Contacts of the strand formed by residues 113 - 119 (chain A) in PDB entry 1LIK
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 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A MET* 3.8 22.9 - - + -
86A GLY* 3.5 22.8 - - - -
88A ALA 2.9 8.8 + - - +
89A GLY* 2.9 4.2 - - - -
90A TYR* 2.6 31.4 + - - +
111A GLY 3.7 2.2 + - - -
112A LEU* 1.3 72.0 - - - +
114A THR* 1.3 55.3 + - - +
157A PHE* 3.8 9.6 - - + -
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Residues in contact with THR 114 (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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90A TYR* 3.2 18.8 - - + +
104A LYS* 4.5 6.4 + - - +
107A CYS* 4.1 7.4 - - + -
108A ASP* 3.8 16.6 + - - -
112A LEU* 3.5 26.9 + - + +
113A ALA* 1.3 81.7 - - - +
115A ARG* 1.3 65.8 + - - +
116A PHE* 3.6 36.4 + - + -
157A PHE* 3.7 8.4 - - - -
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Residues in contact with ARG 115 (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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90A TYR 3.2 6.3 + - - -
91A MET* 3.6 42.6 - - + +
92A GLY 4.2 0.5 + - - -
114A THR* 1.3 77.6 - - - +
116A PHE* 1.3 63.3 + - - +
117A MET* 3.8 1.4 + - - +
148A PHE* 5.5 1.0 - - - -
151A PRO* 4.6 9.3 - - - +
153A ASN* 2.7 57.9 + - - +
156A THR* 5.8 0.2 - - - -
157A PHE* 3.9 29.3 - - + +
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Residues in contact with PHE 116 (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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21A PRO* 3.4 28.7 - - + -
72A LEU* 4.7 0.4 - - + -
90A TYR* 4.0 20.9 - + - -
92A GLY 3.5 15.9 - - - -
94A ILE* 3.4 35.2 - - + -
103A LEU* 3.8 18.8 - - + -
104A LYS* 4.2 27.5 - - + +
107A CYS* 4.2 13.7 - - + -
114A THR* 3.6 32.7 + - + -
115A ARG* 1.3 75.3 - - - +
117A MET* 1.3 60.9 + - - +
118A VAL* 3.9 6.5 + - + +
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Residues in contact with MET 117 (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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92A GLY 3.0 12.4 + - - +
93A ALA* 3.1 11.7 - - + -
94A ILE* 3.0 24.9 + - - +
115A ARG 3.8 1.6 + - - +
116A PHE* 1.3 73.3 - - - +
118A VAL* 1.3 75.2 + - - +
119A ALA* 4.7 3.6 - - + -
120A PRO* 6.0 0.7 - - + -
147A SER* 3.1 44.0 - - - +
148A PHE* 4.4 9.9 - - + -
149A ARG* 3.9 28.0 - - + +
151A PRO* 6.2 1.3 - - + -
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Residues in contact with VAL 118 (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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94A ILE* 3.5 21.1 - - + -
95A GLY 4.0 1.6 - - - +
96A ASP* 3.5 40.2 - - + +
101A GLN* 6.2 1.6 - - - +
116A PHE 3.9 6.9 + - - +
117A MET* 1.3 86.8 - - - +
119A ALA* 1.3 62.6 + - - +
120A PRO* 3.3 16.0 - - + +
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Residues in contact with ALA 119 (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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93A ALA* 5.2 1.8 - - + -
94A ILE 3.2 5.8 + - - +
95A GLY* 4.2 0.3 - - - -
96A ASP 4.0 3.5 + - - -
117A MET* 4.0 6.2 + - + -
118A VAL* 1.3 73.3 - - - +
120A PRO* 1.3 73.4 - - - +
122A GLN* 3.0 46.7 + - - +
144A ALA* 3.8 20.4 - - + +
147A SER* 4.0 15.9 - - - -
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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