Contacts of the strand formed by residues 123 - 133 (chain A) in PDB entry 5J0Z
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 SER 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ASP* 4.6 2.8 - - - +
122A ASP* 1.3 73.7 + - - +
124A GLN* 1.3 79.5 + - - +
163A GLU* 5.1 0.4 + - - -
189A ARG* 6.5 0.2 - - - -
190A ILE 3.2 9.0 - - - -
191A SER* 3.0 28.7 - - - +
192A ARG 4.6 0.2 - - - +
409A PLC 5.5 2.8 + - - -
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Residues in contact with GLN 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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113A PRO 4.6 1.6 - - - +
114A LEU* 3.4 29.2 - - + +
115A ASP* 2.9 46.6 + - - +
116A PHE* 4.9 1.0 - - - +
122A ASP* 2.7 24.9 + - - -
123A SER* 1.3 82.9 + - - +
125A THR* 1.3 65.9 + - - +
126A LEU* 3.9 1.3 - - + -
160A TRP* 3.8 22.6 - - + -
189A ARG* 3.2 8.0 - - - +
190A ILE* 2.7 49.4 + - + +
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Residues in contact with THR 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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112A SER* 3.7 5.0 + - - -
113A PRO 4.6 4.6 - - - +
124A GLN* 1.3 73.6 + - - +
126A LEU* 1.3 69.2 + - - +
127A HIS* 3.3 34.6 - - + +
187A GLN* 4.3 9.6 - - + +
188A LEU 3.6 3.8 - - - +
189A ARG* 3.4 38.4 + - + +
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Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 4.2 7.4 - - + -
37A PHE* 3.7 43.1 - - + -
112A SER* 3.6 9.0 - - - +
114A LEU* 3.6 31.6 - - + -
124A GLN* 4.7 1.1 - - + -
125A THR* 1.3 79.9 - - - +
127A HIS* 1.3 61.8 + - - +
128A ILE* 5.7 0.4 - - - -
157A LEU* 4.8 3.4 - - + -
187A GLN* 3.4 7.1 - - - -
188A LEU* 2.6 63.5 + - + +
190A ILE* 3.8 29.4 - - + -
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Residues in contact with HIS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 4.8 0.2 - - - -
80A ASN* 2.6 33.4 + - - +
110A VAL* 3.3 8.8 - - - +
112A SER* 3.6 14.8 + - - +
113A PRO* 5.5 5.6 - - + -
125A THR* 3.3 38.4 + - + +
126A LEU* 1.3 75.4 + - - +
128A ILE* 1.3 59.1 + - - +
129A TYR* 3.4 31.1 + - + -
185A ASP* 3.2 31.6 + - - -
186A TYR 3.4 2.5 - - - -
187A GLN* 3.7 15.7 - - + +
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Residues in contact with ILE 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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22A ILE* 4.1 11.2 - - + +
24A LEU* 4.4 4.0 - - + -
37A PHE* 4.1 24.0 - - + -
39A VAL* 4.3 26.2 - - + -
78A PHE* 3.3 37.5 - - + -
80A ASN* 3.8 3.1 - - - +
81A VAL* 5.9 0.9 - - + -
106A PHE* 5.3 2.7 - - + -
110A VAL* 4.4 11.2 - - + -
126A LEU 5.7 0.4 - - - -
127A HIS* 1.3 75.6 - - - +
129A TYR* 1.3 60.9 + - - +
130A LEU 3.7 1.7 + - - -
165A PHE* 4.4 23.8 - - + -
186A TYR* 2.9 41.4 + - + +
188A LEU* 5.8 3.8 - - + -
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Residues in contact with TYR 129 (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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78A PHE* 3.4 8.8 - - - +
79A VAL* 2.8 50.4 + - + -
80A ASN* 2.9 22.1 + - + +
127A HIS* 3.4 48.9 + + + -
128A ILE* 1.3 75.4 - - - +
130A LEU* 1.3 60.4 + - - +
183A LYS* 3.5 26.7 - - + -
184A LEU 3.6 6.3 - - - +
185A ASP* 3.4 28.2 + - + -
154E ASP* 3.6 23.3 - - - -
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Residues in contact with LEU 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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20A THR* 4.1 18.8 - - + -
22A ILE* 3.9 13.0 - - + -
43A LEU* 4.0 15.9 - - + -
76A ILE* 3.3 29.2 - - + -
77A ARG 3.9 4.5 - - - +
78A PHE* 3.7 32.8 - - + -
79A VAL* 4.4 0.7 - - - -
128A ILE 3.7 1.8 + - - -
129A TYR* 1.3 71.9 - - - +
131A ILE* 1.3 61.3 + - - +
142A LEU* 3.6 8.0 - - + +
183A LYS* 3.2 4.0 - - - +
184A LEU* 2.7 46.0 + - + +
186A TYR* 3.7 26.2 - - + -
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Residues in contact with ILE 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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76A ILE* 3.5 9.4 - - - +
77A ARG* 2.9 47.5 + - + +
79A VAL* 3.8 20.9 - - + -
130A LEU* 1.3 72.4 - - - +
132A VAL* 1.3 67.6 + - - +
142A LEU* 3.8 2.9 - - - +
174A PHE* 4.4 12.6 - - + -
176A LEU* 5.6 0.4 - - + -
181A GLU* 3.5 38.6 - - + +
182A SER 3.4 11.7 - - - +
183A LYS* 3.8 22.0 - - + -
407A ACT 3.7 24.5 - - + +
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Residues in contact with VAL 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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74A PRO* 4.6 1.8 - - + -
75A GLU 3.3 26.0 - - - +
76A ILE* 3.8 11.7 - - + -
131A ILE* 1.3 78.7 - - - +
133A ARG* 1.3 71.7 + - - +
134A SER* 3.8 1.0 + - - -
140A ILE* 4.1 33.0 - - + +
142A LEU* 3.4 33.2 - - + -
181A GLU* 3.5 6.8 - - - -
182A SER* 3.1 34.1 + - - +
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Residues in contact with ARG 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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75A GLU* 3.9 14.0 + - - +
77A ARG* 4.2 15.4 - - - +
131A ILE* 4.8 0.4 - - - +
132A VAL* 1.3 84.0 - - - +
134A SER* 1.3 71.8 + - - +
135A VAL* 3.8 2.6 + - - +
140A ILE* 4.3 5.9 - - - +
176A LEU* 3.1 34.3 + - - +
177A GLU* 3.1 23.8 + - - +
179A ARG* 4.0 24.5 + - - +
180A LEU 4.0 2.9 - - - +
181A GLU* 2.5 45.6 + - - +
42E PHE* 4.3 7.4 - - - -
90E VAL* 4.2 11.7 - - + -
91E ASP* 5.8 5.6 - - - +
103E LEU* 3.8 29.2 - - - +
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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