Contacts of the helix formed by residues 103 - 112 (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 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B THR* 3.8 24.2 - - + +
56B THR 3.8 12.2 - - - +
57B SER* 3.9 9.9 - - - -
101B GLY 4.4 2.9 - - - +
102B ALA* 1.3 77.0 - - - +
104B LEU* 1.3 65.4 + - - +
105B THR 3.0 4.8 + - - -
106B MET* 3.4 3.8 + - - -
107B GLU* 3.2 24.5 + - - +
174B ASP* 5.3 5.4 - - - +
2002B CL 3.1 12.7 - - + +
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Residues in contact with LEU 104 (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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99B GLY* 4.2 17.7 - - - +
102B ALA* 4.0 13.7 - - - +
103B ALA* 1.3 77.1 - - - +
105B THR* 1.3 66.1 + - - +
107B GLU* 3.1 15.7 + - - +
108B LYS* 3.0 24.6 + - - +
137B PRO* 3.7 10.3 - - + +
139B GLU* 4.1 11.9 - - - +
179B ILE* 3.8 28.3 - - + -
205B GLU* 3.7 17.0 - - + +
206B ASN* 3.4 38.6 - - - +
207B GLY* 3.5 4.7 - - - +
209B PHE* 3.8 13.3 - - + -
2002B CL 3.9 0.6 - - - +
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Residues in contact with THR 105 (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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141A ILE* 4.1 22.4 - - + -
202A GLY 5.6 2.0 - - - +
103B ALA 3.0 1.8 + - - -
104B LEU* 1.3 80.1 - - - +
106B MET* 1.3 67.3 + - + +
108B LYS* 3.3 2.3 + - - +
109B ILE* 3.0 40.2 + - + +
139B GLU* 2.7 30.2 + - - -
175B ASN* 4.9 6.5 - - + +
204B ILE* 3.9 10.9 - - + +
205B GLU* 3.4 26.3 - - + +
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Residues in contact with MET 106 (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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141A ILE* 3.6 28.3 - - + -
143A GLN* 2.3 48.0 - - - +
55B PRO 4.0 8.1 - - - +
56B THR* 3.4 17.7 - - - +
103B ALA* 3.4 3.6 + - - +
105B THR* 1.3 80.6 - - + +
107B GLU* 1.3 62.1 + - - +
109B ILE* 3.8 15.5 - - + -
110B ILE* 3.0 41.1 + - + +
175B ASN* 4.6 13.8 - - - +
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Residues in contact with GLU 107 (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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28B THR* 3.2 19.6 - - - -
56B THR* 3.7 22.2 - - - -
85B ASP* 3.2 21.0 - - - +
98B LYS* 3.5 14.6 - - - +
103B ALA* 3.2 20.8 + - + +
104B LEU* 3.1 22.0 - - - +
106B MET* 1.3 76.7 - - - +
108B LYS* 1.3 57.5 + - - +
110B ILE* 3.9 0.7 - - - +
111B GLU* 2.9 46.4 + - - +
209B PHE* 4.1 4.0 - - + -
1002B DER 3.4 4.9 - - - +
2002B CL 3.0 26.2 - - - +
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Residues in contact with LYS 108 (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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201A PRO* 3.6 19.9 - - + +
104B LEU 3.0 16.3 + - - +
105B THR 4.0 2.2 - - - +
107B GLU* 1.3 73.7 - - - +
109B ILE* 1.3 67.3 + - - +
111B GLU* 4.6 1.3 - - - +
112B TYR* 3.0 28.1 + - - +
194B GLU* 3.0 31.8 + - - +
198B ASN* 4.5 1.3 + - - +
205B GLU* 2.7 41.7 + - - +
206B ASN 3.1 5.9 + - - -
208B ILE 3.0 13.6 + - - -
209B PHE* 3.4 40.1 - - + +
212B ILE* 4.5 10.3 - - + -
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Residues in contact with ILE 109 (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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141A ILE* 3.8 16.4 - - + -
143A GLN* 5.0 0.7 - - + -
144A ALA* 4.1 7.6 - - + -
201A PRO* 3.6 3.4 - - + -
202A GLY* 3.3 37.9 - - - +
74B LEU* 3.6 20.4 - - + +
105B THR* 3.0 29.3 + - + +
106B MET* 3.2 37.2 + - + +
108B LYS* 1.3 78.5 - - - +
110B ILE* 1.3 60.9 + - + +
112B TYR* 4.1 0.2 - - - +
113B ARG* 2.9 45.4 + - - +
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Residues in contact with ILE 110 (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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143A GLN* 4.7 0.7 - - - +
25B GLY* 3.8 27.8 - - - -
54B VAL* 3.8 19.1 - - + +
55B PRO 3.3 27.4 - - - +
56B THR* 3.7 15.0 - - + -
74B LEU* 4.9 9.4 - - + -
80B ILE* 4.1 20.3 - - + +
83B ALA* 4.6 2.7 - - + -
106B MET* 3.0 31.0 + - + +
107B GLU 4.0 1.8 - - - +
109B ILE* 1.3 82.4 - - + +
111B GLU* 1.3 66.5 + - + +
113B ARG* 3.1 16.3 + - - +
114B ALA* 3.4 9.5 + - - +
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Residues in contact with GLU 111 (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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25B GLY 6.0 0.3 - - - -
27B GLY* 4.4 0.7 + - - -
56B THR* 3.8 13.7 - - - +
83B ALA* 3.7 21.4 - - + +
84B VAL 4.7 0.5 - - - +
85B ASP* 2.6 35.1 - - - +
98B LYS* 3.7 0.9 - - - -
107B GLU* 2.9 26.7 + - - +
110B ILE* 1.3 71.0 - - + +
112B TYR* 1.3 65.0 + - - +
114B ALA* 3.2 17.3 + - - +
117B PHE* 3.2 50.9 - - + +
209B PHE* 3.4 15.4 - - - -
212B ILE* 3.9 14.2 - - + +
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Residues in contact with TYR 112 (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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151A GLU* 4.0 14.1 + - - +
199A THR 5.7 0.4 - - - -
200A ILE* 4.7 9.0 - - + +
201A PRO* 3.6 35.4 - - + -
108B LYS* 3.0 21.7 + - + +
109B ILE 4.1 1.6 - - - +
111B GLU* 1.3 77.4 - - - +
113B ARG* 1.3 89.9 + - + +
114B ALA 3.7 3.1 + - - +
212B ILE* 3.7 20.6 - - + +
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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