Contacts of the helix formed by residues 59 - 70 (chain A) in PDB entry 2G9I
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 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ASN 3.3 2.4 + - - -
58A PRO* 1.3 76.2 - - - +
60A GLU* 1.3 63.8 + - - +
61A ARG* 4.1 7.7 + - - +
62A ALA* 3.3 10.6 + - - +
63A LYS* 2.9 28.8 + - - +
77A GLN* 2.7 29.5 + - - +
80A LEU* 4.3 4.0 - - - +
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A SER* 1.3 72.8 - - - +
61A ARG* 1.3 61.4 + - - +
63A LYS* 3.2 23.6 + - - +
64A GLU* 2.8 43.9 + - + +
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Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A SER* 4.3 7.6 - - - +
60A GLU* 1.3 80.4 - - - +
62A ALA* 1.3 58.7 + - - +
64A GLU* 3.4 8.8 + - - +
65A ILE* 3.0 49.8 + - + +
80A LEU* 4.2 13.7 - - + +
86A VAL* 3.7 40.9 - - - +
89A ASP* 5.5 2.8 + - - -
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PRO* 4.2 0.9 - - + -
59A SER* 3.3 11.6 + - - +
61A ARG* 1.3 78.9 - - - +
63A LYS* 1.3 57.0 + - - +
66A ALA* 2.9 32.1 + - - +
73A ALA 3.8 18.6 - - - +
76A VAL* 3.7 13.7 - - - +
77A GLN* 3.3 34.8 - - + +
80A LEU* 3.8 9.9 - - + +
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Residues in contact with LYS 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PRO* 3.7 32.5 + - + +
59A SER 2.9 19.0 + - - +
60A GLU* 3.2 25.2 + - - +
62A ALA* 1.3 71.1 - - - +
64A GLU* 1.3 60.8 + - - +
66A ALA* 3.6 1.4 + - - +
67A ALA* 3.0 30.0 + - - +
73A ALA* 4.1 13.7 - - + -
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLU* 2.8 32.5 + - + +
61A ARG* 3.6 7.4 + - - +
63A LYS* 1.3 70.1 - - + +
65A ILE* 1.3 67.2 + - + +
67A ALA* 3.4 10.7 + - - +
68A ARG* 3.2 43.0 + - - +
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Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ARG* 3.0 45.2 + - + +
62A ALA 4.0 2.7 - - - +
64A GLU* 1.3 77.7 - - + +
66A ALA* 1.3 64.2 + - - +
68A ARG* 3.0 19.6 + - - +
69A ILE* 3.4 20.7 + - + +
76A VAL* 4.0 11.7 - - + -
80A LEU* 4.5 18.2 - - + -
86A VAL* 5.4 2.0 - - + -
89A ASP* 3.9 47.1 - - + +
93A LEU* 4.1 14.8 - - + -
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Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ALA 2.9 18.5 + - - +
63A LYS 3.8 4.0 - - - +
65A ILE* 1.3 76.9 - - - +
67A ALA* 1.3 64.0 + - - +
68A ARG 3.1 1.0 + - - -
69A ILE* 3.3 3.1 + - - -
70A GLY* 3.2 20.4 + - - -
71A LYS 3.2 27.6 + - - +
73A ALA* 3.6 22.7 - - + +
76A VAL* 3.7 14.5 - - + +
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A LYS 3.0 19.1 + - - +
64A GLU* 3.6 8.5 - - - +
65A ILE 3.2 0.2 - - - -
66A ALA* 1.3 79.8 - - - +
68A ARG* 1.3 61.4 + - + +
69A ILE 3.5 0.2 - - - -
70A GLY* 4.4 4.0 + - - -
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Residues in contact with ARG 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLU* 3.2 36.0 + - - +
65A ILE* 3.0 9.9 + - - +
67A ALA* 1.3 78.4 - - + +
69A ILE* 1.3 62.6 + - + +
70A GLY 3.7 0.7 - - - -
89A ASP* 5.1 15.7 + - - +
90A PHE* 3.3 40.0 - - + +
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ILE* 3.4 28.3 - - + +
66A ALA* 3.3 6.3 + - - +
68A ARG* 1.3 82.6 - - + +
70A GLY* 1.3 62.8 + - - +
71A LYS* 4.2 33.2 - - + +
75A PHE* 6.4 0.2 - - + -
76A VAL* 4.3 8.7 - - + -
89A ASP 3.1 28.0 - - - +
90A PHE* 4.3 3.6 - - + -
91A PRO 3.4 28.2 - - - +
92A PHE* 4.4 1.6 - - - +
93A LEU* 4.3 22.0 - - + +
105A ASN* 5.4 0.9 - - - +
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Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ALA 3.2 6.1 + - - -
67A ALA 4.4 3.4 + - - -
68A ARG 3.7 2.0 - - - -
69A ILE* 1.3 78.9 - - - +
71A LYS* 1.3 65.0 + - - +
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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