Contacts of the helix formed by residues 106 - 124 (chain A) in PDB entry 5L5H
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 PRO 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ILE* 4.3 0.2 - - - -
97A TYR* 3.5 23.6 - - + +
104A TYR 4.3 1.1 - - - +
105A PRO* 1.3 91.1 - - + +
107A THR* 1.3 67.0 + - - +
108A LYS* 4.6 7.9 - - + +
109A LEU* 3.1 36.7 + - + +
110A LEU* 3.2 9.4 + - - +
139A HIS 5.6 0.2 - - - +
140A ASP* 3.5 33.4 - - + +
143A ASN* 4.1 9.4 - - - +
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Residues in contact with THR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 3.9 14.6 - - + +
105A PRO 3.8 0.8 + - - -
106A PRO* 1.3 70.5 - - - +
108A LYS* 1.3 58.1 + - - +
110A LEU* 3.3 2.3 + - - +
111A VAL* 2.9 32.6 + - - +
136A ILE* 4.2 18.2 - - + +
137A ALA 4.4 0.7 - - - -
138A GLY* 3.2 42.8 - - - +
139A HIS 3.4 4.4 + - - -
140A ASP* 3.2 13.7 + - - +
146A SER* 3.2 22.8 + - - +
148A TYR* 4.0 13.9 - - + -
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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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106A PRO* 4.6 8.3 - - + +
107A THR* 1.3 77.9 - - - +
109A LEU* 1.3 77.7 + - + +
111A VAL* 3.6 5.5 - - - +
112A SER* 3.0 25.6 + - - -
140A ASP* 4.9 0.8 + - - +
143A ASN* 3.2 39.0 + - - +
148A TYR* 3.4 35.7 - - + +
156A TYR* 4.7 6.7 + - + -
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Residues in contact with LEU 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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97A TYR* 4.0 22.2 - - + +
105A PRO* 4.8 4.3 - - + -
106A PRO* 3.1 32.7 + - + +
108A LYS* 1.3 92.1 - - + +
110A LEU* 1.3 64.8 + - - +
112A SER* 3.2 12.0 + - - +
113A GLU* 3.0 29.4 + - + +
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Residues in contact with LEU 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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67A LEU* 4.1 22.7 - - + -
68A THR* 3.9 18.2 - - + -
71A ILE* 3.6 30.3 - - + -
89A SER 3.6 24.0 - - - +
92A VAL* 3.9 12.8 - - + -
93A ALA* 3.9 14.4 - - + -
105A PRO* 4.1 12.8 - - + +
106A PRO 3.2 11.7 + - - +
107A THR 3.8 6.3 - - - +
109A LEU* 1.3 72.5 - - - +
111A VAL* 1.3 66.0 + - + +
113A GLU* 3.1 6.5 + - + +
114A VAL* 3.0 34.6 + - + +
136A ILE* 5.9 1.3 - - + -
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Residues in contact with VAL 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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107A THR 2.9 21.4 + - - +
108A LYS* 3.6 6.1 - - - +
110A LEU* 1.3 76.1 - - - +
112A SER* 1.3 52.0 + - - +
114A VAL* 3.2 7.2 + - - +
115A ALA* 2.8 33.4 + - - +
136A ILE* 3.8 33.7 - - + -
148A TYR* 3.8 26.9 - - + -
150A VAL* 3.8 16.1 - - + +
156A TYR* 3.7 33.9 - - + -
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Residues in contact with SER 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 3.0 16.0 + - - -
109A LEU* 3.3 20.7 - - - +
111A VAL* 1.3 77.6 - - - +
113A GLU* 1.3 57.1 - - - +
115A ALA* 3.6 7.3 - - - +
116A LYS* 3.0 26.5 + - - +
156A TYR* 4.0 15.6 + - - -
84B GLU* 3.8 15.2 + - - +
88B ASN* 5.2 6.8 + - - -
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Residues in contact with GLU 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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92A VAL* 3.8 30.2 - - + +
96A SER* 3.6 29.3 + - - +
109A LEU* 3.0 21.0 + - + +
110A LEU* 3.1 10.1 + - + +
112A SER* 1.3 75.3 - - - +
114A VAL* 1.3 64.3 + - - +
116A LYS* 3.3 20.2 + - - +
117A ILE* 3.2 27.7 + - - +
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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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67A LEU* 5.3 0.7 - - + -
85A LEU* 4.7 7.4 - - + -
89A SER* 3.1 35.9 - - - +
92A VAL* 5.4 0.2 - - + -
110A LEU* 3.0 26.6 + - + +
111A VAL* 3.6 6.7 - - - +
113A GLU* 1.3 75.2 - - + +
115A ALA* 1.3 63.3 + - - +
117A ILE* 3.2 12.8 + - + +
118A MET* 3.1 30.4 + - + +
134A LEU* 3.5 31.2 - - + -
136A ILE* 4.4 14.6 - - + -
150A VAL* 4.8 2.5 - - + -
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Residues in contact with ALA 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 VAL 2.8 20.7 + - - +
112A SER 3.6 5.6 - - - +
114A VAL* 1.3 74.1 - - - +
116A LYS* 1.3 56.6 + - - +
118A MET* 3.3 1.7 + - - -
119A GLN* 2.9 30.0 + - - +
150A VAL* 4.0 15.0 - - + +
154A GLY* 3.2 29.2 - - - +
156A TYR* 3.5 21.1 - - + -
84B GLU* 5.7 0.2 - - - +
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Residues in contact with LYS 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 SER 3.0 15.1 + - - +
113A GLU* 3.4 24.3 + - - +
114A VAL 3.2 0.4 - - - -
115A ALA* 1.3 76.1 - - - +
117A ILE* 1.3 63.7 + - + +
119A GLN* 3.2 7.5 + - - +
120A GLU* 2.9 50.6 + - - +
85B ILE* 3.7 25.8 - - + -
88B ASN* 6.1 2.9 - - - +
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Residues in contact with ILE 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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85A LEU* 4.1 13.2 - - + -
88A LYS* 4.1 43.3 - - + +
89A SER* 5.1 2.2 - - - +
92A VAL* 4.9 12.3 - - + -
113A GLU 3.2 15.2 + - - +
114A VAL* 3.2 14.0 + - - +
116A LYS* 1.3 79.2 - - + +
118A MET* 1.3 61.6 + - - +
120A GLU* 3.5 16.0 + - - +
121A ALA* 3.3 16.5 + - - +
130A PHE* 3.9 20.7 - - + -
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Residues in contact with MET 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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85A LEU* 3.9 20.2 - - + -
114A VAL* 3.1 22.6 + - - +
115A ALA 3.7 7.0 - - - +
117A ILE* 1.3 74.3 - - - +
119A GLN* 1.3 64.2 + - - +
121A ALA* 3.5 11.6 + - - +
122A THR* 3.6 6.4 + - - -
130A PHE* 3.9 18.8 + - + -
132A VAL* 3.5 35.2 - - + +
134A LEU* 4.2 9.2 - - + -
150A VAL* 3.6 26.7 - - - +
151A ASP 3.3 23.8 - - - +
152A PRO* 3.6 22.9 - - + +
154A GLY* 4.3 7.6 - - - -
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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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115A ALA 2.9 17.2 + - - +
116A LYS* 3.5 7.9 - - - +
118A MET* 1.3 77.7 - - - +
120A GLU* 1.3 65.7 + - - +
122A THR* 2.9 23.5 + - + -
123A GLN* 3.1 30.0 + - - +
153A SER 3.6 13.9 - - - +
154A GLY* 4.1 0.6 - - - -
81B ALA* 3.5 33.9 - - + +
82B ASP* 2.8 27.0 + - - +
85B ILE* 3.4 25.8 - - + +
128B ARG* 3.7 5.5 - - - +
130B PHE* 4.8 0.2 - - - -
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Residues in contact with GLU 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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116A LYS* 2.9 49.1 + - + +
117A ILE* 3.7 17.2 - - - +
118A MET 3.3 0.2 - - - -
119A GLN* 1.3 87.0 - - - +
121A ALA* 1.3 55.8 + - - +
122A THR 3.0 0.2 - - - -
123A GLN* 4.5 2.7 - - - +
124A SER* 2.7 48.8 + - - +
85B ILE* 4.8 3.2 - - + +
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Residues in contact with ALA 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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10A THR* 4.7 0.5 + - - -
117A ILE 3.3 3.8 + - - +
118A MET 3.7 4.7 - - - +
119A GLN 3.2 0.8 - - - -
120A GLU* 1.3 76.5 - - - +
122A THR* 1.3 58.9 + - - +
123A GLN 3.5 0.2 - - - -
127A VAL* 3.6 25.0 - - + +
128A ARG 3.3 33.9 - - - +
129A PRO* 3.4 4.6 - - + +
130A PHE* 3.5 37.0 - - + -
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Residues in contact with THR 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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10A THR* 3.3 24.9 - - + -
21A ILE* 3.3 39.1 - - + +
118A MET 3.6 6.7 + - - -
119A GLN* 2.9 15.8 + - - +
121A ALA* 1.3 79.9 - - - +
123A GLN* 1.3 55.1 + - - +
124A SER 5.2 0.4 - - - -
129A PRO* 3.7 8.1 - - - +
152A PRO 3.6 11.8 + - - -
153A SER 4.4 8.3 - - - +
82B ASP* 4.8 0.4 - - - +
128B ARG* 3.2 35.0 + - - +
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Residues in contact with GLN 123 (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 SER* 2.7 27.8 + - - -
119A GLN* 3.1 35.0 + - - +
120A GLU* 3.2 3.0 + - - +
122A THR* 1.3 79.0 - - - +
124A SER* 1.3 63.8 + - - +
85B ILE* 5.4 0.2 - - - +
121B TYR* 3.5 25.7 + - + -
127B LEU* 3.7 7.7 - - + +
128B ARG* 2.9 41.4 + - + +
129B PRO 4.0 7.5 + - - -
130B PHE* 3.3 30.5 - - - +
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Residues in contact with SER 124 (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 SER* 4.0 7.6 - - - -
9A LEU 4.5 0.5 + - - -
120A GLU* 2.7 38.4 + - - +
121A ALA 4.7 0.4 - - - +
122A THR 5.2 0.5 - - - -
123A GLN* 1.3 78.9 + - - +
125A GLY* 1.3 66.2 + - - +
126A GLY 3.8 1.0 + - - -
127A VAL* 3.7 22.6 + - - +
127B LEU* 4.2 7.4 - - - -
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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