILE 2.8 9.6 + - - +
73G HIS* 1.3 76.5 - - - +
75G ILE* 1.3 54.5 + - + +
77G ASP* 2.8 9.0 + - - +
78G LYS* 2.7 52.0 + - + +
86H LEU* 3.8 23.3 - - + -
87H LYS* 3.2 30.5 + - - -
90H THR* 3.9 22.7 - - + +
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Residues in contact with ILE 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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19G VAL* 4.1 11.7 - - + +
22G VAL* 3.8 25.4 - - + +
23G LEU* 3.8 38.4 - - + -
26G ALA* 5.0 2.2 - - + -
58G VAL* 5.9 2.7 - - + -
60G ILE* 4.6 10.5 - - + -
71G ILE* 3.0 32.5 + - + +
72G LEU* 3.8 7.0 - - + +
74G TYR* 1.3 87.2 - - + +
76G ALA* 1.3 64.3 + - - +
78G LYS* 3.0 5.4 + - - +
79G HIS* 2.9 42.5 + - + +
81G LEU* 5.2 0.4 - - + -
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Residues in contact with ALA 76 (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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22G VAL* 5.1 0.6 - - - +
72G LEU 2.9 18.3 + - - +
75G ILE* 1.3 76.4 - - - +
77G ASP* 1.3 60.0 + - - +
79G HIS 2.9 15.1 + - - -
80G ASN* 3.0 13.3 + - - -
81G LEU* 3.1 32.6 + - + -
82G PHE* 3.6 28.7 + - + -
155G LEU* 4.2 14.8 - - + -
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Residues in contact with ASP 77 (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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73G HIS* 2.9 13.3 + - - +
74G TYR 2.8 8.5 + - - +
76G ALA* 1.3 77.8 - - - +
78G LYS* 1.3 62.8 + - - +
79G HIS 3.3 0.5 + - - -
80G ASN* 4.1 4.2 + - - +
82G PHE* 3.4 12.0 - - - +
89G ARG* 3.0 43.3 + - - -
86H LEU* 4.2 28.3 - - + +
89H ARG* 4.6 3.3 + - - -
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Residues in contact with LYS 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G ILE* 5.4 0.4 - - + -
61G ASP* 4.2 9.0 - - - +
74G TYR* 2.7 57.8 + - + +
75G ILE* 3.0 5.1 + - - +
77G ASP* 1.3 77.0 - - - +
79G HIS* 1.3 83.7 + - + +
80G ASN 3.8 0.4 - - - -
86H LEU* 4.0 18.5 - - + +
87H LYS* 5.6 3.6 - - - +
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Residues in contact with HIS 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G LEU* 5.6 1.3 - - + -
26G ALA* 3.9 21.8 - - + -
28G VAL* 3.3 33.7 - - + +
75G ILE* 2.9 30.5 + - + +
76G ALA 2.9 0.6 + - - +
78G LYS* 1.3 98.8 + - + +
80G ASN* 1.3 73.8 + - - +
81G LEU* 3.1 15.5 + - + +
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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