Contacts of the strand formed by residues 131 - 143 (chain E) in PDB entry 6H25
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 HIS 131 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66E MET* 5.3 14.1 - - + +
67E GLY* 3.8 10.2 + - - +
69E PRO* 4.3 0.8 - - - +
126E ILE* 3.3 35.4 + - + +
127E SER* 3.2 17.7 + - - +
130E GLU* 1.3 103.9 + - + +
132E CYS* 1.3 66.4 + - - +
170E VAL* 4.9 22.0 - - + +
172E GLU* 5.8 2.3 + - - -
178E LYS* 6.3 1.0 - - - +
180E ILE* 6.0 2.5 - - + +
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Residues in contact with CYS 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E MET* 3.9 1.4 - - - -
67E GLY 3.0 32.8 + - - +
69E PRO* 3.7 34.9 - - + +
74E PRO 4.8 0.7 - - - -
75E ASN 4.6 2.5 - - - -
76E GLU* 4.1 13.7 - - - -
77E GLY* 4.2 11.4 - - - -
124E LEU 4.0 6.3 - - - +
125E CYS* 3.8 26.0 - - - -
126E ILE* 4.3 5.1 - - - +
127E SER 4.7 4.9 - - - -
128E PRO* 5.2 1.1 - - - -
131E HIS* 1.3 83.9 - - - +
133E TRP* 1.3 65.1 + - - +
134E VAL* 4.3 2.9 - - + +
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Residues in contact with TRP 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E ALA* 5.0 7.3 - - + +
65E GLU 3.1 23.5 - - - +
66E MET* 3.7 25.7 - - + +
77E GLY* 4.1 5.9 - - - -
78E TYR 3.8 18.0 + - - +
123E THR 4.8 5.6 - - - -
124E LEU* 3.4 48.4 + - + +
125E CYS 5.4 1.8 - - - -
126E ILE* 4.0 16.2 - - + -
132E CYS* 1.3 76.1 - - - +
134E VAL* 1.3 63.3 - - - +
135E LEU* 4.1 3.3 + - + +
165E ILE* 3.6 27.6 - - + -
166E PRO* 3.1 31.6 - - + +
168E VAL* 4.0 30.7 - - + -
190E ILE* 4.1 20.9 - - + -
16J VAL* 5.1 4.6 - - - +
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Residues in contact with VAL 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E LYS 4.1 0.9 - - - +
64E ALA* 4.3 0.6 - - - -
65E GLU* 3.2 33.5 + - + +
66E MET 5.2 0.7 - - - -
67E GLY* 4.9 9.0 - - - +
68E THR 4.7 7.4 - - - +
69E PRO* 6.1 0.4 - - + -
78E TYR* 3.6 52.5 - - + +
80E GLU* 4.3 4.5 - - + -
132E CYS 4.3 7.4 - - - +
133E TRP* 1.3 76.5 - - - +
135E LEU* 1.3 60.9 + - - +
136E TYR* 3.1 44.0 + - + +
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Residues in contact with LEU 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E VAL* 4.3 11.7 - - + -
63E LYS 3.9 13.9 - - - +
64E ALA* 5.1 4.3 - - + -
78E TYR 3.6 7.0 + - - +
79E LEU* 3.9 26.0 - - + -
80E GLU 3.1 26.7 + - - +
119E VAL* 5.9 1.8 - - + -
124E LEU* 4.1 31.2 - - + -
133E TRP* 4.1 3.8 - - + -
134E VAL* 1.3 69.1 - - - +
136E TYR* 1.3 61.5 + - - +
137E VAL* 3.3 12.7 + - + +
160E LEU* 5.4 10.1 - - + -
163E THR* 4.5 5.2 - - + -
165E ILE* 3.9 24.9 - - + -
192E LEU* 4.7 16.6 - - + -
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Residues in contact with TYR 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ARG* 3.5 50.4 + - + +
61E GLY 3.8 1.7 - - - +
62E VAL* 3.4 4.0 - - - -
63E LYS* 3.1 38.6 + - + +
65E GLU* 3.6 36.3 - - + +
78E TYR* 5.4 2.6 + - - -
80E GLU* 3.6 30.1 - - + -
134E VAL* 3.1 30.8 + - + +
135E LEU* 1.3 68.1 - - - +
137E VAL* 1.3 61.6 + - - +
138E ASP* 3.9 6.8 + - - +
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Residues in contact with VAL 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E VAL* 4.0 15.0 - - + -
61E GLY 3.9 2.9 - - - -
62E VAL* 3.7 22.0 - - + -
79E LEU* 4.9 4.3 - - + -
80E GLU 3.0 7.4 + - - +
81E PHE* 3.5 38.9 - - + -
82E PHE 3.2 17.8 + - - +
135E LEU* 4.1 13.9 - - + +
136E TYR* 1.3 71.8 - - - +
138E ASP* 1.3 71.6 + - - +
139E VAL* 4.2 3.7 + - + +
156E VAL* 3.7 17.7 - - + -
160E LEU* 4.0 14.8 - - + -
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Residues in contact with ASP 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B THR* 2.6 38.4 + - - +
81B PHE* 4.2 17.1 + - + +
86B ARG* 3.8 19.6 + - - +
59E LEU 4.2 0.2 - - - +
60E VAL* 3.4 6.0 - - - +
61E GLY 3.0 37.2 + - - +
63E LYS* 5.5 1.7 - - - -
80E GLU 5.3 0.2 - - - +
82E PHE* 3.4 25.1 + - + +
136E TYR* 4.6 5.9 - - - +
137E VAL* 1.3 85.1 + - - +
139E VAL* 1.3 63.9 + - - +
140E LEU* 3.9 1.6 + - + -
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Residues in contact with VAL 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E ILE* 4.1 23.1 - - + -
59E LEU 4.0 2.7 - - - -
60E VAL* 3.8 17.5 - - + -
81E PHE* 5.4 1.1 - - + -
82E PHE 3.0 7.1 + - - +
83E VAL* 3.4 28.0 - - + +
84E ASP* 3.0 26.5 + - - +
109E LEU* 4.7 11.9 - - + -
137E VAL* 4.7 7.9 - - + +
138E ASP* 1.3 75.6 - - - +
140E LEU* 1.3 61.7 + - - +
141E LEU* 4.1 6.0 + - + +
152E ILE* 4.1 31.2 - - + -
156E VAL* 5.4 2.2 - - + -
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Residues in contact with LEU 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ALA* 4.2 25.1 - - + -
81B PHE* 4.5 17.5 - - + -
126B GLN* 2.1 44.4 - - + +
128B LEU* 5.2 7.4 - - + -
59E LEU* 3.0 41.3 + - + +
84E ASP* 3.5 35.9 - - + +
86E SER* 4.0 9.6 - - - -
138E ASP* 3.9 1.2 + - + -
139E VAL* 1.3 72.7 - - - +
141E LEU* 1.3 62.4 + - - +
142E LEU* 3.7 9.8 + - + +
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Residues in contact with LEU 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E ASP 3.4 11.7 - - - +
58E ILE* 3.9 16.8 - - + +
83E VAL* 4.3 15.0 - - + -
84E ASP 3.8 3.7 + - - +
85E CYS* 3.7 40.4 - - + +
86E SER* 3.2 23.0 + - - +
89E ALA* 5.1 5.8 - - + +
105E ILE* 5.4 6.1 - - + -
139E VAL* 3.9 5.1 - - + +
140E LEU* 1.3 73.7 - - - +
142E LEU* 1.3 62.8 + - - +
143E GLU 5.0 0.4 - - - +
144E CYS* 4.2 21.5 - - + +
148E LEU* 3.7 34.3 - - + -
152E ILE* 5.5 2.7 - - + -
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Residues in contact with LEU 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B PHE* 3.8 22.9 - - + -
49B LEU* 3.9 22.7 - - + -
126B GLN* 4.5 20.4 - - - +
128B LEU* 5.3 6.7 - - + -
50E ARG* 5.5 0.2 - - - +
57E ASP* 2.6 45.7 + - + +
59E LEU* 4.8 16.6 - - + -
88E SER* 3.6 13.0 - - - +
89E ALA* 3.4 25.3 + - - +
140E LEU* 4.3 12.1 - - + +
141E LEU* 1.3 77.4 - - - +
143E GLU* 1.3 59.4 + - - +
289E PHE* 4.5 14.8 - - + -
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Residues in contact with GLU 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B PHE* 4.3 22.1 - - + +
34B GLN* 3.3 38.5 - - + +
35B ALA* 5.2 4.7 - - - +
53B TYR* 3.6 6.4 + - - -
55E HIS* 3.9 18.6 - - + +
56E THR* 3.0 9.4 + - - -
57E ASP* 2.9 29.7 + - + +
88E SER 3.6 3.5 - - - +
89E ALA* 3.0 33.7 - - - +
90E THR* 4.9 3.3 - - - +
141E LEU* 5.0 3.1 - - - +
142E LEU* 1.3 80.7 - - - +
144E CYS* 1.3 74.2 + - - +
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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