Contacts of the strand formed by residues 114 - 122 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B ILE* 3.3 15.5 - - + -
82B VAL 4.3 0.2 - - - -
83B ALA* 3.6 24.2 - - + +
110B ILE 3.4 2.6 + - - +
111B GLU 3.2 17.9 + - - +
112B TYR 4.6 2.3 - - - +
113B ARG* 1.3 78.7 - - - +
115B GLY* 1.3 66.7 + - - +
116B THR* 3.3 22.7 + - - +
117B PHE* 4.3 1.5 - - - +
214B ASP* 4.6 2.9 - - - +
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Residues in contact with GLY 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ILE 2.8 16.2 + - - -
81B ASP* 3.1 10.0 + - - -
113B ARG 3.7 0.8 + - - -
114B ALA* 1.3 72.9 - - - +
116B THR* 1.3 64.4 + - - +
214B ASP* 3.7 7.4 - - - +
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Residues in contact with THR 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE* 5.8 1.8 - - + -
81B ASP 2.9 9.2 + - - -
82B VAL* 3.1 15.1 - - - +
83B ALA 2.9 24.3 + - - -
114B ALA* 3.6 4.2 - - - +
115B GLY* 1.3 79.9 + - - +
117B PHE* 1.3 58.9 + - - +
118B ILE* 4.0 12.3 - - + -
214B ASP* 3.3 15.7 - - + -
215B ILE* 3.8 28.9 - - + -
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Residues in contact with PHE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ALA 3.5 9.6 - - - -
85B ASP* 3.9 17.9 - - + -
96B LEU* 4.0 22.2 - - + -
98B LYS* 4.6 4.5 - - + -
111B GLU* 3.2 59.2 - - + +
114B ALA* 4.3 2.6 - - + +
116B THR* 1.3 70.7 - - - +
118B ILE* 1.3 72.1 + - - +
119B VAL* 3.8 14.1 - - + -
209B PHE* 4.3 3.6 - + - -
212B ILE* 3.6 37.0 - - + +
213B ALA* 3.6 16.7 - - - -
214B ASP* 2.8 33.5 + - - +
215B ILE 3.2 7.3 + - - +
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Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ALA* 4.8 5.8 - - + +
17B PHE* 3.6 42.6 - - + -
82B VAL* 3.7 21.1 - - + -
83B ALA 2.8 11.0 + - - +
84B VAL* 3.3 13.0 - - + +
85B ASP 3.1 23.6 + - - -
116B THR* 4.0 16.8 - - + -
117B PHE* 1.3 77.4 - - - +
119B VAL* 1.3 65.2 + - - +
120B LEU* 4.2 9.4 - - + -
215B ILE* 3.3 15.7 - - + +
217B ILE* 3.7 30.5 - - + -
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ASP 3.2 6.7 - - - +
86B GLY 4.2 0.9 - - - +
87B ALA* 3.9 27.1 - - + -
90B VAL* 4.9 0.4 - - + -
96B LEU* 3.7 27.6 - - + -
117B PHE* 3.8 17.0 - - + -
118B ILE* 1.3 77.9 - - - +
120B LEU* 1.3 63.2 + - - +
121B VAL* 4.2 10.1 - - + -
213B ALA* 3.9 18.2 - - + -
215B ILE 2.7 13.1 + - - +
216B VAL* 3.4 14.6 - - + +
217B ILE* 2.7 35.7 + - - +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ALA* 3.6 24.2 - - + +
11B ALA* 4.1 13.9 - - + -
14B ALA* 3.6 14.4 - - + -
31B THR* 3.6 25.6 - - + +
32B THR* 4.3 7.6 - - - +
35B PHE* 4.0 19.3 - - + -
84B VAL* 3.5 28.7 - - + -
85B ASP 2.8 11.8 + - - +
86B GLY* 3.3 15.9 - - - -
87B ALA 4.0 0.3 + - - -
118B ILE* 4.2 4.7 - - + -
119B VAL* 1.3 81.0 - - - +
121B VAL* 1.3 69.2 + - - +
125B LYS* 5.2 0.3 + - - -
217B ILE* 3.6 15.5 - - + -
1002B DER 5.0 0.3 + - - -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B MET 5.4 0.7 - - - -
7B LYS* 5.6 0.2 - - - -
10B ALA* 4.1 5.7 - - - +
31B THR* 4.3 7.2 - - - +
87B ALA* 4.0 26.9 - - + +
90B VAL* 4.1 11.2 - - + -
119B VAL* 4.2 2.7 - - + -
120B LEU* 1.3 81.9 - - - +
122B ASP* 1.3 59.3 + - - +
125B LYS* 3.6 31.9 - - + +
126B LEU* 4.6 2.9 - - + -
216B VAL* 4.0 11.0 - - + -
217B ILE 3.1 5.4 + - - +
218B VAL* 3.2 25.0 - - + -
219B GLY* 2.7 30.8 + - - -
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Residues in contact with ASP 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B VAL* 3.8 11.3 - - - +
6B MET* 3.4 32.1 - - + -
7B LYS* 4.2 13.2 - - + +
31B THR* 5.3 2.9 + - - +
121B VAL* 1.3 80.8 - - - +
123B GLU* 1.3 64.8 + - - +
124B ARG* 2.8 59.4 + - - +
125B LYS* 3.2 22.2 + - - +
126B LEU 4.4 0.5 + - - -
218B VAL* 4.2 2.8 - - - +
219B GLY* 3.6 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