Contacts of the strand formed by residues 65 - 71 (chain A) in PDB entry 2H18
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 VAL 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PHE* 3.5 31.6 - - + +
17A TRP* 3.5 32.7 - - + +
19A GLU 3.2 18.6 - - - +
21A MET* 3.4 10.3 - - + +
23A LEU* 3.7 28.0 - - + -
60A ILE 3.9 0.2 - - - +
61A THR* 3.4 6.6 - - - +
62A LYS 2.9 33.1 + - - +
63A GLY 3.3 0.7 - - - +
64A ASN* 1.3 78.2 - - - +
66A THR* 1.3 64.3 + - - +
67A ILE* 3.9 7.2 - - + -
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Residues in contact with THR 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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21A MET 2.9 9.8 + - - +
22A GLU* 3.4 35.9 - - + +
23A LEU* 3.0 28.4 + - - +
59A LYS* 3.6 31.3 - - - +
60A ILE 3.3 9.6 + - - -
61A THR* 3.6 8.3 - - - +
64A ASN 4.1 0.8 + - - -
65A VAL* 1.3 75.2 - - - +
67A ILE* 1.3 65.0 + - - +
68A LYS* 5.1 5.8 - - + +
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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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16A PHE* 4.9 0.7 - - + -
17A TRP* 3.9 28.9 - - + -
23A LEU* 3.4 29.6 - - + +
25A LEU* 3.6 40.4 - - + +
36A PHE* 5.9 0.7 - - + -
37A VAL* 4.6 14.1 - - + -
40A ILE* 4.2 15.5 - - + -
58A ARG 3.3 3.8 - - - +
59A LYS* 3.6 1.6 - - - -
60A ILE* 2.7 52.1 + - + +
65A VAL* 3.9 6.1 - - + -
66A THR* 1.3 77.4 + - - +
68A LYS* 1.3 65.7 + - - +
69A LEU* 3.5 6.3 + - + +
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Residues in contact with LYS 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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22A GLU* 2.8 36.6 + - + +
23A LEU 2.8 13.6 + - - +
24A THR* 2.7 31.9 + - - +
25A LEU 2.9 11.8 + - - +
57A MET* 4.0 15.5 - - + -
58A ARG 3.6 5.4 - - - +
59A LYS* 5.2 8.3 - - + +
66A THR* 5.1 7.6 - - - +
67A ILE* 1.3 71.7 - - - +
69A LEU* 1.3 59.4 + - - +
70A TRP* 3.6 0.9 - - - -
85A TYR* 2.6 68.7 + - + +
86A CYS* 4.8 1.6 - - - -
87A ARG 4.4 2.4 + - - -
89A VAL* 4.3 10.5 - - + -
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Residues in contact with LEU 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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25A LEU* 3.2 17.7 - - + +
33A LYS* 3.5 37.5 - - + -
34A THR* 4.6 8.1 - - + +
37A VAL* 4.3 14.6 - - + -
56A ASN 3.8 1.7 - - - +
57A MET* 3.6 1.2 - - - -
58A ARG* 2.8 83.1 + - + +
60A ILE* 4.3 23.8 - - + -
67A ILE* 3.5 7.6 + - + -
68A LYS* 1.3 72.1 - - - +
70A TRP* 1.3 67.7 + - - +
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Residues in contact with TRP 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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24A THR* 2.8 28.4 + - - -
25A LEU 3.2 2.6 + - - -
26A VAL* 3.3 52.3 - - + +
33A LYS* 3.3 8.4 - - - -
56A ASN* 3.6 13.7 - - - +
57A MET* 3.4 31.9 - - + -
58A ARG* 5.4 1.6 - - - +
68A LYS 3.6 5.6 - - - -
69A LEU* 1.3 77.9 - - - +
71A ASP* 1.3 77.3 + - - +
72A ILE* 4.0 22.0 - - + -
73A GLY 5.3 0.4 - - - -
79A ARG* 5.0 4.9 - - + -
82A TRP* 3.6 33.4 - + + -
83A GLU* 4.3 10.8 - - + -
86A CYS* 3.5 21.9 - - - -
114A LEU* 4.0 24.9 - - + -
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Residues in contact with ASP 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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27A GLY 3.5 4.7 - - - +
29A GLN* 3.6 35.4 - - + +
33A LYS* 2.7 32.1 + - - -
56A ASN* 2.9 38.1 + - - +
58A ARG* 4.2 13.1 + - - -
70A TRP* 1.3 81.2 - - - +
72A ILE* 1.3 64.3 + - - +
73A GLY 4.0 0.3 + - - -
74A GLY* 4.1 3.8 + - - -
82A TRP* 5.3 0.2 - - - -
201A GDP 3.8 7.2 + - - -
404A UNX 3.8 18.2 - - - -
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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