Contacts of the strand formed by residues 47 - 56 (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 ILE 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A VAL* 3.0 27.1 - - + -
6A ALA 3.4 4.6 + - - -
7A VAL* 3.8 24.0 - - + +
8A SER 2.9 19.2 + - - -
11A VAL* 2.7 42.2 - - + +
38A PHE* 5.6 0.9 - - + -
39A CYS 4.5 0.9 - - - +
40A LEU* 3.0 33.7 - - + -
46A ASN* 1.3 68.5 - - - +
48A ILE* 1.3 59.7 + - - +
82A TYR* 3.8 13.5 - - + +
120A SER* 3.3 17.0 - - - +
124A ILE* 4.3 21.8 - - + +
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Residues in contact with ILE 48 (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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8A SER* 3.3 31.0 - - - +
11A VAL* 3.4 11.6 - - - +
38A PHE* 3.3 8.0 - - - +
39A CYS* 2.7 71.0 + - - +
40A LEU 4.1 3.1 - - - +
41A SER* 3.5 26.7 - - - +
46A ASN* 3.1 8.3 + - + +
47A ILE* 1.3 76.5 - - - +
49A LEU* 1.3 72.2 + - + +
50A GLU* 5.3 0.9 - - - +
51A GLU* 5.5 0.2 - - - +
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Residues in contact with LEU 49 (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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8A SER* 6.4 0.9 - - - -
10A GLY* 3.6 34.3 - - - +
11A VAL* 3.7 2.7 - - + +
14A VAL* 3.2 32.3 - - + -
38A PHE* 3.6 25.4 - - + +
39A CYS* 4.3 0.9 - - - -
48A ILE* 1.3 94.6 - - + +
50A GLU* 1.3 72.7 + - - +
51A GLU* 3.1 12.6 - - + +
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Residues in contact with GLU 50 (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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37A LEU 3.2 26.0 + - - +
38A PHE* 4.1 0.8 - - - +
39A CYS* 2.9 28.3 - - - +
48A ILE* 5.3 0.3 - - - +
49A LEU* 1.3 89.5 - - - +
51A GLU* 1.3 99.4 + - - +
52A GLY 4.0 5.7 + - - +
53A LYS* 3.7 45.5 + - + +
54A GLU* 5.1 5.7 - - - +
81A ARG* 5.4 2.6 + - - +
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Residues in contact with GLU 51 (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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48A ILE* 5.5 0.2 - - - +
49A LEU* 3.1 11.3 - - + +
50A GLU* 1.3 102.3 - - - +
52A GLY* 1.3 59.8 + - - +
53A LYS 3.3 5.7 + - - -
54A GLU* 4.0 16.7 - - - +
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Residues in contact with GLY 52 (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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50A GLU* 4.0 4.2 + - - +
51A GLU* 1.3 79.5 - - - +
53A LYS* 1.3 76.8 + - - +
54A GLU* 4.1 1.3 - - - -
74A MET* 5.1 1.9 - - - +
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Residues in contact with LYS 53 (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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37A LEU* 3.3 50.5 + - + +
50A GLU* 3.7 39.0 + - + +
51A GLU 3.3 3.8 + - - -
52A GLY* 1.3 96.0 + - - +
54A GLU* 1.3 63.0 + - - +
74A MET* 4.1 23.3 - - + +
81A ARG* 4.3 23.1 - - - +
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Residues in contact with GLU 54 (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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31A LYS* 5.7 2.8 + - - -
33A LYS* 4.6 15.1 + - + +
35A ALA 3.6 7.6 - - - -
36A VAL* 4.4 19.0 - - + +
50A GLU 5.1 5.4 - - - +
51A GLU* 4.0 20.3 - - - +
52A GLY 4.1 0.4 - - - -
53A LYS* 1.3 77.5 - - - +
55A ILE* 1.3 65.6 + - - +
56A LEU* 3.9 15.5 + - - +
74A MET* 4.1 4.6 - - - +
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Residues in contact with ILE 55 (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* 3.2 7.4 - - - +
34A LYS* 2.6 27.6 + - + -
35A ALA* 3.3 27.9 + - + -
37A LEU* 4.8 0.9 - - + -
54A GLU* 1.3 74.5 - - - +
56A LEU* 1.3 70.8 + - - +
59A ASP* 4.8 9.0 - - + +
64A VAL* 6.1 1.3 - - + -
67A PRO* 3.7 25.1 - - + +
70A THR* 3.4 27.1 - - + +
71A PHE* 3.2 40.2 - - + +
74A MET* 3.7 15.5 - - + -
85A TYR* 5.8 0.7 - - + -
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Residues in contact with LEU 56 (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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31A LYS* 3.7 41.5 - - + +
32A ARG 3.0 11.0 - - - +
33A LYS* 3.3 32.3 - - + +
34A LYS* 3.1 18.2 - - - +
54A GLU* 4.3 18.4 - - - +
55A ILE* 1.3 88.2 - - - +
57A VAL* 1.3 63.2 + - - +
58A GLY 4.4 2.2 - - - +
59A ASP* 3.3 33.9 + - - +
62A GLN* 5.9 1.1 - - - +
67A PRO* 3.9 4.7 - - - +
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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