Contacts of the strand formed by residues 85 - 91 (chain A) in PDB entry 4LKC
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 ALA 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLN* 3.6 29.8 - - + -
39A GLN 3.3 17.5 - - - +
40A LYS* 4.3 3.6 - - + +
41A PRO* 5.4 0.9 - - - -
83A ASP 3.3 3.3 + - - +
84A PHE* 1.3 83.2 - - - +
86A THR* 1.3 61.5 + - - +
87A TYR* 3.8 9.8 - - + -
103A THR 3.7 1.0 - - - +
104A ARG* 3.7 3.1 - - - +
105A LEU* 2.8 36.1 + - - +
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Residues in contact with THR 86 (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 GLN 3.8 0.2 - - - -
39A GLN* 2.8 41.1 + - - +
85A ALA* 1.3 75.4 + - - +
87A TYR* 1.3 60.5 + - - +
88A TYR* 3.5 36.7 - - + +
101A GLN 5.4 0.2 - - - +
102A GLY* 4.3 2.9 - - - -
103A THR 3.3 21.8 - - - +
104A ARG* 4.1 15.9 - - + +
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Residues in contact with TYR 87 (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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7A GLN* 3.0 10.4 + - - +
22A ILE* 4.1 16.8 - - + -
36A TRP* 5.0 2.9 - - + -
37A TYR 3.3 13.9 - - - +
38A GLN* 2.9 37.1 + - + -
48A LEU* 3.8 13.0 - - + -
63A PHE* 3.7 15.8 - + - -
74A LEU* 3.6 28.5 - - + -
76A ILE* 3.7 10.3 - - + +
83A ASP* 2.5 31.5 + - - -
85A ALA* 3.8 13.2 - - + -
86A THR* 1.3 74.0 - - - +
88A TYR* 1.3 60.5 + - - +
102A GLY* 3.3 2.4 - - - -
103A THR* 2.9 37.5 + - - +
105A LEU* 3.7 19.7 - - + -
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Residues in contact with TYR 88 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLN* 3.4 4.0 - - - -
36A TRP* 3.3 9.7 - - - -
37A TYR* 2.8 48.3 + - + -
39A GLN* 3.6 23.4 + - + -
86A THR* 3.5 36.3 - - + +
87A TYR* 1.3 75.0 - - - +
89A CYS* 1.3 64.7 + - - +
99A PHE* 4.5 5.2 - - + -
100A GLY 3.6 17.9 - - - -
101A GLN 3.7 10.1 + - - -
102A GLY* 3.6 17.7 - - - -
39B GLN* 3.3 20.4 + - - -
43B LYS 3.8 2.8 + - - -
44B GLY* 3.7 8.0 - - - -
45B LEU* 3.7 42.8 - - + -
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Residues in contact with CYS 89 (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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5A LEU* 4.1 3.1 - - - -
7A GLN* 3.2 22.3 + - - -
24A CYS* 2.0 54.1 - - + -
34A LEU* 3.9 10.5 - - + -
35A ALA 3.2 9.2 - - - +
36A TRP* 3.9 9.2 - - + -
88A TYR* 1.3 75.3 - - - +
90A GLN* 1.3 62.2 + - - +
99A PHE* 3.3 7.1 - - - +
100A GLY* 2.9 30.8 + - - -
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Residues in contact with GLN 90 (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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5A LEU* 3.8 4.0 - - - +
33A ALA 4.0 0.2 - - - +
34A LEU* 3.4 3.9 - - - -
35A ALA* 2.8 31.8 + - - +
37A TYR* 2.7 38.9 + - + -
89A CYS* 1.3 77.1 - - - +
91A GLN* 1.3 82.8 + - - +
92A PHE* 3.2 36.6 - - - -
97A ILE* 3.5 16.5 - - + +
98A THR 3.4 17.5 - - - +
99A PHE* 3.6 26.2 - - + -
115B MET* 4.0 7.2 - - - +
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Residues in contact with GLN 91 (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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3A ILE* 3.9 33.3 - - + +
5A LEU* 3.6 8.9 - - + +
30A ILE* 3.8 19.5 - - + -
33A ALA 3.3 10.3 - - - +
90A GLN* 1.3 92.1 + - - +
92A PHE* 1.4 55.5 + - - +
93A ASN* 2.8 32.4 + - - +
94A SER* 3.1 11.2 + - - +
96A LEU 3.2 23.8 + - - -
97A ILE* 3.7 13.1 - - - +
98A THR* 2.8 42.7 + - - +
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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