Contacts of the strand formed by residues 88 - 95 (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 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A VAL* 3.4 11.0 - - + +
75A VAL* 3.8 24.7 - - + +
78A VAL* 4.5 9.4 - - + -
79A GLN* 2.9 13.4 - - - +
86A GLY 4.2 2.7 - - - -
87A SER* 1.3 80.3 - - - +
89A GLY* 1.3 59.7 + - - +
112A LEU* 2.8 36.2 - - + +
113A ALA 2.9 12.4 + - - -
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Residues in contact with GLY 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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13A MET* 3.4 30.1 - - - -
15A VAL 2.9 9.4 + - - +
16A PHE* 3.5 7.9 - - - -
17A ALA* 3.1 23.6 + - - +
75A VAL* 4.7 3.5 - - - +
88A ALA* 1.3 73.5 - - - +
90A TYR* 1.3 62.2 + - - +
112A LEU* 4.9 0.4 - - - -
113A ALA 2.9 9.0 - - - -
157A PHE* 4.2 2.0 - - - -
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Residues in contact with TYR 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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16A PHE* 4.7 0.2 - - - -
17A ALA* 3.2 18.8 - - + -
18A ILE 4.1 1.3 - - - -
19A GLY* 3.0 36.6 - - - -
20A ASN 3.2 2.4 + - - -
21A PRO* 3.1 17.8 - - + +
71A ALA* 4.2 1.8 - - + -
72A LEU* 3.8 38.3 + - + +
75A VAL* 3.9 25.8 - - + -
89A GLY* 1.3 74.3 - - - +
91A MET* 1.3 82.1 + - - +
92A GLY* 4.0 1.6 - - - -
112A LEU* 4.6 3.1 - - + -
113A ALA 2.6 10.1 + - - +
114A THR* 3.2 16.3 - - + -
115A ARG 3.2 23.7 + - - -
116A PHE* 4.0 30.7 - + - -
157A PHE* 4.0 2.8 - - - -
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Residues in contact with MET 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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16A PHE* 4.0 10.5 - - + -
17A ALA 3.0 6.7 + - - -
18A ILE* 3.3 11.2 - - + +
19A GLY 3.2 24.1 + - - -
90A TYR* 1.3 89.5 - - - +
92A GLY* 1.3 58.5 + - - +
115A ARG* 3.6 34.3 - - + +
148A PHE* 3.7 15.7 - - + -
150A ILE* 4.0 5.2 - - - -
151A PRO* 3.9 19.7 - - + -
154A TRP* 3.9 29.2 - - + -
157A PHE* 3.1 46.0 - - + -
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Residues in contact with GLY 92 (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 GLY 3.6 15.5 - - - -
21A PRO* 4.1 4.9 - - - -
90A TYR* 4.0 3.6 - - - -
91A MET* 1.3 78.8 - - - +
93A ALA* 1.3 59.8 + - - -
115A ARG 4.2 1.2 + - - +
116A PHE* 3.5 12.1 - - - -
117A MET* 3.0 24.3 + - - +
148A PHE* 3.6 18.0 - - - -
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Residues in contact with ALA 93 (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 GLY 4.6 0.2 + - - -
21A PRO* 3.5 20.7 - - - +
92A GLY* 1.3 73.7 - - - -
94A ILE* 1.3 61.5 + - - +
117A MET* 3.1 24.0 - - + +
119A ALA* 5.2 1.3 - - + -
125A GLY 5.7 0.2 + - - -
144A ALA* 3.8 20.0 - - + +
145A CYS* 3.6 20.7 + - - +
147A SER* 4.5 1.6 - - - -
148A PHE* 3.9 23.5 - - + +
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Residues in contact with ILE 94 (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* 3.8 12.1 - - + -
92A GLY 4.2 0.6 + - - -
93A ALA* 1.3 73.9 - - - +
95A GLY* 1.3 67.5 + - - +
100A GLY* 3.5 33.2 - - - +
101A GLN* 4.8 7.9 - - - +
103A LEU* 4.6 6.3 - - + -
104A LYS* 4.4 8.7 - - + -
116A PHE* 3.4 44.4 - - + -
117A MET 3.0 8.2 + - - +
118A VAL* 3.5 15.3 - - + -
119A ALA 3.2 21.5 + - - -
124A THR* 3.8 14.4 - - + +
144A ALA* 3.6 6.7 - - - +
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Residues in contact with GLY 95 (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* 1.3 92.1 - - - +
96A ASP* 1.3 57.2 + - - -
97A ASP* 3.2 15.0 + - - +
100A GLY* 4.3 0.2 - - - -
118A VAL* 4.0 5.9 - - - +
119A ALA 4.2 2.9 - - - -
122A GLN 3.0 18.8 - - - -
124A THR* 2.7 19.1 + - - +
144A ALA* 3.6 12.7 - - - +
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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