Contacts of the helix formed by residues 70 - 80 (chain G) in PDB entry 1G3I
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 HIS 70 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A GLU* 2.8 41.2 + - + -
387A LYS* 4.8 5.6 - - - -
388A THR 4.5 5.0 + - - -
67G HIS* 2.9 28.8 + - + +
68G GLN* 3.8 30.1 + - + +
69G GLY* 1.3 67.5 + - - -
71G LEU* 1.3 71.3 + - - +
72G LEU* 3.3 2.5 - - + -
73G LYS* 3.1 25.1 + - + +
74G SER* 2.9 21.5 + - - -
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Residues in contact with LEU 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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42G VAL* 3.9 22.4 - - + -
60G PHE* 3.6 23.5 - - + -
64G LEU* 4.1 5.8 - - + -
69G GLY 2.9 10.0 + - - +
70G HIS* 1.3 70.8 - - - +
72G LEU* 1.3 71.7 + - - +
74G SER* 3.3 2.4 + - - -
75G ALA* 3.1 14.9 + - - +
97G VAL* 3.9 25.6 - - + +
98G ALA* 4.3 6.1 - - - +
99G ASP* 3.6 32.1 + - + +
102G GLU* 4.3 14.8 - - + -
104G LEU* 3.7 27.8 - - + -
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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
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436A ASN* 6.0 0.4 - - - +
438A ASP* 5.1 2.0 - - + -
439A LEU* 3.3 42.2 - - + +
443A ILE* 3.5 17.3 - - + -
70G HIS* 3.3 1.9 - - + -
71G LEU* 1.3 85.6 - - - +
73G LYS* 1.3 67.7 + - - +
75G ALA* 3.1 3.8 + - - +
76G VAL* 3.1 22.6 + - + -
102G GLU* 3.8 33.5 - - + +
104G LEU* 3.9 23.3 - - + -
114G GLN* 4.6 1.3 - - - +
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Residues in contact with LYS 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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437A GLU* 5.9 0.9 - - - -
438A ASP* 3.7 35.8 + - - +
315B ARG* 6.1 1.2 - - - +
67G HIS* 3.6 27.9 - - + -
70G HIS* 3.1 25.9 + - + +
72G LEU* 1.3 75.9 - - - +
74G SER* 1.3 70.0 + - - +
76G VAL* 2.7 12.6 + - + +
77G GLU* 2.7 52.5 + - + +
80G LYS* 4.5 3.8 - - - +
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Residues in contact with SER 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G PHE* 4.0 9.0 - - - -
63G LYS* 3.6 12.5 + - - +
64G LEU* 3.3 45.7 - - - +
67G HIS* 4.1 5.5 - - - +
70G HIS 2.9 26.8 + - - -
71G LEU 3.4 4.3 - - - -
73G LYS* 1.3 74.0 - - - +
75G ALA* 1.3 53.6 + - - +
77G GLU* 3.0 8.4 + - - +
78G LEU* 2.7 34.8 + - - +
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Residues in contact with ALA 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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60G PHE* 3.7 19.9 - - + -
71G LEU* 3.1 6.7 + - + +
72G LEU 3.2 10.3 - - - +
73G LYS 3.0 0.4 - - - -
74G SER* 1.3 79.0 - - - +
76G VAL* 1.3 57.7 - - + +
78G LEU* 3.3 3.2 + - - +
79G ALA* 2.9 28.2 + - - +
104G LEU* 3.5 27.8 - - + -
106G ILE* 4.1 9.5 - - + +
112G VAL* 3.6 14.6 - - + +
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Residues in contact with VAL 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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438A ASP* 4.8 6.7 - - + +
439A LEU 4.8 5.6 - - - +
442A PHE* 3.4 46.7 - - + +
443A ILE* 4.4 13.9 - - + -
72G LEU* 3.2 34.5 - - + +
73G LYS* 2.7 14.2 + - + +
75G ALA* 1.3 73.3 - - + +
77G GLU* 1.3 53.2 + - - +
79G ALA* 3.0 7.3 + - + +
80G LYS* 2.6 45.3 + - + +
112G VAL* 4.3 4.0 - - + -
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Residues in contact with GLU 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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63G LYS* 3.8 23.2 + - + -
66G MET* 6.1 0.5 - - - +
67G HIS* 3.8 23.4 + - + +
73G LYS* 2.7 40.2 + - + +
74G SER* 3.2 11.2 - - - +
76G VAL* 1.3 72.9 - - + +
78G LEU* 1.3 65.5 + - - +
80G LYS* 2.5 59.2 + - - +
81G ASP* 3.3 9.0 + - - +
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Residues in contact with LEU 78 (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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56G LEU* 4.2 15.9 - - + -
59G LEU* 4.2 22.4 - - + +
60G PHE* 3.5 44.6 - - + +
63G LYS* 3.7 19.4 - - + +
74G SER 2.7 15.7 + - - +
75G ALA* 3.4 8.5 - - - +
77G GLU* 1.3 71.4 - - - +
79G ALA* 1.3 53.9 + - - +
81G ASP* 2.8 36.4 + - + +
82G TRP* 3.2 33.2 - - + -
88G LEU* 5.2 2.0 - - + -
106G ILE* 4.6 8.7 - - + -
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Residues in contact with ALA 79 (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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75G ALA 2.9 14.1 + - - +
76G VAL* 3.4 8.5 - - + +
78G LEU* 1.3 70.9 - - - +
80G LYS* 1.3 52.3 + - - +
81G ASP 2.8 4.9 - - - -
82G TRP* 2.6 44.6 + - - +
83G ARG* 3.1 30.4 - - - +
106G ILE* 5.4 2.2 - - + +
110G GLY 3.9 13.5 - - - +
111G ASP 4.2 3.1 - - - +
112G VAL* 4.2 13.5 - - + -
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Residues in contact with LYS 80 (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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438A ASP* 4.9 4.9 + - - -
442A PHE* 4.9 19.5 - - + -
315B ARG* 4.8 16.4 - - - +
73G LYS* 4.5 7.3 - - - +
76G VAL* 2.6 28.3 + - + +
77G GLU* 2.5 63.7 + - - +
79G ALA* 1.3 71.8 - - - +
81G ASP* 1.3 59.2 + - - +
82G TRP 3.0 5.1 + - - -
83G ARG* 3.4 25.5 + - - +
84G THR* 3.9 9.5 + - - -
58H GLU* 5.4 5.6 - - - +
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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