Contacts of the helix formed by residues 100 - 118 (chain A) in PDB entry 5LUQ
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A PHE* 5.1 7.0 - - + -
63A PHE* 3.8 21.5 - - + -
93A LEU* 3.5 32.1 - - + +
96A MSE 3.8 25.4 - - + +
97A GLY 5.2 0.4 - - - +
98A GLN 2.9 17.8 + - - +
99A LYS* 1.3 84.1 - - + +
101A ALA* 1.3 54.4 + - - +
102A PRO* 3.8 0.9 - - - -
103A TYR* 3.3 29.4 - - + -
104A SER* 2.4 40.9 + - - +
107A ILE* 4.4 1.3 - - + -
143A LEU* 5.9 1.7 - - - +
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LYS* 3.8 1.5 - - - +
100A ILE* 1.3 73.6 - - - +
102A PRO* 1.3 73.8 - - + +
104A SER* 2.3 35.4 + - - -
105A VAL* 3.0 10.0 + - + +
143A LEU* 5.7 10.5 - - + +
146A GLU* 4.4 18.2 - - - +
149A ILE* 5.8 0.9 - - + -
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Residues in contact with PRO 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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100A ILE 4.3 0.2 - - - -
101A ALA* 1.3 92.1 - - + +
103A TYR* 1.3 72.7 + - + +
105A VAL* 3.4 7.7 + - + +
106A GLU* 3.1 36.7 + - - +
149A ILE* 5.9 2.0 - - + -
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Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A SER* 3.1 46.2 + - - -
63A PHE* 3.7 24.0 - + + +
64A GLY 5.7 1.1 - - - -
99A LYS 5.4 1.8 - - - -
100A ILE* 3.3 31.9 - - + +
102A PRO* 1.3 86.7 - - + +
104A SER* 1.3 62.4 + - - +
106A GLU* 3.3 18.4 + - - +
107A ILE* 2.9 28.1 + - - +
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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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93A LEU* 5.2 8.7 - - - -
100A ILE* 2.4 30.5 + - - -
101A ALA* 2.3 32.5 + - - -
103A TYR* 1.3 67.3 - - - +
105A VAL* 1.3 71.0 + - - +
107A ILE* 2.9 25.8 + - - +
108A LYS* 2.9 27.3 + - - +
141A SER* 5.3 4.3 - - - -
143A LEU* 5.9 7.9 - - - +
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Residues in contact with VAL 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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101A ALA 3.0 14.7 + - - +
102A PRO* 4.0 6.3 - - + +
104A SER* 1.3 78.4 + - - +
106A GLU* 1.3 63.6 + - + +
108A LYS* 3.2 13.4 + - - +
109A ASN* 3.1 24.9 + - + +
149A ILE* 3.4 44.6 - - + -
152A LEU* 3.6 38.8 - - + -
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Residues in contact with GLU 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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63A PHE* 6.1 1.6 - - + +
64A GLY* 6.1 1.0 - - - -
67A VAL* 5.7 3.4 - - + -
102A PRO* 3.1 23.6 + - - +
103A TYR* 3.3 26.0 - - - +
105A VAL* 1.3 78.5 - - + +
107A ILE* 1.3 61.9 + - + +
108A LYS 3.1 0.3 + - - -
109A ASN* 3.4 4.3 + - - +
110A THR* 2.8 29.4 + - - +
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Residues in contact with ILE 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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63A PHE* 3.5 48.9 - - + -
67A VAL* 5.6 2.5 - - - -
86A LEU* 4.6 13.7 - - + -
89A LEU* 4.6 9.6 - - + -
93A LEU* 4.2 18.4 - - + -
100A ILE* 4.4 1.3 - - + -
103A TYR 2.9 24.8 + - - +
104A SER* 2.9 16.0 + - - +
106A GLU* 1.3 70.9 - - + +
108A LYS* 1.3 58.8 + - + +
110A THR* 3.2 9.1 + - - -
111A CYS* 2.9 38.9 + - - -
137A THR* 4.8 10.5 - - + -
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Residues in contact with LYS 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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104A SER* 2.9 31.0 + - - +
105A VAL* 3.7 10.9 - - + +
106A GLU 3.1 0.2 - - - -
107A ILE* 1.3 76.5 - - + +
109A ASN* 1.3 63.0 + - - +
111A CYS* 2.8 25.3 + - - +
112A THR* 3.1 9.9 + - - +
137A THR 4.8 3.4 - - - +
138A PHE* 4.2 30.1 - - + +
141A SER* 3.7 35.4 - - - +
144A MSE 5.2 3.0 - - - -
149A ILE* 4.5 11.7 - - - +
152A LEU* 6.0 1.3 - - + -
153A PHE* 3.2 43.9 - - + -
156A PHE* 6.0 0.4 - - - -
157A TYR* 4.1 8.0 + - - +
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Residues in contact with ASN 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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71A LYS* 5.9 2.6 - - - +
105A VAL* 3.1 13.6 + - + +
106A GLU* 4.1 4.0 - - - +
108A LYS* 1.3 77.2 - - - +
110A THR* 1.3 55.9 + - - +
112A THR* 3.0 28.2 - - - +
113A SER* 2.7 29.1 + - - -
152A LEU* 5.3 12.8 - - + +
156A PHE* 4.9 8.2 - - + -
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Residues in contact with THR 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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66A LEU* 4.5 10.1 - - + -
67A VAL* 3.4 48.8 - - + +
71A LYS* 5.5 7.9 + - + +
86A LEU* 5.4 3.8 - - + -
106A GLU* 2.8 19.4 + - - +
107A ILE* 3.3 12.6 - - - +
108A LYS 3.1 0.2 - - - -
109A ASN* 1.3 77.7 - - - +
111A CYS* 1.3 62.2 + - - +
113A SER* 3.0 10.1 + - - -
114A VAL* 2.9 38.3 + - + +
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Residues in contact with CYS 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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86A LEU* 4.2 10.1 - - - -
107A ILE* 2.9 24.7 + - - -
108A LYS* 2.8 10.7 + - - +
110A THR* 1.3 75.7 - - - +
112A THR* 1.3 63.5 + - - +
114A VAL* 3.0 9.8 + - - -
115A TYR* 3.1 11.4 + - - +
134A LEU* 3.2 47.5 - - + +
137A THR* 2.8 37.9 - - - +
138A PHE* 5.6 1.6 - - + -
157A TYR* 5.2 3.6 - - - +
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Residues in contact with THR 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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108A LYS 3.1 4.2 + - - -
109A ASN* 3.0 36.6 - - - +
111A CYS* 1.3 77.1 - - - +
113A SER* 1.3 57.1 + - - +
115A TYR* 3.4 9.9 + - - +
116A THR* 2.6 35.7 + - - +
119A ARG* 5.3 2.1 + - - -
156A PHE* 2.9 46.2 - - + -
157A TYR* 4.1 9.2 + - - -
160A LEU* 4.1 8.3 - - - +
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Residues in contact with SER 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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70A ARG* 5.4 1.1 - - - -
71A LYS* 3.8 31.3 + - - -
109A ASN* 2.7 28.5 + - - -
110A THR* 3.0 11.2 + - - -
112A THR* 1.3 77.4 - - - +
114A VAL* 1.3 60.2 + - - +
116A THR* 3.1 10.8 - - - -
117A LYS* 2.9 34.0 + - - +
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Residues in contact with VAL 114 (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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70A ARG* 4.8 7.9 - - - +
82A ARG* 3.2 45.2 + - + +
86A LEU* 4.0 13.7 - - + -
110A THR* 2.9 28.7 + - + +
111A CYS 3.0 6.9 + - - +
113A SER* 1.3 73.6 - - - +
115A TYR* 1.3 65.1 + - - +
116A THR 3.1 0.8 + - - -
117A LYS* 3.3 7.5 + - - +
118A ASP* 3.0 20.3 + - - +
130A LEU* 3.3 30.3 - - + +
134A LEU* 3.7 4.9 - - + -
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Residues in contact with TYR 115 (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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111A CYS 3.1 11.9 + - - +
112A THR* 3.9 10.5 - - - +
114A VAL* 1.3 75.2 - - - +
116A THR* 1.3 63.4 + - - +
118A ASP* 2.9 28.7 + - + +
119A ARG* 3.1 36.2 + - + +
130A LEU* 4.9 0.9 - - - -
131A LEU* 3.5 29.7 - - + +
134A LEU* 3.5 13.0 - - + +
160A LEU* 5.5 15.3 - - + -
164A LYS* 5.2 7.9 - - + +
166A ILE* 3.1 34.2 - - + +
173A LYS* 3.3 26.9 - - - -
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Residues in contact with THR 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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112A THR* 2.6 25.0 + - - +
113A SER* 3.1 13.9 - - - -
114A VAL 3.1 0.2 - - - -
115A TYR* 1.3 76.3 - - - +
117A LYS* 1.3 60.3 + - + +
119A ARG* 2.7 65.7 + - - +
120A ALA 4.2 1.0 + - - -
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Residues in contact with LYS 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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70A ARG* 3.3 46.6 - - - +
71A LYS* 3.9 28.5 + - - +
79A ARG* 3.7 25.2 + - - +
82A ARG* 4.7 6.1 - - - +
113A SER* 2.9 19.6 + - - +
114A VAL* 3.3 6.3 + - - +
116A THR* 1.3 76.8 - - + +
118A ASP* 1.3 59.6 + - - +
119A ARG 3.1 1.3 + - - -
120A ALA* 3.8 10.9 + - - +
121A ALA 4.8 0.3 + - - -
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Residues in contact with ASP 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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79A ARG* 5.1 13.6 + - - +
82A ARG* 5.3 1.5 - - - +
114A VAL 3.0 13.1 + - - +
115A TYR* 2.9 29.2 + - + +
117A LYS* 1.3 74.7 - - - +
119A ARG* 1.3 59.0 + - - +
120A ALA 3.4 0.2 - - - -
121A ALA* 3.0 25.4 + - - +
127A ALA* 3.1 45.2 + - - +
130A LEU* 4.0 14.8 - - + +
131A LEU* 5.1 0.3 - - - +
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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