Contacts of the helix formed by residues 63 - 76 (chain I) in PDB entry 3G5G
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 SER 63 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ARG* 2.8 28.3 + - - -
44C ASN* 4.2 11.2 - - - +
45C SER* 3.4 8.7 - - - -
57I MET* 5.3 0.2 - - - -
62I VAL* 1.3 80.4 - - - +
64I ASP* 1.3 66.7 + - - +
65I VAL* 3.7 6.4 + - - +
66I VAL* 3.2 30.0 + - - +
67I PHE* 3.0 22.5 + - - +
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Residues in contact with ASP 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ARG* 4.0 8.1 + - - +
45C SER* 3.5 20.1 + - - -
54I GLU* 5.2 1.9 - - - +
57I MET* 3.1 32.5 - - - +
62I VAL 3.9 0.8 + - - -
63I SER* 1.3 72.1 - - - +
65I VAL* 1.3 63.9 + - - +
67I PHE* 3.2 1.4 + - - +
68I PHE* 3.0 33.7 + - + -
4J PHE* 3.4 31.6 - - - -
5J LEU* 4.3 13.2 - - - +
75J ILE* 3.9 24.2 - - + +
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Residues in contact with VAL 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C GLU* 5.0 12.3 - - + -
44C ASN 5.7 4.7 - - - +
45C SER* 6.5 0.2 - - - -
63I SER* 3.3 6.1 + - - +
64I ASP* 1.3 72.7 - - - +
66I VAL* 1.3 57.8 + - + +
68I PHE* 3.2 3.0 + - - +
69I GLU* 2.8 54.2 + - - +
72J ILE* 4.0 29.4 - - + +
75J ILE* 3.6 23.1 - - + -
76J LEU* 3.4 34.1 - - + -
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Residues in contact with VAL 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I VAL* 3.6 20.2 - - + -
63I SER* 3.2 20.7 + - - +
65I VAL* 1.3 77.8 - - + +
67I PHE* 1.3 63.0 + - - +
69I GLU* 3.3 12.4 + - - +
70I MET* 3.0 36.6 + - + +
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Residues in contact with PHE 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I VAL* 4.1 19.5 - - + -
12I VAL* 3.6 22.7 - - + +
13I ILE* 4.0 17.9 - - + -
16I ILE* 3.8 19.5 - - + -
53I LEU* 3.8 28.3 - - + -
57I MET* 3.9 28.9 - - + -
60I LEU* 4.9 3.4 - - + -
62I VAL* 4.1 11.2 - - + +
63I SER 3.0 15.0 + - - +
64I ASP 3.5 7.4 - - - +
65I VAL 3.2 0.2 - - - -
66I VAL* 1.3 75.8 - - - +
68I PHE* 1.3 81.4 + + - +
70I MET* 3.1 9.5 + - - +
71I LEU* 3.0 32.4 + - + +
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Residues in contact with PHE 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I VAL* 6.4 0.2 - - + -
50I ILE* 6.4 0.4 - - + -
53I LEU* 4.5 12.6 - - + -
57I MET* 4.7 4.9 - - - -
64I ASP* 3.0 33.3 + - + +
65I VAL* 5.0 0.2 - - - -
67I PHE* 1.3 86.8 - + - +
69I GLU* 1.3 65.7 + - - +
71I LEU* 3.4 13.3 - - + +
72I ILE* 3.0 28.4 + - - +
5J LEU* 3.7 39.5 - - + -
9J VAL* 5.6 1.6 - - + -
68J PHE* 3.7 33.0 - + + -
71J LEU* 3.7 26.7 - - + -
72J ILE* 4.0 20.6 - - + -
75J ILE* 4.2 9.0 - - + -
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Residues in contact with GLU 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I VAL* 2.8 42.0 + - - +
66I VAL* 3.6 11.6 - - - +
68I PHE* 1.3 72.8 - - - +
70I MET* 1.3 64.2 + - + +
72I ILE* 3.4 6.9 + - + +
73I LYS* 3.2 26.4 + - + +
72J ILE* 3.9 21.2 - - + +
76J LEU* 6.0 0.2 - - - +
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Residues in contact with MET 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I VAL* 3.9 17.5 - - + +
15I LYS* 3.6 40.4 - - + +
16I ILE* 3.7 36.1 - - + -
19I GLU* 4.7 8.1 - - - +
62I VAL* 5.8 0.2 - - - -
66I VAL* 3.0 26.6 + - + +
67I PHE 3.1 8.9 + - - +
69I GLU* 1.3 74.8 - - + +
71I LEU* 1.3 58.6 + - - +
73I LYS* 3.5 11.2 - - + +
74I GLU* 3.0 28.9 + - - +
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Residues in contact with LEU 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I LEU* 4.5 1.1 - - + -
8I LYS* 3.8 41.7 - - + +
9I VAL* 3.9 21.1 - - + +
12I VAL* 4.0 10.0 - - + +
67I PHE* 3.0 18.0 + - + +
68I PHE* 3.2 23.8 + - + +
70I MET* 1.3 75.0 - - - +
72I ILE* 1.3 60.5 + - + +
74I GLU* 3.1 3.8 + - - +
75I ILE* 2.8 41.2 + - + +
68J PHE* 3.7 41.5 - - + -
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Residues in contact with ILE 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68I PHE 3.0 14.9 + - - +
69I GLU* 3.7 6.7 - - + +
71I LEU* 1.3 73.5 - - - +
73I LYS* 1.3 64.3 + - - +
75I ILE* 3.1 9.5 + - - +
76I LEU* 3.0 37.3 + - + +
65J VAL* 4.0 28.7 - - + +
68J PHE* 3.8 17.9 - - + -
69J GLU* 3.9 34.8 - - + +
72J ILE* 3.6 31.6 - - + -
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Residues in contact with LYS 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69I GLU* 3.2 14.5 + - + +
70I MET* 3.5 15.5 - - + +
72I ILE* 1.3 79.3 - - - +
74I GLU* 1.3 64.8 + - - +
76I LEU* 3.4 17.9 + - - +
77I LYS* 3.9 8.7 + - - +
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Residues in contact with GLU 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I LYS* 4.0 33.4 + - + +
11I PHE* 3.1 47.4 - - + -
12I VAL* 4.0 13.2 - - + +
15I LYS* 4.6 12.6 + - - +
70I MET 3.0 14.9 + - - +
71I LEU* 3.1 10.1 + - + +
73I LYS* 1.3 76.8 - - - +
75I ILE* 1.3 63.8 + - - +
77I LYS* 3.2 24.8 + - - +
78I HIS 5.2 0.2 - - - +
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Residues in contact with ILE 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I PHE* 4.6 10.5 - - + -
5I LEU* 4.4 5.6 - - + -
8I LYS* 4.0 26.5 - - + +
71I LEU* 2.8 44.1 + - + +
72I ILE* 3.1 8.2 + - + +
74I GLU* 1.3 72.7 - - - +
76I LEU* 1.3 57.2 + - + +
77I LYS 3.1 5.0 + - - -
78I HIS* 3.6 15.9 - - - +
64J ASP* 4.0 32.3 - - + +
65J VAL* 3.8 20.6 - - + +
68J PHE* 4.2 14.1 - - + -
44N ASN* 4.5 10.1 - - - +
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Residues in contact with LEU 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I ILE* 3.0 33.5 + - + +
73I LYS* 3.8 9.0 - - - +
74I GLU 3.2 0.8 - - - -
75I ILE* 1.3 76.6 - - + +
77I LYS* 1.3 56.6 + - - +
78I HIS* 3.4 14.0 - - - +
65J VAL* 3.5 30.7 - - + -
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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