Contacts of the strand formed by residues 33 - 40 (chain A) in PDB entry 1Q8G
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 33 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 4.0 10.1 - - + +
17A ASP* 3.7 38.3 + - - +
18A MET* 2.9 43.7 - - + +
21A ARG 5.4 1.9 + - - -
31A LYS 5.0 5.5 + - - -
32A ARG* 1.3 79.7 - - + +
34A LYS* 1.3 58.8 + - - +
35A ALA 3.4 2.5 - - - +
36A VAL* 3.0 37.9 - - + -
54A GLU* 4.6 10.1 + - + +
55A ILE 3.2 11.0 - - - +
56A LEU* 3.3 12.5 - - + +
57A VAL* 4.5 0.7 - - - +
86A ASP* 4.6 0.7 - - - -
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Residues in contact with LYS 34 (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 MET* 4.4 2.5 - - - -
32A ARG 3.2 1.6 + - - -
33A LYS* 1.3 73.2 - - - +
35A ALA* 1.3 63.5 + - - +
55A ILE* 2.6 12.5 + - + +
56A LEU 3.1 18.2 - - - +
57A VAL* 3.3 37.1 + - + +
60A VAL* 4.5 6.9 - - - +
67A PRO* 3.7 14.8 - - + -
84A LEU 3.9 4.9 - - - -
85A TYR* 2.9 49.6 - - + +
86A ASP* 3.4 11.0 - - - +
88A THR* 2.7 49.8 + - - +
162A GLU* 5.2 4.7 - - - +
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Residues in contact with ALA 35 (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 3.4 1.2 - - - -
34A LYS* 1.3 83.8 - - - +
36A VAL* 1.3 62.3 + - - +
37A LEU* 2.9 20.3 + - + +
55A ILE* 3.3 32.6 + - + -
71A PHE* 3.3 33.0 - - + -
84A LEU 3.5 12.7 + - - -
85A TYR* 3.7 5.6 - - + -
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Residues in contact with VAL 36 (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 VAL* 4.2 17.0 - - + +
18A MET* 4.3 7.4 - - + -
33A LYS* 3.0 42.4 - - + +
35A ALA* 1.3 69.3 - - - +
37A LEU* 1.3 60.6 + - - +
38A PHE* 2.9 56.1 - - + -
53A LYS 4.3 0.2 - - - -
54A GLU* 4.4 14.6 - - + +
83A ALA* 3.3 4.7 - - - -
84A LEU* 3.6 25.3 + - + +
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Residues in contact with LEU 37 (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* 2.9 25.7 + - + +
36A VAL* 1.3 68.0 - - - +
38A PHE* 1.3 66.1 + - - +
50A GLU* 3.2 25.6 + - - +
53A LYS* 3.3 27.2 + - + +
55A ILE* 4.8 0.2 - - + -
71A PHE* 3.0 39.5 - - + -
74A MET* 3.4 49.1 - - + +
75A LEU* 4.1 12.6 - - + -
81A ARG* 4.7 8.9 - - - +
82A TYR 3.4 7.6 - - - +
83A ALA* 3.7 3.4 - - + -
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Residues in contact with PHE 38 (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* 4.0 24.0 - - + -
14A VAL* 3.5 25.1 - - + -
15A PHE* 4.9 3.4 - - + -
36A VAL* 2.9 49.8 - - + -
37A LEU* 1.3 78.1 - - - +
39A CYS* 1.3 69.4 + - - +
47A ILE* 5.6 0.4 - - + -
48A ILE 3.3 10.3 - - - +
49A LEU* 3.6 24.5 - - + +
81A ARG* 3.2 22.0 - - - +
82A TYR* 3.1 37.8 + - + -
83A ALA* 3.9 8.7 - - - -
84A LEU* 3.7 20.9 - - + -
101A PHE* 4.1 8.5 - + - -
124A ILE* 5.5 0.2 - - + -
127A LYS* 6.0 0.2 - - - -
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Residues in contact with CYS 39 (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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38A PHE* 1.3 83.0 - - - +
40A LEU* 1.3 67.5 + - - +
47A ILE* 5.3 0.2 - - - -
48A ILE* 2.7 69.0 + - - +
50A GLU* 2.9 35.4 - - - +
81A ARG* 3.3 27.8 - - - +
82A TYR* 4.8 5.1 - - - -
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Residues in contact with LEU 40 (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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39A CYS* 1.3 81.2 - - - +
41A SER* 1.3 75.8 + - - +
44A LYS* 3.6 10.5 - - + -
45A LYS* 3.4 15.5 - - - +
46A ASN 3.3 35.0 - - - +
47A ILE* 3.0 32.3 - - + +
48A ILE* 3.8 4.1 - - - +
80A CYS 5.4 4.6 + - - +
82A TYR* 4.3 12.9 - - + +
113A SER* 5.9 8.3 - - - -
116A ILE* 4.2 24.2 - - + -
117A TYR* 4.9 6.5 - - + +
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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