Contacts of the strand formed by residues 104 - 117 (chain A) in PDB entry 1J71
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 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A VAL* 3.3 33.0 - - + -
100A GLY* 3.2 3.1 - - - -
101A PHE* 3.0 40.2 + - + +
102A GLY 4.6 0.7 - - - +
103A GLY* 1.3 84.4 - - - +
105A SER* 1.3 64.0 + - - +
106A ILE* 5.4 0.4 - - + -
145A LEU* 3.6 21.3 - - + -
150A ILE* 3.5 26.2 - - + -
572A EOH 3.6 30.3 - - + +
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Residues in contact with SER 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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24A GLN* 6.2 2.0 - - - -
98A THR* 4.1 13.8 - - - +
99A VAL 3.3 10.5 - - - -
100A GLY* 4.1 5.8 - - - -
104A ILE* 1.3 80.1 - - - +
106A ILE* 1.3 67.2 + - - +
107A LYS* 2.9 36.2 + - - -
148A GLN* 4.5 0.5 - - - +
150A ILE* 4.1 9.1 - - - +
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Residues in contact with ILE 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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97A ASP 4.1 1.0 - - - +
98A THR* 3.4 3.1 - - - +
99A VAL* 2.8 45.1 + - + +
101A PHE* 4.8 7.9 - - + -
104A ILE* 5.4 0.2 - - + -
105A SER* 1.3 76.4 - - - +
107A LYS* 1.3 64.2 + - - +
109A GLN* 3.5 35.4 - - + +
141A VAL* 4.4 20.2 - - + +
144A THR* 4.0 17.7 - - + -
145A LEU* 3.7 28.5 - - + -
148A GLN* 3.5 13.2 - - - +
150A ILE* 3.8 11.7 - - + -
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Residues in contact with LYS 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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98A THR* 3.9 22.7 - - + +
105A SER* 2.9 42.5 + - - -
106A ILE* 1.3 75.9 - - - +
108A ASN* 1.3 84.9 + - - +
109A GLN* 3.2 4.6 + - - -
144A THR* 4.6 0.7 - - - +
148A GLN* 3.0 32.5 + - - +
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Residues in contact with ASN 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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72A SER 5.7 0.7 - - - +
74A GLN* 4.4 14.0 + - - -
96A LYS* 3.5 31.2 + - + +
97A ASP* 3.5 19.8 + - - +
98A THR* 4.8 1.0 + - - -
107A LYS* 1.3 83.9 + - - +
109A GLN* 1.3 62.7 + - - +
110A GLN 3.6 0.3 + - - -
144A THR* 5.8 1.1 - - - +
148A GLN* 5.9 0.2 - - - +
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Residues in contact with GLN 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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38A LEU* 4.8 2.9 - - + +
96A LYS* 3.3 1.2 - - - -
97A ASP 2.9 29.7 + - - +
99A VAL* 3.9 18.6 - - + -
106A ILE* 3.5 24.7 - - + +
107A LYS 3.2 2.5 - - - +
108A ASN* 1.3 77.5 - - - +
110A GLN* 1.3 85.5 + - - +
111A PHE* 3.3 8.7 - - - -
139A ASP 3.1 21.6 + - - -
140A ASN* 3.6 10.7 - - - +
141A VAL* 3.6 20.1 - - + +
144A THR* 2.7 35.2 + - - -
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Residues in contact with GLN 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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38A LEU* 5.0 3.1 + - - +
76A LEU* 3.6 20.3 - - + +
78A GLN* 4.5 8.7 - - - +
94A PHE* 3.4 35.2 - - + +
95A TYR 3.2 11.7 - - - +
96A LYS* 4.2 18.5 - - + +
108A ASN 3.6 3.4 + - - -
109A GLN* 1.3 95.4 + - - +
111A PHE* 1.3 65.0 + - - +
136A ASN* 5.6 0.9 - - - +
138A TYR* 3.6 55.7 + - + +
139A ASP 4.8 1.0 + - - +
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Residues in contact with PHE 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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20A VAL* 3.6 23.1 - - + -
38A LEU* 3.3 34.1 - - + +
40A VAL* 3.9 28.7 - - + -
65A PHE* 3.8 20.0 - + - -
94A PHE* 3.5 10.1 - - - -
95A TYR* 2.8 43.3 + - + +
96A LYS 4.2 2.2 - - - -
97A ASP* 3.5 33.0 - - + -
99A VAL* 4.2 11.7 - - + -
109A GLN 3.3 12.8 - - - -
110A GLN* 1.3 76.1 - - - +
112A ALA* 1.3 72.1 + - - +
113A ASP 4.7 0.9 - - - -
138A TYR* 5.1 0.7 - - - -
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Residues in contact with ALA 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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38A LEU 3.0 9.4 + - - +
39A TRP* 3.1 12.3 - - + +
40A VAL 2.9 27.0 + - - -
80A PHE* 3.4 49.1 - - + -
93A SER 3.5 6.3 - - - +
94A PHE* 3.9 6.2 - - + -
111A PHE* 1.3 80.0 - - - +
113A ASP* 1.3 61.0 + - - +
114A VAL 3.7 0.2 - - - -
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Residues in contact with ASP 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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40A VAL* 3.8 4.4 - - - +
42A ASP* 2.5 49.8 + - - +
65A PHE* 3.6 20.7 - - + +
67A PRO* 3.5 16.1 - - + +
92A GLY* 3.3 2.1 - - - -
93A SER* 2.9 28.2 + - - +
95A TYR* 3.7 28.4 + - + -
111A PHE* 4.1 1.9 + - + -
112A ALA* 1.3 70.5 - - - +
114A VAL* 1.3 59.5 + - - +
115A THR* 3.8 6.8 + - - +
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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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39A TRP* 3.3 41.7 - - + -
40A VAL 2.8 16.3 + - - +
41A VAL* 3.8 1.0 - - - -
42A ASP* 2.8 27.5 + - - +
45A ALA* 3.4 5.2 - - - +
80A PHE* 4.0 14.8 - - + -
90A SER* 3.8 13.0 - - - -
91A GLN 3.4 7.4 - - - +
113A ASP* 1.3 73.8 - - - +
115A THR* 1.3 60.9 + - - +
116A THR 3.2 27.8 - - - +
117A THR* 3.7 20.0 - - + -
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Residues in contact with THR 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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42A ASP* 3.9 23.3 - - + +
44A ASP 4.6 2.2 - - - +
45A ALA* 3.2 10.1 - - - +
46A GLU* 2.7 37.9 + - - +
91A GLN* 3.0 10.2 + - - +
92A GLY* 4.1 6.2 - - - -
113A ASP* 3.8 10.0 + - - +
114A VAL* 1.3 75.3 - - - +
116A THR* 1.3 63.3 + - - +
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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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46A GLU* 3.3 27.0 + - + +
48A GLN* 2.9 42.2 - - + +
90A SER* 3.4 0.7 - - - -
91A GLN* 2.9 48.5 + - - +
114A VAL* 3.2 3.1 - - - +
115A THR* 1.3 85.4 + - - +
117A THR* 1.3 63.8 + - - +
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Residues in contact with THR 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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39A TRP* 3.7 9.5 - - + -
41A VAL* 5.0 4.5 - - + -
45A ALA* 5.4 1.3 - - + -
46A GLU 3.2 6.2 + - - +
47A CYS* 3.5 3.5 - - - -
48A GLN* 2.8 35.9 + - - +
58A PHE* 4.4 1.6 - - - -
59A CYS* 3.8 22.0 - - + -
89A SER 3.0 5.7 + - - -
90A SER* 2.7 25.4 + - - -
114A VAL* 3.7 12.6 - - + -
116A THR* 1.3 79.2 - - - +
118A SER* 1.3 57.9 + - - +
119A VAL* 3.0 27.4 + - - +
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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