Contacts of the helix formed by residues 108 - 122 (chain A) in PDB entry 2LKT
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 ILE 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PRO* 5.5 0.4 - - - -
106A TYR 4.2 1.3 + - - +
107A SER* 1.3 72.7 - - - +
109A VAL* 1.3 56.0 + - + +
110A SER* 4.0 12.1 - - - +
111A ARG* 3.1 30.2 + - + +
112A ASN* 2.8 29.0 + - - -
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Residues in contact with VAL 109 (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 TYR* 3.0 40.2 + - + +
38A PRO* 4.4 5.6 - - + -
39A PRO* 4.1 19.2 - - + +
40A SER* 3.6 32.5 - - - +
107A SER 4.1 0.4 + - - -
108A ILE* 1.3 71.9 - - + +
110A SER* 1.3 69.3 + - - +
112A ASN* 3.3 7.6 + - - +
113A CYS* 3.0 21.7 + - - -
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Residues in contact with SER 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 3.6 12.8 + - - -
108A ILE* 3.3 11.5 - - - +
109A VAL* 1.3 84.1 - - - +
111A ARG* 1.3 60.9 + - - +
113A CYS* 3.5 4.9 - - - +
114A GLU* 3.3 27.4 + - - +
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Residues in contact with ARG 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A SER* 4.4 13.5 - - - -
108A ILE* 3.1 19.6 + - + +
110A SER* 1.3 76.6 - - - +
112A ASN* 1.3 57.3 + - - +
114A GLU* 2.8 43.9 + - - +
115A HIS* 2.7 48.6 + - + +
118A THR* 5.7 3.3 + - - -
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Residues in contact with ASN 112 (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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36A LEU* 3.6 11.8 - - + +
39A PRO* 3.5 19.1 - - + +
58A ALA* 3.4 20.1 - - - +
104A MET* 3.6 34.8 - - - +
105A LYS 4.4 1.0 - - - +
107A SER* 2.9 32.2 + - - +
108A ILE 2.8 18.8 + - - +
109A VAL* 3.5 11.7 - - - +
111A ARG* 1.3 74.4 - - - +
113A CYS* 1.3 55.8 + - - +
115A HIS* 4.0 2.0 - - - -
116A PHE* 3.1 29.5 + - - +
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Residues in contact with CYS 113 (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 TYR* 3.3 35.9 - - - +
22A GLU 3.9 9.6 - - - +
23A HIS* 4.7 6.3 - - - -
24A TRP* 3.4 31.2 - - + +
36A LEU* 3.8 21.1 - - - -
38A PRO* 5.1 4.0 - - - -
109A VAL* 3.0 8.4 + - - +
110A SER 3.5 10.3 - - - +
112A ASN* 1.3 71.6 - - - +
114A GLU* 1.3 65.2 + - + +
116A PHE* 3.2 5.4 + - - +
117A VAL 3.1 17.7 + - - -
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TRP* 4.5 8.5 - - + +
110A SER* 3.3 14.9 + - - +
111A ARG* 2.8 47.1 + - - +
113A CYS* 1.3 75.1 - - + +
115A HIS* 1.3 53.8 + - - +
117A VAL* 3.3 12.6 + - + +
118A THR* 2.7 39.3 + - - +
121A ARG* 5.0 0.2 + - - -
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Residues in contact with HIS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A MET* 3.7 15.7 - - - -
107A SER* 4.9 10.3 - - - +
111A ARG* 2.7 35.9 + - + +
112A ASN* 4.1 3.8 - - - +
114A GLU* 1.3 72.4 - - - +
116A PHE* 1.3 55.7 + - - +
118A THR* 3.5 9.3 + - - +
119A GLN* 2.9 67.3 + - + +
122A TYR* 6.0 3.1 - + - -
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Residues in contact with PHE 116 (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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24A TRP* 3.6 37.5 - - + -
34A ILE* 4.2 3.8 - - + -
35A HIS* 3.8 23.1 - - - -
36A LEU* 3.6 22.7 - - + -
60A VAL* 3.6 41.1 - - + -
99A MET* 4.5 6.5 - - + -
104A MET* 4.0 6.2 - - + +
112A ASN 3.1 20.5 + - - +
113A CYS 3.2 5.1 + - - +
115A HIS* 1.3 74.8 - - - +
117A VAL* 1.3 59.0 + - - +
119A GLN* 3.1 14.1 + - - +
120A LEU* 2.9 61.5 + - + +
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Residues in contact with VAL 117 (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 LEU* 4.0 24.2 - - + -
24A TRP* 3.4 55.6 - - + +
25A ALA 5.2 0.2 - - - +
79A SER* 5.6 0.2 - - - +
113A CYS 3.1 11.4 + - - +
114A GLU* 3.5 15.5 - - + +
116A PHE* 1.3 74.7 - - + +
118A THR* 1.3 56.3 + - - +
120A LEU* 3.7 20.8 - - + +
121A ARG* 3.1 48.1 + - - +
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Residues in contact with THR 118 (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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80A LEU* 4.7 9.7 - - + +
111A ARG* 5.7 2.9 + - - -
114A GLU* 2.7 25.7 + - - +
115A HIS* 3.8 11.7 - - - +
116A PHE 3.2 0.2 - - - -
117A VAL* 1.3 76.3 - - - +
119A GLN* 1.3 54.8 + - - +
121A ARG* 4.3 12.2 + - - +
122A TYR* 2.8 45.7 + - + +
125A SER* 4.7 17.7 - - - +
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Residues in contact with GLN 119 (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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95A SER* 4.5 5.7 - - - -
99A MET* 3.7 41.6 - - + +
102A GLN* 4.6 7.4 + - - -
104A MET* 3.4 18.7 - - - +
115A HIS* 2.9 64.7 + - + +
116A PHE* 3.5 6.4 - - - +
118A THR* 1.3 74.3 - - - +
120A LEU* 1.3 63.6 + - - +
121A ARG 4.2 0.2 - - - +
122A TYR* 3.7 30.3 - - + +
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Residues in contact with LEU 120 (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 LEU* 5.2 0.4 - - + -
25A ALA 5.0 0.4 - - - -
26A LEU* 3.8 31.2 - - + +
34A ILE* 4.3 7.2 - - + -
92A ILE* 3.5 18.0 - - - +
95A SER* 3.6 15.9 - - - -
96A ALA* 3.7 33.9 - - + -
99A MET* 4.3 8.3 - - + -
116A PHE* 2.9 58.4 + - + +
117A VAL* 3.7 24.2 - - + +
118A THR 3.4 0.2 - - - -
119A GLN* 1.3 74.5 - - - +
121A ARG* 1.3 66.1 + - + +
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Residues in contact with ARG 121 (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 LEU* 3.7 22.6 - - + +
78A ASN* 2.9 36.7 + - - -
79A SER* 3.0 30.1 + - - +
80A LEU* 3.4 34.0 - - - +
85A GLN* 4.1 24.7 - - - +
87A ARG* 4.4 12.1 - - - +
92A ILE* 3.7 19.3 - - + +
95A SER* 4.5 6.2 + - - -
117A VAL* 3.1 40.5 + - - +
118A THR* 4.0 5.6 + - - +
119A GLN 4.2 0.3 - - - +
120A LEU* 1.3 78.1 - - - +
122A TYR* 1.3 59.8 + - - +
123A GLY* 2.9 16.2 + - - -
125A SER* 3.6 9.9 - - - +
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Residues in contact with TYR 122 (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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95A SER* 5.9 0.7 - - - +
115A HIS* 6.0 3.4 - + - -
118A THR* 2.8 32.9 + - + +
119A GLN* 3.7 32.8 - - + +
121A ARG* 1.3 76.4 - - - +
123A GLY* 1.3 59.1 + - - +
124A LYS 4.0 0.2 - - - -
125A SER* 3.8 17.3 + - - +
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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