Contacts of the helix formed by residues 110 - 128 (chain A) in PDB entry 5LN3
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 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1132 THR* 5.7 4.5 - - + -
1152 ARG* 4.3 22.4 - - - +
76A ILE* 4.6 1.0 - - - +
101A TRP* 4.0 16.2 - - + -
107A TYR* 4.6 14.6 - - + +
108A GLU 3.4 9.6 - - - +
109A ILE* 1.3 92.3 - - - +
111A VAL* 1.4 64.7 + - - +
112A ASP* 3.4 18.8 - - - +
113A MET* 3.3 32.6 + - + +
114A LEU* 3.5 5.2 + - - +
144A ASP* 4.5 7.6 - - - +
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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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75A ASN* 4.6 5.4 - - - +
76A ILE* 4.0 27.8 - - + -
109A ILE 5.1 0.7 - - - +
110A PRO* 1.4 70.5 - - - +
112A ASP* 1.3 64.1 + - - +
114A LEU* 3.3 17.3 + - - +
115A CYS* 3.3 9.0 + - - +
140A LEU* 3.8 36.5 - - + +
141A ILE 4.3 10.1 - - - +
142A GLY* 4.2 16.6 - - - +
144A ASP* 4.0 25.8 + - - +
150A GLN* 4.9 12.1 - - + +
152A TYR* 5.2 5.6 - - + -
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Residues in contact with ASP 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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1132 THR 4.9 1.9 - - - +
1152 ARG* 3.2 39.3 + - - -
110A PRO* 3.4 10.4 - - - +
111A VAL* 1.3 77.3 + - - +
113A MET* 1.3 73.6 + - - +
115A CYS* 3.2 9.6 + - - +
116A LYS* 3.1 22.7 + - - +
144A ASP* 4.4 4.5 - - - +
150A GLN* 5.3 6.1 - - + +
152A TYR* 4.5 30.2 - - + +
160A TYR* 5.2 1.9 - - - -
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Residues in contact with MET 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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1092 HIS* 4.2 4.0 - - + -
1122 SER* 4.2 33.7 - - - +
1132 THR* 4.2 16.8 - - + -
1152 ARG* 6.1 0.2 - - - +
101A TRP* 3.6 41.7 - - + +
109A ILE* 4.6 2.2 - - + -
110A PRO* 3.3 26.9 + - + +
111A VAL 3.1 0.6 - - - -
112A ASP* 1.3 86.5 - - - +
114A LEU* 1.4 55.9 + - - +
116A LYS* 3.2 16.7 + - - +
117A ARG* 3.0 48.1 + - + +
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Residues in contact with LEU 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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72A ILE* 3.5 30.7 - - + -
76A ILE* 5.4 8.7 - - + -
94A ALA* 4.3 13.9 - - + +
97A GLU* 3.4 24.2 - - + +
98A ALA* 4.1 24.7 - - + +
109A ILE* 4.3 13.0 - - + +
110A PRO 3.5 5.2 + - - +
111A VAL* 3.3 12.0 + - - +
113A MET* 1.4 76.2 - - - +
115A CYS* 1.4 65.9 + - - +
117A ARG* 4.4 4.9 - - - +
118A ILE* 3.0 40.4 + - + +
138A MET* 4.8 4.0 - - + -
140A LEU* 4.4 15.3 - - + -
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Residues in contact with CYS 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 3.3 5.3 + - - +
112A ASP* 3.2 14.1 + - - +
114A LEU* 1.4 78.2 - - - +
116A LYS* 1.4 57.5 + - - +
118A ILE* 3.5 5.4 + - - +
119A ALA* 3.0 27.0 + - - +
138A MET* 5.8 0.7 - - - -
140A LEU* 3.6 31.8 - - + +
152A TYR* 4.2 15.7 - - + -
153A LYS 4.4 0.9 - - - -
154A CYS* 4.2 13.5 - - - -
160A TYR* 3.4 36.1 - - + -
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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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1112 LEU 5.6 0.4 + - - -
1122 SER* 3.9 23.8 + - - +
112A ASP 3.1 10.0 + - - +
113A MET* 3.4 17.7 - - - +
115A CYS* 1.4 77.8 - - - +
117A ARG* 1.3 57.8 + - + +
119A ALA* 3.0 21.1 + - - +
120A ASP* 2.9 22.7 - - - +
160A TYR* 3.4 38.3 - - + +
66B GLU* 4.9 11.7 + - - -
84B ARG* 5.4 13.2 - - + +
91B ARG* 5.2 11.0 - - - +
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Residues in contact with ARG 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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1092 HIS* 5.4 0.6 + - - -
97A GLU* 3.1 40.7 + - + +
101A TRP* 3.5 30.2 - - - +
104A LYS* 5.7 3.0 - - - +
105A TYR* 3.9 22.0 + - - -
113A MET* 3.0 35.7 + - + +
114A LEU* 3.3 7.2 + - - +
116A LYS* 1.3 74.1 - - + +
118A ILE* 1.3 67.4 + - + +
120A ASP* 3.2 26.5 + - - +
121A ILE* 3.4 11.7 + - - +
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Residues in contact with ILE 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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90A GLN* 3.9 31.4 - - + +
93A ARG* 5.6 1.8 - - + -
94A ALA* 4.4 19.1 - - + +
97A GLU* 5.3 11.7 - - + +
114A LEU* 3.0 33.5 + - + +
115A CYS* 3.7 4.9 - - - +
117A ARG* 1.3 77.4 - - + +
119A ALA* 1.4 65.5 + - - +
121A ILE* 3.1 33.3 + - + +
122A SER* 3.0 23.1 + - - +
138A MET* 4.8 11.2 - - - -
154A CYS* 5.3 9.0 - - - -
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Residues in contact with ALA 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 CYS 3.0 14.6 + - - +
116A LYS 3.0 11.2 + - - +
118A ILE* 1.4 76.8 - - - +
120A ASP* 1.4 56.0 + - - +
122A SER* 3.1 24.4 + - - -
123A GLN* 3.1 13.5 + - - +
154A CYS* 4.9 7.6 - - - -
158A GLY* 4.0 15.6 - - - +
160A TYR* 3.6 31.6 - - + -
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Residues in contact with ASP 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 26.9 - - - +
117A ARG* 3.4 16.8 - - - +
119A ALA* 1.4 71.2 - - - +
121A ILE* 1.4 65.4 + - + +
123A GLN* 3.4 19.8 + - - +
124A VAL* 3.6 17.0 + - - +
84B ARG* 4.7 10.0 - - - +
85B VAL* 3.6 25.5 - - + +
88B HIS* 5.7 9.4 - - - +
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Residues in contact with ILE 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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90A GLN* 6.2 2.7 - - + +
93A ARG* 4.7 19.5 - - + -
117A ARG 3.6 14.6 - - - +
118A ILE* 3.1 35.7 + - + +
120A ASP* 1.4 75.9 - - + +
122A SER* 1.3 64.2 + - - +
124A VAL* 3.3 13.5 - - + +
125A TYR* 3.1 49.6 - - + +
134A LEU* 6.4 1.8 - - + -
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Residues in contact with SER 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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118A ILE* 3.0 21.6 + - - +
119A ALA* 3.1 14.5 + - - -
121A ILE* 1.3 79.0 - - - +
123A GLN* 1.3 58.2 + - - +
125A TYR* 3.3 24.9 + - - +
126A THR* 3.0 16.8 + - - -
133A PRO* 4.2 5.9 - - - +
154A CYS* 5.3 4.4 - - - -
156A PRO* 4.2 23.6 - - - +
158A GLY* 4.6 7.4 - - - -
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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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119A ALA 3.1 11.7 + - - +
120A ASP* 3.5 14.6 - - - +
121A ILE 3.3 0.2 - - - -
122A SER* 1.3 76.0 - - - +
124A VAL* 1.3 61.9 + - - +
126A THR* 3.1 29.7 - - - +
127A GLN* 3.2 24.1 + - - +
157A ALA 5.4 1.6 - - - +
158A GLY* 5.2 5.6 - - - -
81B PRO* 3.9 30.5 - - + +
82B ASP* 3.1 27.7 + - - +
85B VAL* 3.7 23.5 - - + +
130B PHE* 3.8 16.6 - - - -
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Residues in contact with VAL 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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120A ASP 3.7 13.7 - - - +
121A ILE* 3.3 19.3 - - + +
123A GLN* 1.3 76.0 - - - +
125A TYR* 1.4 74.0 + - + +
127A GLN* 3.0 38.0 + - + +
128A ASN* 3.1 21.2 + - - +
85B VAL* 5.5 2.7 - - + -
89B ARG* 4.3 12.1 - - - +
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Residues in contact with TYR 125 (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 ARG* 3.2 25.1 + - - -
121A ILE* 3.1 50.3 - - + +
122A SER* 3.6 14.6 - - - +
123A GLN 3.2 0.4 - - - -
124A VAL* 1.4 87.0 - - + +
126A THR* 1.3 57.9 + - - +
128A ASN* 3.2 18.8 + - - +
131A MET* 3.2 48.3 - - + +
132A ARG 4.0 5.6 - - - +
133A PRO* 3.8 35.1 - - + +
134A LEU* 4.4 17.7 - - + +
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Residues in contact with THR 126 (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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14A THR* 4.8 9.0 + - - +
22A LEU* 4.9 17.9 - - + +
25A VAL* 4.9 11.2 - - + -
122A SER 3.0 15.6 + - - -
123A GLN* 3.1 19.3 + - - -
125A TYR* 1.3 77.4 - - - +
127A GLN* 1.4 58.7 + - - +
128A ASN 3.9 4.2 - - - +
133A PRO* 3.9 15.0 - - + +
156A PRO 4.9 2.9 + - - -
157A ALA* 4.7 12.3 + - - +
128B ARG* 5.1 16.6 + - - +
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Residues in contact with GLN 127 (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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14A THR* 5.4 2.1 - - - +
123A GLN* 3.2 31.0 + - - +
124A VAL* 3.0 18.1 + - + +
126A THR* 1.4 75.4 - - - +
128A ASN* 1.4 62.6 + - - +
129A ALA* 3.7 1.2 + - - +
10B LEU* 5.9 0.9 - - - +
89B ARG* 3.6 16.3 + - - +
121B TYR* 4.8 10.5 - - - -
126B GLY 3.4 11.4 - - - +
127B VAL* 3.6 27.5 - - + +
128B ARG* 3.4 36.7 + - + +
129B PRO 5.8 0.2 - - - +
130B PHE* 3.3 31.3 - - + -
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Residues in contact with ASN 128 (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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14A THR* 4.0 7.5 - - - +
124A VAL* 3.1 23.5 + - - +
125A TYR* 3.2 33.1 + - - +
126A THR 3.9 4.9 - - - +
127A GLN* 1.4 74.0 - - - +
129A ALA* 1.3 57.4 + - - +
130A GLU* 3.2 7.4 + - - +
131A MET* 3.3 34.3 - - + +
126B GLY 3.6 7.3 - - - +
127B VAL* 4.4 12.0 - - - +
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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