Contacts of the strand formed by residues 128 - 142 (chain A) in PDB entry 5I7L
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 ARG 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A GLN* 3.6 7.8 - - - +
123A SER* 2.8 54.8 + - - +
124A PRO* 4.0 10.3 - - - +
125A ASP* 2.7 36.5 + - - -
126A GLY 3.5 0.6 - - - -
127A HIS* 1.3 85.6 - - + +
129A LEU* 1.3 63.7 + - - +
130A TYR* 2.8 44.5 + - + +
162A GLU* 3.9 8.3 - - - +
163A ILE 3.4 7.4 - - - +
164A LEU* 3.4 22.7 - - + -
246A LEU* 3.8 2.9 - - - +
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 3.6 28.0 - - + -
120A LEU* 3.7 28.9 - - + -
121A VAL 3.5 10.8 - - - +
122A GLN* 4.6 3.1 - - + -
128A ARG* 1.3 76.6 - - - +
130A TYR* 1.3 67.2 + - - +
131A VAL 4.1 0.2 - - - -
162A GLU* 3.4 5.4 - - - +
163A ILE* 2.8 47.8 + - + +
242A ILE* 4.4 3.4 - - + -
246A LEU* 4.0 27.6 - - + -
252A PHE* 4.1 15.0 - - + -
253A CYS* 3.7 21.1 - - + -
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Residues in contact with TYR 130 (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 GLY 3.5 4.5 - - - +
120A LEU* 3.5 2.3 - - - -
121A VAL* 2.9 56.3 + - + +
123A SER* 4.2 10.5 - - - -
128A ARG* 2.8 46.8 + - + -
129A LEU* 1.3 75.3 - - - +
131A VAL* 1.3 62.5 + - - +
132A THR* 4.0 2.2 + - - +
160A THR* 4.7 17.0 - - + -
161A ALA 3.6 1.1 - - - -
162A GLU* 3.0 46.1 + - + -
179A ASP* 6.2 0.2 - - + -
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Residues in contact with VAL 131 (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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55A LEU* 4.1 16.8 - - + -
118A LEU* 4.6 10.5 - - + -
119A GLY 3.3 4.3 - - - +
120A LEU* 3.4 26.2 - - + -
129A LEU* 5.2 0.7 - - + -
130A TYR* 1.3 75.6 - - - +
132A THR* 1.3 66.2 + - - +
133A ILE* 4.0 20.4 - - + +
159A ILE 3.5 0.7 - - - +
160A THR* 3.2 11.1 + - - -
161A ALA* 2.8 52.0 + - + +
163A ILE* 3.6 29.4 - - + -
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Residues in contact with THR 132 (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 LEU* 3.3 6.9 - - - +
119A GLY* 2.8 36.5 + - - -
121A VAL* 5.9 2.9 - - - +
130A TYR* 4.9 2.4 + - - +
131A VAL* 1.3 74.2 + - - +
133A ILE* 1.3 63.0 + - - +
134A PRO* 3.1 17.9 - - + +
158A ASP* 3.7 33.0 - - + +
159A ILE 3.7 2.7 - - - +
160A THR* 4.4 7.6 + - - +
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Residues in contact with ILE 133 (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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55A LEU* 6.4 0.7 - - + -
59A LEU* 4.1 17.5 - - + -
64A LEU* 5.2 0.2 - - + -
115A LEU* 3.9 14.4 - - + -
118A LEU* 3.8 10.8 - - + -
131A VAL* 4.0 16.4 - - + -
132A THR* 1.3 76.7 - - - +
134A PRO* 1.3 62.0 - - - +
135A LEU* 3.5 30.6 + - + +
158A ASP* 3.6 1.1 - - - -
159A ILE* 2.9 46.1 + - + +
161A ALA* 4.5 13.0 - - + -
223A VAL* 5.0 4.3 - - + -
227A VAL* 3.9 30.3 - - + -
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Residues in contact with PRO 134 (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 LEU* 3.7 6.1 - - - +
116A LEU* 2.8 60.2 + - + +
117A GLU 3.2 26.7 - - - +
118A LEU* 4.2 3.1 - - + -
132A THR* 3.1 20.0 - - + +
133A ILE* 1.3 85.1 - - - +
135A LEU* 1.3 57.0 + - - +
158A ASP* 3.4 22.0 - - - +
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Residues in contact with LEU 135 (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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64A LEU* 3.7 27.1 - - + -
68A LEU* 4.2 17.9 - - + -
114A GLN 3.4 4.9 - - - +
115A LEU* 4.0 3.1 - - + -
116A LEU* 5.2 3.9 - - - +
133A ILE* 3.5 28.7 - - + +
134A PRO* 1.3 77.7 - - - +
136A GLY* 1.3 59.6 + - - +
137A ILE* 6.0 0.7 - - + -
156A LYS* 3.5 8.8 - - - +
157A LEU* 2.8 37.7 + - + +
159A ILE* 3.9 17.7 - - + -
219A VAL* 3.8 28.9 - - + -
223A VAL* 4.1 13.5 - - + -
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Residues in contact with GLY 136 (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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68A LEU* 4.7 0.4 - - - +
112A ASP* 3.2 3.9 - - - +
113A PRO* 3.3 2.1 - - - +
114A GLN* 2.5 50.1 + - - +
116A LEU* 5.5 2.0 - - - +
135A LEU* 1.3 77.4 - - - +
137A ILE* 1.3 64.3 + - - +
155A VAL 3.5 8.3 - - - -
156A LYS* 4.2 11.2 - - - -
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Residues in contact with ILE 137 (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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68A LEU* 3.9 34.1 - - + +
71A LEU* 4.9 13.2 - - + -
73A LEU* 5.0 0.4 - - + -
110A VAL* 3.7 22.0 - - + -
111A THR 3.9 0.7 - - - +
112A ASP 3.8 6.1 - - - -
113A PRO* 4.3 4.7 - - + -
135A LEU* 6.0 0.4 - - + -
136A GLY* 1.3 79.9 - - - +
138A LYS* 1.3 64.2 + - - +
139A LEU* 3.7 27.8 - - + -
154A ALA* 3.8 1.7 - - - -
155A VAL* 2.9 43.7 + - + +
156A LYS* 5.4 1.4 + - - +
215A LEU* 4.6 19.1 - - + -
219A VAL* 6.0 1.6 - - + -
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Residues in contact with LYS 138 (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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109A LYS 3.8 0.5 - - - +
110A VAL* 3.5 5.7 - - - +
111A THR* 2.9 47.4 + - - +
112A ASP* 3.2 38.2 + - + +
137A ILE* 1.3 77.0 - - - +
139A LEU* 1.3 64.2 + - - +
140A GLN 4.1 0.2 - - - -
152A ARG* 4.1 31.4 - - + +
153A LEU 3.1 10.5 - - - +
154A ALA* 4.7 12.4 - - + +
156A LYS* 5.3 5.1 - - - +
192A LEU* 4.2 14.6 - - + +
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Residues in contact with LEU 139 (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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73A LEU* 3.6 32.5 - - + -
108A ILE* 3.8 14.4 - - + -
109A LYS 3.7 1.1 - - - -
110A VAL* 3.7 16.8 - - + -
137A ILE* 3.7 20.6 - - + -
138A LYS* 1.3 73.6 - - - +
140A GLN* 1.3 60.1 + - - +
141A VAL* 4.0 4.4 + - + +
151A LEU 4.4 0.2 - - - -
152A ARG* 3.2 4.7 - - - -
153A LEU* 2.8 49.1 + - + +
155A VAL* 3.9 18.2 - - + -
207A LEU* 6.1 2.5 - - + -
211A LEU* 3.8 33.4 - - + -
215A LEU* 4.9 1.8 - - + -
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Residues in contact with GLN 140 (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 ASP 3.5 2.8 - - - +
108A ILE* 3.7 1.9 - - - -
109A LYS* 3.2 65.1 + - + +
111A THR* 4.5 13.8 + - + +
138A LYS 4.1 1.0 + - - -
139A LEU* 1.3 72.7 - - - +
141A VAL* 1.3 62.5 + - - +
142A ASN* 3.4 24.3 + - - +
149A SER* 4.1 11.8 + - - +
151A LEU 3.4 5.4 - - - +
152A ARG* 3.7 31.4 + - + +
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Residues in contact with VAL 141 (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 ILE* 5.5 4.0 - - + -
107A ASP 3.6 8.1 - - - +
108A ILE* 3.6 19.3 - - + -
139A LEU* 5.0 5.6 - - + +
140A GLN* 1.3 70.9 - - - +
142A ASN* 1.3 66.9 + - - +
149A SER* 3.3 1.6 - - - -
150A LEU* 2.6 55.1 + - + -
151A LEU* 2.8 30.9 + - + +
153A LEU* 5.7 1.3 - - + -
203A LEU* 4.8 6.7 - - + -
207A LEU* 3.5 30.7 - - + -
91B LEU* 6.3 1.3 - - + -
95B VAL* 5.4 5.4 - - + -
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Residues in contact with ASN 142 (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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105A ILE 3.3 0.9 - - - +
106A ILE* 3.8 2.4 - - - -
107A ASP* 2.9 41.6 + - + +
109A LYS* 4.8 6.4 - - - +
140A GLN* 3.4 30.0 + - - +
141A VAL* 1.3 82.2 - - - +
143A THR* 1.3 68.0 + - - +
144A PRO* 4.2 3.8 - - + -
146A VAL* 5.7 0.7 - - + -
148A ALA 5.7 0.4 - - - -
149A SER* 2.5 33.4 + - - +
150A LEU* 4.4 3.5 - - - +
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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