Contacts of the strand formed by residues 60 - 69 (chain A) in PDB entry 2JQZ
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 LYS 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.6 16.4 - - + +
20A CYS* 3.6 11.2 - - + +
51A ASP* 4.9 2.9 - - - +
53A VAL* 4.1 11.2 - - + +
58A ASP* 5.3 2.7 - - - +
59A PRO* 1.3 82.6 - - + +
61A TRP* 1.3 75.8 + - - +
62A ASN* 4.7 17.0 - - + +
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Residues in contact with TRP 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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18A VAL* 3.3 37.7 - - + +
19A LEU 3.3 3.8 + - - -
20A CYS* 4.7 1.8 - - - -
21A ALA* 4.1 23.6 - - + -
35A PRO* 3.6 28.2 + - + -
36A PHE* 3.8 5.8 - - - +
37A ALA* 4.9 0.2 - - + -
50A THR* 3.4 30.7 + - + -
51A ASP* 2.7 46.9 + - - +
53A VAL* 3.3 13.7 - - + +
59A PRO* 4.1 8.1 - - + -
60A LYS* 1.3 82.4 - - - +
62A ASN* 1.3 86.8 + - - +
63A GLN* 2.8 19.3 + - + +
79A VAL* 4.1 21.8 - - + -
132A ILE* 3.6 12.3 - - + -
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Residues in contact with ASN 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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17A THR* 4.6 10.6 - - - +
18A VAL 3.1 12.5 + - - -
19A LEU* 3.3 20.2 + - + +
60A LYS* 4.7 17.8 - - + +
61A TRP* 1.3 91.3 + - - +
63A GLN* 1.3 60.9 + - - +
64A HIS* 4.9 3.5 - - - -
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Residues in contact with GLN 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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17A THR* 4.1 1.6 - - - -
18A VAL* 2.8 32.4 + - - +
49A SER 5.1 1.7 + - - -
50A THR* 3.9 23.7 - - + +
51A ASP* 3.2 37.0 + - - +
61A TRP* 2.9 19.4 - - - +
62A ASN* 1.3 83.1 - - - +
64A HIS* 1.3 63.8 + - - +
65A TYR* 5.4 0.7 - - + -
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Residues in contact with HIS 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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15A ARG* 4.1 25.9 + - + +
16A LEU 3.1 17.7 - - - +
17A THR* 3.4 31.9 - - + +
62A ASN 4.9 2.7 - - - -
63A GLN* 1.3 77.5 - - - +
65A TYR* 1.3 73.5 + - - +
66A ASP* 4.0 19.7 + - - +
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Residues in contact with TYR 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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14A LEU 3.1 5.7 - - - +
15A ARG* 3.2 2.0 - - - -
16A LEU 3.0 28.4 + - - +
18A VAL* 4.5 2.7 - - + -
37A ALA* 3.1 15.0 + - + +
39A VAL* 3.3 33.9 - - + -
48A HIS* 3.5 19.1 - + + -
49A SER* 2.9 25.8 - - - -
50A THR* 2.6 49.5 + - + +
63A GLN* 5.4 1.3 - - + -
64A HIS* 1.3 86.1 - - - +
66A ASP* 1.3 63.0 + - - +
67A LEU* 3.2 17.8 - - + +
77A ILE* 3.3 30.1 - - + -
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Residues in contact with ASP 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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13A LYS* 3.6 27.2 + - + +
14A LEU 3.6 6.1 - - - -
15A ARG* 3.1 28.9 - - + +
46A GLN* 2.8 16.9 - - - +
48A HIS* 4.5 9.3 + - + +
64A HIS* 4.0 14.9 + - - +
65A TYR* 1.3 76.3 - - - +
67A LEU* 1.3 64.6 + - - +
68A TYR* 4.2 6.8 + - - -
139A ARG* 4.4 5.4 + - - +
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Residues in contact with LEU 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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13A LYS* 3.1 10.6 - - - +
14A LEU* 2.9 32.6 + - + +
16A LEU* 4.8 9.4 - - + -
39A VAL* 3.9 13.2 - - + -
41A VAL* 3.7 11.4 - - + -
46A GLN* 3.4 28.3 - - + +
48A HIS* 3.7 18.2 - - + -
65A TYR* 3.2 30.3 - - + +
66A ASP* 1.3 72.1 - - - +
68A TYR* 1.3 65.1 + - - +
69A ILE* 4.7 2.0 - - + -
75A VAL* 3.6 40.6 - - + -
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Residues in contact with TYR 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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11A PRO* 4.0 20.2 - - + -
12A VAL 3.2 5.2 - - - -
13A LYS* 3.6 37.4 - - + +
41A VAL* 4.4 4.9 - - - +
44A SER* 4.6 13.5 - - - +
46A GLN* 3.2 34.4 + - + +
66A ASP 4.2 6.7 + - - -
67A LEU* 1.3 80.8 - - - +
69A ILE* 1.3 67.9 + - - +
73A ASP* 3.0 18.6 - - - +
75A VAL* 4.1 3.8 - - - +
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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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10A GLY 4.8 0.2 - - - +
11A PRO* 3.3 3.7 - - - +
12A VAL* 2.8 64.1 + - + +
14A LEU* 4.0 21.3 - - + -
67A LEU* 4.7 0.7 - - + -
68A TYR* 1.3 84.6 - - - +
70A GLY* 1.3 58.8 + - - +
71A LYS 4.3 0.6 + - - +
73A ASP* 3.2 37.2 - - + +
74A SER* 4.3 1.1 - - - +
75A VAL* 3.9 19.1 - - + -
101A SER* 4.4 13.2 - - - -
104A ILE* 4.1 24.7 - - + -
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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