Contacts of the helix formed by residues 66 - 76 (chain G) in PDB entry 1GMO
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 66 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64G VAL* 3.2 18.0 - - - +
65G ASN* 1.3 90.4 - - + +
67G ALA* 1.3 65.1 + - - +
68G ASP* 3.1 30.9 + - - +
69G GLN* 3.1 18.7 + - - +
89G PHE* 4.1 3.4 - - - -
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Residues in contact with ALA 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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39G ILE* 4.1 13.7 - - + -
66G THR* 1.3 71.4 - - - +
68G ASP* 1.3 66.6 + - - +
70G CYS* 2.8 17.6 + - - +
71G ALA* 3.0 11.6 + - - +
87G PHE* 4.1 2.3 - - + -
89G PHE* 3.6 45.3 - - + -
119G TYR* 4.1 17.0 - - + +
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Residues in contact with ASP 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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39G ILE* 3.9 26.9 - - + +
66G THR* 3.1 28.2 + - - +
67G ALA* 1.3 78.3 + - - +
69G GLN* 1.3 62.1 + - - +
71G ALA* 3.0 10.0 + - - +
72G ASP* 2.9 24.3 + - - +
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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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64G VAL* 3.9 22.7 - - + -
65G ASN 5.2 0.4 - - - +
66G THR* 3.1 20.9 + - - +
68G ASP* 1.3 80.4 - - - +
70G CYS* 1.3 63.1 + - - +
71G ALA 3.3 0.2 + - - -
72G ASP* 3.4 4.6 + - - +
73G ARG* 3.2 25.6 + - - +
96G CYS* 4.7 0.4 - - - -
98G TRP* 5.1 0.7 - - - -
6N IDS 5.0 6.9 + - - +
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Residues in contact with CYS 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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64G VAL* 4.1 2.2 - - - -
67G ALA* 2.8 12.9 + - - +
69G GLN* 1.3 77.5 - - - +
71G ALA* 1.3 64.1 + - - +
74G CYS* 3.1 12.3 + - - +
87G PHE* 3.4 22.9 - - + -
89G PHE* 3.5 31.2 - - - -
96G CYS* 2.0 51.8 - - + -
98G TRP* 3.0 24.6 + - - +
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Residues in contact with ALA 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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38G THR* 3.9 4.7 - - - +
39G ILE* 3.7 36.3 - - + +
42G PHE* 3.9 3.7 - - + -
67G ALA 3.0 8.9 + - - +
68G ASP* 3.2 9.0 - - - +
70G CYS* 1.3 74.3 - - - +
72G ASP* 1.3 68.2 + - - +
74G CYS* 2.9 5.0 + - - +
75G THR* 2.8 25.7 + - - -
87G PHE* 3.4 20.3 - - + -
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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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38G THR* 3.5 14.6 + - + +
68G ASP 2.9 18.2 + - - +
69G GLN* 3.4 5.8 + - - +
71G ALA* 1.3 71.8 - - - +
73G ARG* 1.3 51.6 + - - +
74G CYS 2.8 1.9 + - - -
75G THR* 2.7 25.8 + - - -
76G ARG* 2.8 44.7 + - - +
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Residues in contact with ARG 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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62G LYS* 4.1 2.6 - - - +
69G GLN 3.2 13.8 + - - +
72G ASP* 1.3 76.5 - - - +
74G CYS* 1.3 57.6 + - - +
76G ARG* 4.5 12.9 - - - +
77G ASN* 3.1 4.2 + - - -
78G LYS* 3.0 50.8 + - + +
79G GLY 3.7 14.8 + - - -
80G LEU* 3.7 8.8 - - + +
98G TRP* 3.3 46.7 - - + -
4N IDS 3.1 29.7 + - - -
5N SGN 3.6 20.2 + - - -
6N IDS 2.7 49.3 + - - +
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Residues in contact with CYS 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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42G PHE* 3.8 22.2 - - + -
70G CYS 3.1 13.5 + - - +
71G ALA 2.9 9.8 + - - +
72G ASP 2.8 1.2 + - - -
73G ARG* 1.3 73.2 - - - +
75G THR* 1.3 64.6 + - - +
77G ASN* 2.8 21.3 + - - +
80G LEU* 4.3 0.4 - - - -
84G CYS* 2.0 64.8 - - - +
86G ALA 4.7 2.5 - - - -
87G PHE* 4.0 10.5 - - + -
98G TRP* 3.8 5.8 - - + +
121G ASN* 5.2 2.7 + - - -
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Residues in contact with THR 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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38G THR* 3.1 36.8 + - + -
41G GLU* 4.7 11.4 - - + +
42G PHE* 3.6 15.7 - - + -
71G ALA 2.8 13.9 + - - -
72G ASP* 2.7 11.5 + - - -
74G CYS* 1.3 75.3 - - - +
76G ARG* 1.3 60.0 + - + -
77G ASN* 3.2 4.7 + - - +
121G ASN* 5.8 4.9 - - - +
142H ILE* 5.4 5.2 - - - +
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Residues in contact with ARG 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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72G ASP* 2.8 41.1 + - - +
73G ARG* 4.5 6.3 - - - +
75G THR* 1.3 75.9 - - + +
77G ASN* 1.3 58.1 + - - +
78G LYS* 2.6 38.6 + - + +
142H ILE* 5.9 1.3 - - - -
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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