Contacts of the strand formed by residues 114 - 122 (chain C) in PDB entry 1LK7
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 114 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C ILE* 3.3 17.9 - - + -
83C ALA* 3.7 30.5 - - + +
110C ILE 3.5 3.1 + - - +
111C GLU 3.2 15.9 + - - +
112C TYR 3.5 1.8 - - - +
113C ARG* 1.3 78.2 - - - +
115C GLY* 1.3 65.6 + - - +
116C THR* 3.7 15.0 - - - +
117C PHE* 4.6 2.2 + - - +
214C ASP* 4.9 1.9 - - - +
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Residues in contact with GLY 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ILE 2.8 15.0 + - - -
81C ASP* 3.2 8.9 + - - -
113C ARG 3.7 1.2 + - - -
114C ALA* 1.3 72.1 - - - +
116C THR* 1.3 63.9 + - - +
214C ASP* 4.1 6.6 - - - +
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Residues in contact with THR 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C PHE* 5.9 1.1 - - + -
81C ASP 3.0 9.7 + - - -
82C VAL* 3.2 13.8 - - - +
83C ALA 2.9 24.8 + - - +
114C ALA* 3.7 4.6 - - - +
115C GLY* 1.3 79.9 + - - +
117C PHE* 1.3 61.7 + - - +
118C ILE* 3.9 21.1 - - + -
214C ASP* 3.5 21.1 - - + -
215C ILE* 4.1 14.4 - - + -
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Residues in contact with PHE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ALA* 3.5 9.9 - - + +
85C ASP* 3.7 20.4 - - + -
86C GLY 5.1 0.2 - - - -
96C LEU* 3.9 24.9 - - + -
98C LYS* 4.5 3.8 - - + -
111C GLU* 3.3 56.1 - - + +
114C ALA* 4.8 2.6 + - + +
116C THR* 1.3 71.7 - - - +
118C ILE* 1.3 72.7 + - - +
119C VAL* 3.9 13.4 + - + -
209C PHE* 4.5 3.4 - + - -
212C ILE* 3.6 31.0 - - + +
213C ALA* 3.7 20.7 - - + -
214C ASP* 2.7 34.0 + - - +
215C ILE 3.2 9.9 + - - +
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Residues in contact with ILE 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ALA* 4.7 4.9 - - + +
17C PHE* 3.6 43.5 - - + -
82C VAL* 3.8 19.7 - - + -
83C ALA 2.8 12.7 + - - +
84C VAL* 3.3 11.6 - - + +
85C ASP 3.0 25.1 + - - -
116C THR* 3.9 15.7 - - + -
117C PHE* 1.3 78.8 - - - +
119C VAL* 1.3 62.9 + - - +
120C LEU* 4.0 11.0 - - + -
215C ILE* 3.4 14.6 - - + +
217C ILE* 3.7 30.3 - - + -
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Residues in contact with VAL 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ASP 3.1 8.7 - - - +
86C GLY 4.1 2.5 - - - +
87C ALA* 3.8 28.5 - - + -
90C VAL* 4.6 0.4 - - + -
96C LEU* 3.8 25.4 - - + -
117C PHE* 3.9 11.4 - - + -
118C ILE* 1.3 76.3 - - - +
120C LEU* 1.3 63.8 + - - +
121C VAL* 4.0 11.0 - - + -
213C ALA* 3.8 21.1 - - + -
215C ILE 2.9 11.1 + - - +
216C VAL* 3.6 15.5 - - + +
217C ILE* 2.7 33.3 + - - +
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ALA* 3.7 13.9 - - + +
11C ALA* 4.0 12.6 - - - -
14C ALA* 3.6 24.0 - - + -
31C THR* 3.4 24.4 + - + +
32C THR* 4.4 11.2 - - - +
35C PHE* 3.9 21.5 - - + -
84C VAL* 3.4 27.4 - - + -
85C ASP 2.8 13.6 + - - +
86C GLY* 3.4 14.9 - - - -
87C ALA 4.1 0.2 + - - -
118C ILE* 4.0 8.1 - - + -
119C VAL* 1.3 79.0 - - - +
121C VAL* 1.3 68.3 + - - +
125C LYS* 5.4 0.3 + - - -
217C ILE* 3.6 13.7 - - + -
1003C DER 5.1 0.2 + - - -
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Residues in contact with VAL 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C MET 5.3 0.4 - - - -
7C LYS* 5.5 0.2 - - - -
10C ALA* 3.9 5.7 - - - +
31C THR* 4.2 7.8 - - - +
87C ALA 4.0 10.5 - - - +
90C VAL* 4.0 11.2 - - + -
119C VAL* 4.0 16.4 - - + -
120C LEU* 1.3 80.0 - - - +
122C ASP* 1.3 63.2 + - - +
125C LYS* 3.7 31.2 - - + +
126C LEU* 4.7 3.4 - - + -
216C VAL* 4.0 9.6 - - + -
217C ILE 3.0 5.5 + - - +
218C VAL* 3.3 27.0 - - + -
219C GLY* 2.8 31.2 + - - -
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Residues in contact with ASP 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C VAL* 4.2 4.5 - - - +
6C MET* 3.7 27.4 - - + -
7C LYS* 3.6 23.9 - - + +
31C THR* 5.1 0.6 + - - +
121C VAL* 1.3 78.9 - - - +
123C GLU* 1.3 65.1 + - - +
124C ARG* 2.5 62.6 + - - +
125C LYS* 3.1 24.5 + - - +
126C LEU* 4.6 0.3 + - - +
218C VAL* 4.2 2.2 - - - -
219C GLY* 3.4 8.1 - - - +
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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