Contacts of the helix formed by residues 100 - 113 (chain A) in PDB entry 1LKO
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 GLU 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A HIS* 2.9 35.5 + - + +
99A THR* 1.3 98.3 + - - +
101A MET* 1.3 63.3 - - - +
102A TYR 3.7 1.1 - - - -
103A PRO* 3.6 2.1 - - - +
104A SER* 2.7 36.5 + - - -
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Residues in contact with MET 101 (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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15A THR* 5.0 7.4 - - - +
16A ALA* 4.2 12.3 - - + +
19A GLY* 6.2 3.6 - - - -
96A HIS* 3.0 30.9 + - + +
97A GLU* 4.1 18.8 - - + +
100A GLU* 1.3 76.7 - - - +
102A TYR* 1.3 103.4 + - + +
104A SER* 3.2 2.3 + - - -
105A PHE* 2.9 66.0 + - + -
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Residues in contact with TYR 102 (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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16A ALA* 3.8 13.9 - - + +
20A GLU* 2.5 32.9 + - - +
60A LEU* 4.1 4.1 - - + +
97A GLU* 2.9 38.3 + - + +
101A MET* 1.3 100.5 - - + +
103A PRO* 1.3 63.7 - - + +
105A PHE* 3.7 4.2 - + - +
106A ALA* 2.8 31.9 + - - +
121A PHE* 3.3 52.4 - + - +
122A ALA* 5.5 0.4 - - - -
124A ILE* 3.6 27.4 - - + -
125A ALA* 4.0 8.5 - - + -
128A GLU* 3.6 15.7 - - + -
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Residues in contact with PRO 103 (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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97A GLU 3.5 6.7 - - - +
98A TYR 3.1 28.9 - - - +
99A THR 3.9 10.8 - - - +
100A GLU 3.6 11.9 - - - +
102A TYR* 1.3 91.7 - - + +
104A SER* 1.3 56.4 + - - +
106A ALA* 3.6 6.4 - - + +
107A ARG* 3.0 29.7 + - - +
110A ARG* 4.8 1.9 + - - -
122A ALA* 6.1 1.6 - - - -
125A ALA* 4.8 5.4 - - + -
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Residues in contact with SER 104 (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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100A GLU* 2.7 29.2 + - - -
101A MET* 3.5 4.3 - - - -
103A PRO* 1.3 75.6 - - - +
105A PHE* 1.3 70.9 + - - +
107A ARG* 3.3 6.6 + - - +
108A ILE* 3.0 33.7 + - - +
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Residues in contact with PHE 105 (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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9A THR* 4.9 0.7 + - - -
12A ASN* 3.3 64.7 + - + +
15A THR* 4.1 13.5 - - + -
16A ALA* 4.1 7.4 - - + -
101A MET* 2.9 53.5 + - + +
102A TYR* 3.8 7.9 - + - +
104A SER* 1.3 81.5 - - - +
106A ALA* 1.3 57.1 + - - +
108A ILE* 3.4 5.2 + - + +
109A ALA* 2.9 29.3 + - - +
121A PHE* 3.8 33.7 - + + -
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Residues in contact with ALA 106 (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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102A TYR 2.8 17.1 + - - +
103A PRO* 3.6 6.7 - - + +
105A PHE* 1.3 78.8 - - - +
107A ARG* 1.3 57.7 + - - +
109A ALA 3.2 0.7 + - - -
110A ARG* 2.9 42.1 + - - +
118A ALA* 3.3 32.0 - - - +
121A PHE* 3.8 13.2 - - + -
122A ALA* 4.2 9.2 - - + +
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Residues in contact with ARG 107 (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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103A PRO 3.0 17.5 + - - +
104A SER* 3.7 7.9 - - - +
106A ALA* 1.3 75.5 - - - +
108A ILE* 1.3 59.2 + - + +
110A ARG* 3.3 30.0 + - - +
111A GLU* 2.5 52.7 + - + +
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Residues in contact with ILE 108 (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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8A ARG* 3.6 54.3 - - + +
9A THR* 4.1 5.8 - - - +
12A ASN* 3.8 26.5 - - - +
104A SER* 3.0 27.0 + - - +
105A PHE* 3.8 6.7 - - + +
107A ARG* 1.3 78.7 - - + +
109A ALA* 1.3 62.7 + - - +
111A GLU* 3.2 7.1 + - - +
112A GLU* 2.9 26.8 + - - +
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Residues in contact with ALA 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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9A THR* 3.3 25.4 - - + +
105A PHE 2.9 18.9 + - - +
106A ALA* 3.4 6.1 - - - +
108A ILE* 1.3 77.1 - - - +
110A ARG* 1.3 60.5 + - - +
112A GLU 3.2 2.3 + - - -
113A GLY 3.1 5.0 + - - -
114A TYR* 2.8 39.7 + - + +
117A ILE* 4.4 3.4 - - + -
118A ALA* 3.6 21.3 - - + +
121A PHE* 4.5 0.2 - - + -
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Residues in contact with ARG 110 (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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103A PRO 4.8 1.8 + - - -
106A ALA* 2.9 32.7 + - - +
107A ARG* 3.4 50.7 - - - +
109A ALA* 1.3 76.4 - - - +
111A GLU* 1.3 70.2 + - - +
113A GLY* 3.1 13.0 + - - +
114A TYR 4.7 0.7 - - - +
115A GLU* 3.8 32.7 - - - +
118A ALA* 3.4 20.6 + - + +
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Residues in contact with GLU 111 (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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8A ARG* 5.0 8.7 - - - +
107A ARG* 2.5 50.4 + - + +
108A ILE* 3.2 8.9 + - - +
110A ARG* 1.3 85.6 + - - +
112A GLU* 1.3 62.2 + - + +
113A GLY 3.5 0.7 + - - -
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Residues in contact with GLU 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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2A LYS* 2.7 36.8 + - - -
7A SER* 3.4 10.9 - - - -
8A ARG* 3.0 41.9 + - - +
9A THR* 2.7 40.4 + - - -
108A ILE* 2.9 21.7 + - + +
109A ALA 3.2 0.2 + - - -
111A GLU* 1.3 76.6 - - + +
113A GLY* 1.3 52.6 + - - +
114A TYR* 3.6 13.8 - - + -
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Residues in contact with GLY 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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2A LYS* 4.2 12.3 + - - +
109A ALA 3.1 2.0 + - - -
110A ARG 3.1 12.6 + - - -
111A GLU 3.2 1.8 + - - -
112A GLU* 1.3 80.1 - - - +
114A TYR* 1.3 65.2 + - - +
115A GLU* 3.5 11.8 + - - +
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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