Contacts of the helix formed by residues 61 - 74 (chain A) in PDB entry 2JG1
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 GLY 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLY* 1.3 70.5 - - - -
62A GLU* 1.3 71.6 + - - -
63A LEU 4.4 0.2 - - - -
64A GLY* 3.2 1.7 + - - -
65A GLN* 3.1 26.8 + - - +
83A ILE 4.6 3.2 + - - -
84A LYS 5.7 0.2 + - - -
85A GLY 3.7 2.8 + - - -
86A GLU* 4.5 12.6 - - - -
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Residues in contact with GLU 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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61A GLY* 1.3 74.5 - - - -
63A LEU* 1.3 64.8 + - + +
65A GLN* 3.2 11.3 + - + +
66A PHE* 2.9 23.4 + - - +
86A GLU* 4.4 8.9 - - - +
62D GLU* 3.5 39.0 - - + +
63D LEU* 5.5 1.3 - - + -
65D GLN* 3.9 9.9 - - + +
66D PHE* 3.5 45.1 - - + +
69D LYS* 3.6 24.9 - - - +
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Residues in contact with LEU 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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11A VAL* 3.5 31.2 - - + +
60A GLY 4.6 0.7 - - - +
61A GLY 3.3 0.6 - - - -
62A GLU* 1.3 76.1 - - + +
64A GLY* 1.3 65.2 + - - +
66A PHE* 3.3 10.5 + - + +
67A ILE* 3.2 19.1 + - - +
86A GLU* 5.9 2.6 - - + +
87A THR* 3.3 33.0 - - - +
88A ARG 4.0 5.8 - - - +
89A ASN* 3.3 36.8 - - - +
33D LYS* 4.0 8.7 - - + +
62D GLU* 6.1 0.4 - - + -
63D LEU* 4.0 27.1 - - + -
66D PHE* 6.4 2.2 - - + -
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Residues in contact with GLY 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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59A ILE* 3.7 31.7 - - - +
60A GLY 3.1 14.8 + - - -
61A GLY 3.2 4.2 + - - -
63A LEU* 1.3 77.3 - - - +
65A GLN* 1.3 60.1 + - - +
67A ILE* 3.3 5.9 + - - +
68A ALA 3.1 18.2 + - - -
87A THR* 3.5 18.5 - - - -
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Residues in contact with GLN 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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59A ILE* 3.9 17.5 - - - +
61A GLY 3.1 17.3 + - - +
62A GLU* 3.2 11.4 + - - +
64A GLY* 1.3 73.2 - - - +
66A PHE* 1.3 67.1 + - - +
68A ALA* 3.4 11.3 + - - +
69A LYS* 3.0 24.3 + - - +
82A ASN* 4.2 10.0 + - - -
62D GLU* 4.0 15.5 - - + +
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Residues in contact with PHE 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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11A VAL* 3.6 34.1 - - + -
33A LYS* 3.6 30.3 - - + -
34A THR 4.2 8.7 - - - -
62A GLU 2.9 13.5 + - - +
63A LEU* 3.3 17.0 + - + +
65A GLN* 1.3 75.2 - - - +
67A ILE* 1.3 64.8 + - + +
69A LYS* 3.0 27.0 + - - -
70A LYS* 3.0 54.2 + - + +
62D GLU* 3.9 24.4 - - + +
63D LEU* 6.2 3.6 - - + -
86D GLU* 5.1 11.4 - - + -
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Residues in contact with ILE 67 (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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9A PRO* 3.7 22.7 - - + -
10A SER 4.0 13.5 - - - +
11A VAL* 4.1 9.2 - - + -
35A ALA* 4.1 22.4 - - + +
40A LEU* 4.2 20.2 - - + -
59A ILE* 4.5 4.5 - - + -
63A LEU 3.2 8.3 + - - +
64A GLY* 3.3 10.1 + - - +
66A PHE* 1.3 76.7 - - + +
68A ALA* 1.3 62.9 + - - +
70A LYS* 3.2 4.3 + - - +
71A LEU* 3.1 24.1 + - + +
80A PHE* 4.3 22.0 - - + -
87A THR* 3.6 30.3 - - + -
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Residues in contact with ALA 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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59A ILE* 4.6 11.2 - - + -
64A GLY 3.1 13.3 + - - +
65A GLN* 3.6 19.3 - - - +
67A ILE* 1.3 75.9 - - - +
69A LYS* 1.3 52.1 + - - +
71A LEU* 3.2 4.1 + - - +
72A ASP* 2.8 42.0 + - - +
78A HIS* 3.4 30.9 + - + +
80A PHE* 5.0 2.2 - - + -
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Residues in contact with LYS 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 GLN 3.0 13.5 + - - +
66A PHE* 3.0 54.3 + - - +
68A ALA* 1.3 74.1 - - - +
70A LYS* 1.3 86.4 + - - +
72A ASP* 3.3 10.7 + - - +
73A HIS* 2.9 57.4 + - + +
62D GLU* 3.4 27.1 - - - +
86D GLU* 5.2 11.2 - - - +
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Residues in contact with LYS 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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33A LYS 3.7 14.4 + - - -
34A THR* 5.0 1.3 - - - +
35A ALA* 3.9 22.9 - - + +
44A ARG* 6.0 0.7 - - - +
66A PHE* 3.0 46.7 + - + +
67A ILE 3.2 7.2 + - - +
69A LYS* 1.3 97.6 - - - +
71A LEU* 1.3 65.1 + - + +
73A HIS* 3.4 16.6 + - + +
74A ALA* 3.3 20.6 + - - +
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Residues in contact with LEU 71 (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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35A ALA* 5.4 3.1 - - + -
40A LEU* 4.1 15.7 - - + -
43A THR* 5.2 2.7 - - + -
44A ARG* 4.9 15.7 - - + +
55A ALA* 4.1 9.9 - - + -
67A ILE* 3.1 17.7 + - + +
68A ALA 3.5 7.6 - - - +
70A LYS* 1.3 75.9 - - + +
72A ASP* 1.3 63.7 + - - +
74A ALA* 3.1 9.4 + - + +
76A ILE* 3.0 55.8 + - + +
78A HIS* 3.7 20.2 - - + -
80A PHE* 3.6 37.2 - - + -
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Residues in contact with ASP 72 (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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68A ALA* 2.8 25.4 + - - +
69A LYS* 3.5 12.1 - - + +
71A LEU* 1.3 72.8 - - - +
73A HIS* 1.3 65.2 + - + +
75A ASP* 3.1 20.5 + - - +
76A ILE 4.6 3.0 - - - +
78A HIS* 2.9 25.9 + - - -
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Residues in contact with HIS 73 (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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69A LYS* 2.9 54.0 + - + +
70A LYS* 3.7 17.2 + - + +
71A LEU 3.3 0.4 - - - -
72A ASP* 1.3 78.7 - - + +
74A ALA* 1.3 58.0 + - - +
75A ASP* 3.3 7.7 + - - +
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Residues in contact with ALA 74 (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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44A ARG* 5.9 2.7 - - + -
47A ALA* 5.8 0.9 - - - +
70A LYS 3.3 10.0 + - - +
71A LEU* 3.1 9.6 + - + +
73A HIS* 1.3 76.8 - - - +
75A ASP* 1.3 70.3 + - - +
76A ILE* 3.4 25.8 + - + +
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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