Contacts of the helix formed by residues 74 - 85 (chain Q) in PDB entry 2J28
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 74 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1011B G 3.7 5.4 - - - -
1012B U 3.3 19.9 + - - -
65Q ASN* 4.5 2.5 - - - -
73Q ILE* 1.3 92.6 + - - +
75Q TYR* 1.3 57.9 + - - +
76Q SER* 2.9 15.3 - - - -
77Q LYS* 2.7 57.1 + - - +
78Q PHE 2.9 11.1 + - - -
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Residues in contact with TYR 75 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010B A 3.4 22.7 - - - +
1011B G 3.0 2.2 + - - -
1152B C 3.2 31.4 - - - -
1153B C 2.9 29.8 + - - -
61Q ILE* 4.2 13.3 - - + +
64Q ILE* 3.4 44.9 - - + -
65Q ASN* 3.0 39.9 + - + +
68Q ALA* 5.7 0.9 - - - -
73Q ILE* 4.3 1.9 - - - +
74Q SER* 1.3 70.2 - - - +
76Q SER* 1.3 61.8 + - - +
78Q PHE* 3.6 11.8 + - + -
79Q ILE* 3.4 34.1 + - + +
92Q LYS* 3.6 15.9 - - - -
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Residues in contact with SER 76 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010B A 3.7 1.0 + - - -
1011B G 2.8 33.8 + - - -
1151B A 2.5 40.7 + - - -
1152B C 3.5 29.9 - - - +
74Q SER* 3.6 9.7 - - - -
75Q TYR* 1.3 79.3 - - - +
77Q LYS* 1.3 66.2 + - - +
80Q ASN* 3.3 11.3 + - - +
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Residues in contact with LYS 77 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1013B C 5.9 4.3 + - - -
1151B A 4.7 0.2 - - - -
73Q ILE* 4.6 11.8 - - + -
74Q SER* 2.7 42.3 + - - +
76Q SER* 1.3 79.1 + - - +
78Q PHE* 1.3 70.3 + - - +
80Q ASN* 2.8 18.6 + - - +
81Q GLY* 2.9 10.7 + - - -
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Residues in contact with PHE 78 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64Q ILE* 4.7 11.7 - - + -
68Q ALA* 3.4 27.4 - - + -
73Q ILE* 4.3 14.6 - - + +
74Q SER 2.9 10.1 + - - +
75Q TYR* 3.8 14.6 - - + +
76Q SER 3.6 0.2 - - - -
77Q LYS* 1.3 78.9 - - - +
79Q ILE* 1.3 77.9 + - + +
81Q GLY* 3.1 1.4 + - - -
82Q LEU* 3.0 46.0 + - + -
91Q ARG* 6.0 0.4 - - + -
105Q PHE 5.5 0.2 - - - -
108Q LEU* 4.3 12.8 - - + -
109Q VAL* 3.5 47.1 - - + -
112Q ALA* 3.7 13.5 - - + +
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Residues in contact with ILE 79 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998B C 4.7 9.4 - - - +
1152B C 4.4 20.2 - - - +
1153B C 5.2 1.1 - - - +
64Q ILE* 5.1 7.0 - - + -
75Q TYR* 3.4 46.6 + - + +
77Q LYS 3.5 0.4 - - - -
78Q PHE* 1.3 94.1 - - + +
80Q ASN* 1.3 56.8 + - - +
82Q LEU* 3.6 4.6 - - + -
83Q LYS* 2.8 29.7 + - + +
91Q ARG* 3.7 52.7 - - + +
92Q LYS* 5.4 3.6 - - - +
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Residues in contact with ASN 80 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1151B A 3.5 40.6 + - - +
1152B C 4.1 11.4 + - - -
76Q SER 3.3 16.9 + - - +
77Q LYS* 2.8 18.7 + - - +
79Q ILE* 1.3 78.1 - - - +
81Q GLY* 1.3 61.2 + - - +
83Q LYS* 3.1 17.5 + - - +
84Q LYS* 3.2 29.6 + - - +
115Q ALA* 5.8 2.9 - - - +
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Residues in contact with GLY 81 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77Q LYS 2.9 11.8 + - - -
78Q PHE 3.7 0.9 - - - -
80Q ASN* 1.3 72.2 - - - +
82Q LEU* 1.3 52.6 + - - +
83Q LYS 2.8 5.1 + - - -
84Q LYS* 3.1 12.3 + - - +
85Q ALA* 2.7 37.7 + - - +
112Q ALA 3.6 20.9 - - - -
115Q ALA* 4.3 15.6 - - - +
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Residues in contact with LEU 82 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78Q PHE* 3.0 41.8 + - + +
79Q ILE* 3.9 6.5 - - + +
81Q GLY* 1.3 73.6 - - - +
83Q LYS* 1.3 58.9 + - - +
85Q ALA* 3.4 9.6 - - - -
88Q GLU* 2.8 65.3 - - + +
91Q ARG* 3.3 42.3 + - + +
108Q LEU* 3.5 22.2 - - + -
112Q ALA* 3.5 13.7 - - + +
53R PHE* 3.7 4.5 - - + -
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Residues in contact with LYS 83 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1151B A 4.2 16.6 + - - -
1152B C 3.7 24.9 + - - +
79Q ILE* 2.8 20.4 + - + +
80Q ASN* 3.3 13.8 - - - +
81Q GLY 2.8 1.6 + - - -
82Q LEU* 1.3 77.1 - - - +
84Q LYS* 1.3 75.0 + - - +
85Q ALA 2.8 11.5 + - - +
86Q SER 4.0 4.7 - - - +
88Q GLU* 5.3 0.2 - - - +
91Q ARG* 4.0 23.1 - - - +
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Residues in contact with LYS 84 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80Q ASN* 3.4 35.0 - - - +
81Q GLY* 3.5 10.3 - - - +
83Q LYS* 1.3 84.9 - - - +
85Q ALA* 1.3 66.9 + - - +
115Q ALA* 4.5 21.1 - - + +
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Residues in contact with ALA 85 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81Q GLY 2.7 17.5 + - - +
82Q LEU* 3.3 9.0 - - - +
83Q LYS 2.8 3.6 - - - +
84Q LYS* 1.3 85.8 - - - +
86Q SER* 1.3 72.8 + - - +
88Q GLU* 3.3 22.9 - - + +
111Q LYS* 4.7 13.2 - - + +
112Q ALA* 4.8 0.4 - - - -
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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