Contacts of the strand formed by residues 83 - 89 (chain M) in PDB entry 1LK3
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 83 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36M GLN* 3.9 20.4 - - + -
37M GLN 3.4 22.9 - - - +
38M LYS* 4.0 8.3 - - + +
39M PRO* 4.8 4.9 - - - -
81M ASP 3.0 10.4 + - - +
82M THR* 1.3 78.7 + - - +
84M ILE* 1.3 66.1 + - - +
85M TYR* 4.1 3.8 - - + -
101M THR 3.7 0.7 - - - +
102M LYS* 3.6 3.3 - - - +
103M LEU* 2.8 30.0 + - - +
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Residues in contact with ILE 84 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I LYS* 3.2 40.8 - - + +
35M TYR 3.9 0.3 - - - +
36M GLN* 3.7 1.0 - - - -
37M GLN* 2.8 41.6 + - + +
83M ALA* 1.3 79.4 - - - +
85M TYR* 1.3 64.7 + - - +
86M PHE* 3.8 28.8 + - + -
100M GLY* 4.0 1.3 - - - -
101M THR 3.3 20.0 - - - +
102M LYS* 4.0 30.5 - - - +
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Residues in contact with TYR 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6M GLN* 2.8 8.6 + - - -
20M ILE* 3.8 27.1 - - + -
34M TRP* 4.9 3.4 - - + -
35M TYR 3.2 7.6 - - - +
36M GLN* 3.0 37.1 + - + -
46M LEU* 3.7 27.6 - - + -
61M PHE* 4.3 0.2 - + - -
72M LEU* 3.8 13.2 - - + -
74M ILE* 3.5 18.5 - - + +
81M ASP* 2.7 39.6 + - - +
83M ALA 3.9 8.3 - - - -
84M ILE* 1.3 74.7 - - - +
86M PHE* 1.3 60.1 + - - +
100M GLY* 3.2 0.9 - - - -
101M THR 2.7 43.5 + - - +
103M LEU* 3.8 20.2 - - + -
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Residues in contact with PHE 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I GLN* 3.8 6.1 - - - -
43I LYS* 3.2 32.8 - - + -
45I LEU* 3.9 26.5 - - + -
6M GLN* 3.5 2.7 - - - -
34M TRP* 3.2 9.4 - - - -
35M TYR* 2.8 49.2 + - + +
37M GLN* 3.4 28.5 - - + -
43M PRO* 5.4 0.9 - - + -
84M ILE* 3.8 24.5 - - + -
85M TYR* 1.3 75.6 - - - +
87M CYS* 1.3 66.5 + - - +
97M PHE* 4.5 10.3 - - + -
98M GLY 3.5 17.9 - - - -
99M ALA 3.7 16.8 - - - -
100M GLY* 3.6 7.9 - - - -
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Residues in contact with CYS 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4M LEU* 3.9 10.8 - - - -
6M GLN* 3.2 23.2 + - - -
22M CYS* 2.0 53.6 - - + -
32M MET* 3.9 6.3 - - - -
33M HIS 3.1 9.0 - - - +
34M TRP* 3.7 13.6 - - + -
86M PHE* 1.3 76.6 - - - +
88M GLN* 1.3 63.5 + - - +
97M PHE* 3.4 6.6 - - - +
98M GLY* 2.9 23.4 + - - -
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Residues in contact with GLN 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I ASN 2.9 26.1 + - - +
105I TRP* 3.9 0.3 - - - -
106I PHE* 4.2 6.3 - - - -
4M LEU* 3.7 1.3 - - - -
32M MET* 3.4 4.8 - - - +
33M HIS* 2.7 53.7 + - - +
35M TYR* 2.5 46.8 + - + -
87M CYS* 1.3 77.6 - - - +
89M GLN* 1.3 83.9 + - - +
90M SER* 4.0 0.8 - - - -
95M LEU* 4.0 11.0 - - + +
96M THR 3.4 17.0 - - - +
97M PHE* 3.7 21.1 - - + -
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Residues in contact with GLN 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2M THR* 4.1 14.2 - - + -
4M LEU* 3.6 15.4 - - + +
28M VAL* 3.8 25.1 - - + +
31M ARG 3.1 11.2 - - - +
32M MET* 4.2 5.6 - - - -
88M GLN* 1.3 87.1 + - - +
90M SER* 1.3 59.2 + - - +
91M TRP* 3.0 7.8 + - - -
92M ASN* 2.9 46.7 + - - +
94M PRO 3.2 15.6 + - - -
95M LEU* 3.7 2.4 - - - +
96M THR* 3.1 38.1 + - - +
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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