Contacts of the strand formed by residues 133 - 143 (chain A) in PDB entry 3IAB
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 LEU 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A PHE 3.3 5.5 - - - +
119A ASP* 3.4 3.6 - - - -
120A ILE* 3.1 58.6 + - + +
121A LYS* 5.3 0.4 - - - -
131A GLU* 3.8 37.9 - - + +
132A ARG* 1.3 73.5 - - - +
134A LYS* 1.3 63.3 + - - +
135A VAL* 3.7 1.9 + - + -
71R A 3.5 45.8 - - + +
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Residues in contact with LYS 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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117A SER* 3.3 15.4 + - - -
118A PHE 3.5 2.5 - - - -
119A ASP* 2.8 31.4 + - - +
132A ARG* 4.6 6.3 - - - +
133A LEU* 1.3 70.8 - - - +
135A VAL* 1.3 62.6 + - - +
136A PRO* 3.5 9.4 - - - +
41B TYR* 4.5 2.7 - - - +
77B ALA* 3.5 21.1 - - - +
80B CYS* 3.6 32.8 - - + -
81B HIS* 4.4 6.3 - - + +
84B ASP* 3.2 19.8 + - - +
85B GLN* 3.2 30.8 + - - +
68R A 5.4 0.3 + - - -
71R A 2.9 36.9 + - + +
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Residues in contact with VAL 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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16A ILE* 4.1 22.2 - - + -
84A TYR* 4.1 19.3 - - + -
85A GLY* 3.9 22.4 - - - -
86A PRO* 4.9 2.7 - - + -
117A SER* 3.3 1.3 - - - -
118A PHE* 2.7 49.2 + - + +
120A ILE* 3.8 28.0 - - + -
133A LEU* 5.0 1.3 - - + -
134A LYS* 1.3 72.9 - - - +
136A PRO* 1.3 65.2 - - + +
137A ILE* 4.0 1.6 - - - +
73B GLU* 4.6 6.3 - - - +
71R A 6.0 0.7 - - - +
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Residues in contact with PRO 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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84A TYR* 3.2 5.9 - - - +
85A GLY* 2.9 25.3 + - - -
88A ILE* 3.8 17.9 - - + -
115A LEU* 4.0 2.2 - - + -
116A THR 3.6 6.1 - - - +
134A LYS 3.5 10.2 - - - +
135A VAL* 1.3 92.1 - - + +
137A ILE* 1.3 59.7 + - - +
73B GLU* 3.6 40.8 - - + +
76B LEU* 3.8 22.0 - - + -
77B ALA* 4.4 2.5 - - + -
80B CYS* 3.9 15.5 - - - -
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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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7A TYR* 4.4 6.7 - - + -
26A LEU* 3.8 26.0 - - + -
30A VAL* 4.8 0.4 - - + -
83A SER 3.5 11.0 - - - +
84A TYR* 4.0 3.1 - - + -
88A ILE* 4.7 0.2 - - - -
114A LYS 3.4 1.6 - - - +
115A LEU* 3.4 10.4 - - - +
116A THR* 2.6 50.7 + - + +
117A SER* 3.6 30.5 - - - +
118A PHE* 3.6 33.9 - - + -
136A PRO* 1.3 79.6 - - - +
138A LEU* 1.3 62.2 + - - +
139A VAL* 4.1 16.6 - - + -
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Residues in contact with LEU 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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82A PHE* 3.3 4.5 - - - -
83A SER 2.9 36.5 + - - +
88A ILE* 3.9 24.0 - - + +
91A MSE 3.8 25.4 - - + +
92A LEU* 3.7 30.3 - - + -
113A ASN* 4.7 9.4 - - + -
114A LYS 3.9 14.8 - - - +
115A LEU* 4.7 7.4 - - + -
137A ILE* 1.3 72.6 - - - +
139A VAL* 1.3 62.7 + - - +
140A THR* 4.1 3.6 - - - +
76B LEU* 4.9 7.6 - - + -
92B VAL* 4.0 26.0 - - + -
94B THR* 4.3 9.0 - - + -
134B VAL* 5.2 2.2 - - + -
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Residues in contact with VAL 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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30A VAL* 4.8 2.2 - - + -
31A ILE* 3.6 27.1 - - + -
34A LEU* 4.7 11.9 - - + -
80A CYS* 3.8 25.8 - - - -
81A ILE 3.8 2.2 - - - -
82A PHE* 4.2 3.8 - - + -
112A TRP 3.6 1.2 - - - +
113A ASN* 3.3 3.3 - - - +
114A LYS* 2.8 42.7 + - + +
116A THR* 5.3 2.0 - - + -
137A ILE* 4.1 18.4 - - + -
138A LEU* 1.3 77.2 - - - +
140A THR* 1.3 63.0 + - - +
141A MSE 4.1 14.6 - - + -
155A PHE* 3.7 13.7 - - + -
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Residues in contact with THR 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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79A VAL 3.6 1.0 - - - +
80A CYS* 3.4 4.0 - - - -
81A ILE* 2.7 48.0 + - + +
91A MSE 3.2 21.2 - - - +
95A LEU* 3.9 15.2 - - + +
111A GLN* 3.6 13.9 - - + +
112A TRP 3.2 3.6 - - - +
113A ASN* 2.7 27.4 + - - +
138A LEU* 4.1 4.5 - - - +
139A VAL* 1.3 73.0 - - - +
141A MSE 1.3 72.9 + - - +
142A VAL* 4.0 13.0 - - + -
94B THR* 4.8 0.2 - - - +
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Residues in contact with MSE 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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31A ILE* 3.9 18.2 - - + +
34A LEU* 5.9 0.7 - - + -
35A ALA* 4.2 19.1 - - + -
44A ILE* 5.4 4.0 - - + -
78A VAL* 4.4 18.8 - - + -
79A VAL 3.4 2.2 - - - +
80A CYS* 3.6 39.0 - - + -
111A GLN* 3.0 8.1 - - - +
112A TRP* 2.8 49.8 + - + +
139A VAL* 4.1 2.2 - - + -
140A THR* 1.3 73.6 - - - +
142A VAL* 1.3 61.1 + - - +
148A ILE* 5.1 0.4 - - + -
150A LEU* 4.6 6.5 - - + -
152A LEU* 3.8 15.5 - - + -
155A PHE* 3.7 35.4 - - + -
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Residues in contact with VAL 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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62A LEU* 5.9 0.2 - - + -
66A ILE* 3.9 7.4 - - + +
77A GLN 3.8 0.5 - - - +
78A VAL* 3.4 3.8 - - - +
79A VAL* 2.8 62.7 + - + +
81A ILE* 3.8 15.7 - - + -
95A LEU* 4.0 15.9 - - + -
98A PHE* 4.7 11.9 - - + -
99A LYS* 5.4 0.2 - - + -
109A ILE* 4.5 17.3 - - + -
110A TYR 3.4 4.5 - - - +
111A GLN* 3.8 17.9 - - + +
112A TRP* 5.0 0.4 - - - -
140A THR* 4.0 11.7 - - + -
141A MSE 1.3 78.8 - - - +
143A SER* 1.3 62.6 + - - +
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Residues in contact with SER 143 (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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66A ILE* 4.1 2.9 - - - -
76A GLN* 4.9 0.3 - - - +
77A GLN 3.1 19.2 + - - -
78A VAL* 4.2 2.5 - - - +
109A ILE* 3.5 9.5 - - - +
110A TYR* 2.9 33.6 + - - +
112A TRP* 4.3 2.0 - - - -
142A VAL* 1.3 77.1 - - - +
144A ASP* 1.3 68.8 + - - +
145A SER* 2.9 27.2 + - - -
148A ILE* 3.5 27.8 - - - +
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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