Contacts of the helix formed by residues 70 - 81 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64P LEU* 4.3 1.0 - - - +
67P HIS* 2.9 19.1 + - + +
68P GLN* 3.6 35.8 + - - -
69P GLY* 1.3 73.9 - - - +
71P LEU* 1.3 69.5 + - - +
72P LEU 3.7 1.3 - - - -
73P LYS* 3.0 16.7 + - + +
74P SER* 2.8 19.5 + - - -
386V GLU* 3.1 39.4 + - + +
387V LYS* 4.2 9.3 - - - -
388V THR* 4.2 8.6 + - - -
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Residues in contact with LEU 71 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42P VAL* 4.0 15.5 - - + -
60P PHE* 3.5 31.0 - - + -
64P LEU* 4.2 3.1 - - + -
69P GLY 2.9 9.8 + - - +
70P HIS* 1.3 67.3 - - - +
72P LEU* 1.3 58.0 + - - +
73P LYS 2.5 14.9 + - - -
74P SER* 2.7 21.2 + - - -
75P ALA* 3.0 10.2 + - + +
97P VAL* 3.9 20.0 - - + +
98P ALA* 3.8 10.1 - - - +
99P ASP* 3.5 52.2 + - - +
102P GLU* 3.8 16.8 - - + +
103P SER 4.4 0.4 - - - +
104P LEU* 5.2 4.7 - - + +
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Residues in contact with LEU 72 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70P HIS 3.7 0.4 - - - -
71P LEU* 1.3 78.2 - - - +
73P LYS* 1.3 56.0 + - - +
75P ALA* 4.0 1.9 - - - +
76P VAL* 2.8 29.7 + - + +
102P GLU* 4.2 31.2 - - + +
104P LEU* 3.8 27.6 - - + -
114P GLN* 4.5 17.3 - - - +
435V GLU* 5.3 11.9 - - - +
438V ASP* 3.5 19.4 - - + +
439V LEU* 5.4 12.6 - - + +
443V ILE* 4.8 12.1 - - + -
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Residues in contact with LYS 73 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67P HIS* 5.4 8.1 - - + -
70P HIS* 3.0 19.8 + - + +
71P LEU 2.5 6.1 + - - -
72P LEU* 1.3 72.8 - - - +
74P SER* 1.3 53.7 + - - +
75P ALA 2.7 5.0 + - - -
76P VAL* 2.6 28.7 + - - +
77P GLU* 2.9 12.3 + - - +
438V ASP* 3.5 16.4 - - - +
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Residues in contact with SER 74 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60P PHE* 4.0 6.0 - - - -
63P LYS* 2.9 46.7 - - - +
64P LEU* 3.0 24.5 - - - +
67P HIS* 4.5 8.8 - - - +
70P HIS* 2.8 15.6 + - - +
71P LEU* 2.7 18.5 + - - -
73P LYS* 1.3 72.2 - - - +
75P ALA* 1.3 59.2 + - - +
77P GLU* 3.5 7.9 + - - +
78P LEU* 3.1 18.2 + - - +
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Residues in contact with ALA 75 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60P PHE* 3.6 20.1 - - + -
71P LEU 3.0 13.9 + - - +
72P LEU 4.0 5.8 - - - +
73P LYS 2.7 4.2 + - - -
74P SER* 1.3 73.8 + - - +
76P VAL* 1.3 54.9 + - - +
78P LEU* 2.7 25.8 + - - +
79P ALA* 2.9 11.4 + - - +
97P VAL* 5.5 0.9 - - + -
104P LEU* 4.1 9.4 - - + -
106P ILE* 4.1 11.9 - - + +
112P VAL* 4.0 26.7 - - + +
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Residues in contact with VAL 76 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P LEU* 2.8 25.4 - - + +
73P LYS* 2.6 10.5 + - - +
75P ALA* 1.3 72.8 - - + +
77P GLU* 1.3 60.9 + - - +
79P ALA* 3.3 3.6 + - + +
80P LYS* 3.0 26.1 + - + +
83P ARG* 5.9 1.8 - - - +
112P VAL* 4.1 8.7 - - + +
438V ASP* 3.6 18.8 - - - +
442V PHE* 3.5 44.9 - - + +
443V ILE* 4.1 18.6 - - + -
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Residues in contact with GLU 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63P LYS* 3.7 25.8 + - + +
67P HIS* 4.6 16.6 - - + +
73P LYS 2.9 10.3 + - - +
74P SER* 3.6 12.6 - - - +
76P VAL* 1.3 77.6 - - - +
78P LEU* 1.3 62.4 + - - +
80P LYS* 3.7 12.0 + - - +
81P ASP* 3.7 9.7 + - - +
265U LYS* 5.0 2.4 + - - -
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Residues in contact with LEU 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56P LEU* 4.6 7.9 - - + +
59P LEU* 3.7 35.0 - - + +
60P PHE* 3.5 46.4 - - + +
63P LYS* 4.1 10.5 - - + +
74P SER 3.1 11.3 + - - +
75P ALA* 2.7 15.0 + - - +
77P GLU* 1.3 74.9 - - - +
79P ALA* 1.3 63.5 + - - +
81P ASP* 3.0 32.7 + - + +
82P TRP* 3.7 20.7 - - + -
106P ILE* 4.8 10.5 - - + -
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Residues in contact with ALA 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75P ALA 2.9 4.8 + - - -
76P VAL* 3.3 10.1 + - + +
78P LEU* 1.3 76.3 - - - +
80P LYS* 1.3 52.5 + - - +
81P ASP 2.7 0.3 + - - -
82P TRP* 2.7 46.9 + - - +
83P ARG* 3.6 33.4 + - - +
106P ILE* 5.5 2.2 - - + +
110P GLY* 4.4 2.2 - - - -
111P ASP 4.2 7.2 - - - +
112P VAL* 3.8 22.0 - - + -
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Residues in contact with LYS 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76P VAL* 3.0 17.2 + - + +
77P GLU* 3.8 9.4 - - - +
78P LEU 3.3 0.2 - - - -
79P ALA* 1.3 74.1 - - - +
81P ASP* 1.3 57.6 + - - +
82P TRP 3.0 0.7 - - - -
83P ARG* 3.0 32.5 + - - +
84P THR* 3.3 15.1 - - - +
265U LYS* 4.7 13.9 - - - +
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Residues in contact with ASP 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59P LEU* 5.8 1.0 - - - +
63P LYS* 3.4 27.6 + - - -
77P GLU 3.7 9.9 + - - +
78P LEU* 3.0 19.0 + - + +
79P ALA 2.7 5.3 + - - -
80P LYS* 1.3 73.6 - - - +
82P TRP* 1.3 57.6 + - + -
84P THR* 4.1 15.1 + - - +
86P ARG 4.3 2.9 - - - +
87P ALA* 4.4 0.2 - - - -
88P LEU* 4.0 34.8 + - + +
85Q ASP* 5.6 1.2 - - - +
265U LYS* 4.2 15.1 + - - -
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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