Contacts of the strand formed by residues 43 - 51 (chain A) in PDB entry 1QL6
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 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ILE* 3.6 2.1 - - - -
38A HIS* 2.9 26.4 + - - +
41A THR* 3.1 36.1 + - + +
42A CYS* 1.3 79.5 - - - +
44A GLU* 1.3 60.1 + - - +
45A TYR* 3.5 29.1 - - + +
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Residues in contact with GLU 44 (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 ARG* 2.7 38.2 + - + -
36A CYS 3.5 5.4 - - - +
37A ILE* 3.8 16.6 - - + -
42A CYS 5.5 0.7 - - - +
43A LYS* 1.3 73.2 - - - +
45A TYR* 1.3 75.8 + - - +
104A ASP* 5.2 0.2 - - - -
105A LEU* 3.6 19.8 + - + +
107A LYS* 2.6 33.5 + - - +
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Residues in contact with TYR 45 (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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19A TYR* 4.1 17.3 - + - -
35A ARG* 3.4 10.4 - - - +
36A CYS* 3.0 35.1 + - - -
38A HIS* 3.9 16.5 + + + -
41A THR* 4.5 1.0 + - - -
43A LYS* 3.5 50.7 - - + +
44A GLU* 1.3 80.4 - - - +
46A ALA* 1.3 63.1 - - - +
90A LYS* 4.2 21.1 - - + -
102A VAL* 3.8 17.9 - - + -
103A PHE 3.1 22.0 - - - +
104A ASP* 3.8 18.6 - - - -
105A LEU* 3.7 8.7 - - - +
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Residues in contact with ALA 46 (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* 3.9 15.9 - - + -
33A VAL* 4.2 3.1 - - + -
34A ARG 3.3 4.5 - - - +
36A CYS* 4.5 0.2 - - - -
45A TYR* 1.3 79.5 - - - +
47A VAL* 1.3 59.1 + - - +
101A LEU 3.6 1.0 - - - +
102A VAL* 3.4 1.4 - - - +
103A PHE* 2.5 41.6 + - + +
104A ASP 4.0 2.9 - - - +
105A LEU* 4.1 3.8 - - + +
301A ATP 3.6 42.0 - - + +
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Residues in contact with VAL 47 (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 PHE* 3.3 43.5 - - + -
21A PRO* 6.0 0.9 - - + -
32A VAL 3.8 0.3 - - - +
33A VAL* 3.1 5.5 - - - -
34A ARG* 2.9 54.9 + - + +
36A CYS* 4.0 14.3 - - + -
46A ALA* 1.3 74.3 - - - +
48A LYS* 1.3 67.3 + - - +
49A ILE* 3.7 23.9 + - + +
100A PHE* 4.2 8.1 - - + -
101A LEU 3.1 7.6 - - - +
102A VAL* 4.2 4.5 - - + +
103A PHE* 5.2 0.2 - - - -
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Residues in contact with LYS 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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31A SER* 4.3 9.0 - - - +
32A VAL 3.7 2.7 - - - -
33A VAL* 3.6 19.3 - - + -
46A ALA 4.2 0.4 - - - -
47A VAL* 1.3 73.9 - - - +
49A ILE* 1.3 60.2 + - - +
50A ILE* 3.7 32.7 + - + +
73A GLU* 3.1 31.3 + - - +
99A PHE 3.5 2.3 - - - +
100A PHE* 3.5 3.3 - - - -
101A LEU* 2.6 41.4 + - + +
103A PHE* 4.1 22.1 - - + -
167A ASP* 3.7 4.6 + - - +
301A ATP 2.9 53.5 + - - +
302A MN 4.5 0.2 + - - -
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Residues in contact with ILE 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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15A PHE* 5.5 2.0 - - + -
16A TYR* 4.6 9.9 - - + +
21A PRO* 6.2 0.9 - - + -
31A SER* 3.2 23.3 - - - -
32A VAL* 2.7 27.4 + - + +
34A ARG* 4.1 28.9 - - + +
47A VAL* 4.0 24.0 - - + -
48A LYS* 1.3 72.7 - - - +
50A ILE* 1.3 63.0 + - - +
51A ASP* 3.9 0.9 + - - +
98A PHE* 3.8 30.5 - - + -
99A PHE 3.4 5.6 - - - +
100A PHE* 4.1 21.3 - - + -
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Residues in contact with ILE 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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30A SER* 3.7 15.3 - - - +
31A SER* 4.1 5.8 - - - -
48A LYS* 3.7 39.5 + - + +
49A ILE* 1.3 74.6 - - - +
51A ASP* 1.3 70.4 + - - +
52A VAL* 3.5 8.4 + - + +
66A LEU* 4.8 7.9 - - + -
70A THR* 3.3 46.0 - - + +
73A GLU* 4.6 3.4 - - - +
97A THR 3.5 1.0 - - - +
98A PHE* 3.2 8.8 - - - -
99A PHE* 2.8 43.5 + - + +
101A LEU* 4.4 11.4 - - + -
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Residues in contact with ASP 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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30A SER* 3.1 29.0 + - - +
49A ILE 3.9 2.0 + - - +
50A ILE* 1.3 72.6 - - - +
52A VAL* 1.3 57.3 + - - +
53A THR* 3.9 9.4 - - - -
54A GLY* 3.3 19.3 + - - +
55A GLY* 2.4 39.5 + - - -
66A LEU* 4.2 3.5 - - - +
97A THR* 3.6 6.7 - - - +
98A PHE* 3.4 33.6 - - + -
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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