Contacts of the helix formed by residues 103 - 112 (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 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C THR* 3.9 11.2 - - + +
56C THR 3.8 17.5 - - - +
57C SER* 3.9 16.6 - - - -
101C GLY 4.4 2.5 - - - +
102C ALA* 1.3 78.2 - - - +
104C LEU* 1.3 63.5 + - - +
105C THR* 3.2 3.4 + - - -
106C MET* 3.4 3.5 + - + -
107C GLU* 3.1 26.6 + - - +
174C ASP* 5.0 6.5 - - - +
2003C CL 3.1 13.2 - - + +
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Residues in contact with LEU 104 (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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99C GLY* 4.1 11.9 - - - -
102C ALA* 3.5 11.6 + - - +
103C ALA* 1.3 79.1 - - - +
105C THR* 1.3 63.2 + - - +
107C GLU* 3.4 14.8 + - - +
108C LYS* 3.1 26.3 + - - +
137C PRO* 3.3 30.5 - - + +
139C GLU* 4.3 12.5 + - + +
179C ILE* 3.5 29.6 - - + -
205C GLU* 3.9 16.1 - - + +
206C ASN* 3.4 10.5 - - - -
207C GLY* 3.4 17.3 - - - +
209C PHE* 4.0 13.9 - - + -
2003C CL 4.2 0.2 - - - +
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Residues in contact with THR 105 (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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103C ALA 3.2 1.4 + - - -
104C LEU* 1.3 81.5 - - - +
106C MET* 1.3 63.3 + - + +
108C LYS* 4.0 1.9 - - - +
109C ILE* 3.2 29.5 + - + +
139C GLU* 2.7 32.7 + - - -
175C ASN* 4.5 12.1 - - - +
204C ILE* 3.8 10.0 - - + +
205C GLU* 3.6 22.3 - - + +
141D ILE* 3.9 33.2 - - + -
202D GLY* 5.8 1.6 - - - +
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Residues in contact with MET 106 (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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55C PRO 3.9 7.2 - - - +
56C THR* 3.3 17.5 - - - +
57C SER* 5.4 0.7 - - - -
103C ALA* 3.4 3.9 + - + +
105C THR* 1.3 77.6 - - + +
107C GLU* 1.3 67.0 + - - +
109C ILE* 3.2 17.0 + - + +
110C ILE* 3.0 42.8 + - + +
175C ASN* 4.4 16.7 - - - +
141D ILE* 3.8 25.1 - - + -
143D GLN* 3.0 43.3 - - + +
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Residues in contact with GLU 107 (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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28C THR* 3.2 19.6 - - - +
56C THR* 3.7 21.2 + - - +
85C ASP* 3.3 15.0 - - - +
98C LYS* 3.3 25.2 + - - +
103C ALA* 3.1 16.4 + - - +
104C LEU* 3.4 16.4 - - - +
106C MET* 1.3 75.6 - - - +
108C LYS* 1.3 57.1 + - - +
110C ILE* 3.8 0.3 - - - +
111C GLU* 2.8 50.5 + - - +
209C PHE* 4.1 4.0 - - + -
1003C DER 3.3 1.9 - - - +
2003C CL 3.2 29.2 - - - +
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Residues in contact with LYS 108 (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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104C LEU 3.1 14.3 + - - +
105C THR 4.1 2.5 - - - +
107C GLU* 1.3 76.4 - - - +
109C ILE* 1.3 62.1 + - - +
111C GLU* 4.4 0.4 - - - +
112C TYR* 2.8 34.7 + - + +
194C GLU* 3.0 34.8 + - - +
198C ASN* 4.7 0.2 + - - -
205C GLU* 2.8 36.8 + - - +
206C ASN* 3.0 15.7 + - - +
208C ILE 3.0 8.3 + - - -
209C PHE* 3.6 40.6 - - + -
212C ILE* 4.8 9.0 - - + -
201D PRO* 3.8 21.1 - - + -
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Residues in contact with ILE 109 (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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74C LEU* 3.3 26.1 - - + +
105C THR* 3.2 22.7 + - + +
106C MET* 3.6 26.0 - - + +
108C LYS* 1.3 77.3 - - - +
110C ILE* 1.3 60.7 + - + +
113C ARG* 3.0 43.3 + - - +
141D ILE* 3.7 29.6 - - + -
144D ALA* 4.0 9.9 - - + -
201D PRO* 3.7 3.1 - - + -
202D GLY* 3.6 36.6 - - - +
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Residues in contact with ILE 110 (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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25C GLY* 3.9 26.7 - - - -
54C VAL* 3.8 18.6 - - + +
55C PRO 3.1 34.5 - - - +
56C THR* 3.8 11.2 - - + -
74C LEU* 4.7 11.4 - - + -
80C ILE* 4.0 19.9 - - + +
83C ALA* 4.7 2.7 - - + -
106C MET* 3.0 32.1 + - + +
107C GLU 4.0 1.8 - - - +
109C ILE* 1.3 82.6 - - + +
111C GLU* 1.3 67.3 + - + +
113C ARG* 3.1 13.9 + - - +
114C ALA* 3.5 9.7 + - - +
143D GLN* 4.8 1.3 - - - +
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Residues in contact with GLU 111 (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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25C GLY 6.1 0.2 - - - -
27C GLY* 4.6 0.3 + - - -
56C THR* 3.8 12.0 - - - +
83C ALA* 3.7 25.7 - - + +
84C VAL 4.8 0.7 - - - +
85C ASP* 2.4 36.0 - - - +
98C LYS* 3.7 1.7 - - - -
107C GLU* 2.8 28.3 + - - +
108C LYS* 4.7 1.1 - - - +
110C ILE* 1.3 72.4 - - + +
112C TYR* 1.3 64.9 + - - +
113C ARG 3.1 0.9 + - - -
114C ALA* 3.2 15.9 + - - +
117C PHE* 3.3 36.4 - - + +
209C PHE* 3.5 16.1 - - - -
212C ILE* 3.7 21.9 - - + +
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Residues in contact with TYR 112 (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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108C LYS* 2.8 21.7 + - + +
109C ILE 4.1 2.5 - - - +
111C GLU* 1.3 78.6 - - - +
113C ARG* 1.3 81.0 + - + +
114C ALA 3.8 1.6 + - - +
212C ILE* 3.6 19.2 - - + +
151D GLU* 4.0 24.7 + - - -
199D THR 5.2 1.6 - - - -
200D ILE* 4.8 10.7 - - + +
201D PRO* 3.4 35.2 - - + +
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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