Contacts of the strand formed by residues 132 - 139 (chain E) in PDB entry 6R7H
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 ASN 132 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36E GLN* 4.2 3.6 + - - +
40E LEU* 3.6 21.5 - - - +
82E LEU* 3.5 17.7 - - - +
83E GLY 3.3 18.5 + - - +
121E ILE* 3.7 24.3 - - + +
125E LYS* 4.2 17.6 - - - +
130E LEU* 3.1 20.0 + - - +
131E GLU* 1.3 84.0 + - - +
133E ALA* 1.3 68.9 + - - +
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Residues in contact with ALA 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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80E LEU* 5.0 2.0 - - + -
81E MET 4.7 2.5 - - - +
82E LEU* 3.9 9.3 - - - +
83E GLY 4.7 1.0 - - - +
117E MET* 3.8 25.9 - - + +
132E ASN* 1.3 84.8 - - - +
134E ILE* 1.3 63.1 + - - +
162E GLN* 5.3 7.9 - - + +
163E GLU 4.8 1.9 - - - +
164E PRO* 3.8 19.4 - - - +
165E PHE* 3.8 23.8 - - + -
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Residues in contact with ILE 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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81E MET* 3.5 13.1 + - + +
82E LEU 3.5 8.3 - - - +
83E GLY* 3.5 26.7 - - - +
84E LYS* 3.5 22.7 - - - +
85E VAL* 3.8 20.0 - - + -
90E MET* 3.6 22.5 - - + +
91E ILE 3.5 15.0 - - - +
92E ILE* 3.7 24.0 - - + -
132E ASN 3.8 0.4 + - - -
133E ALA* 1.3 76.8 - - - +
135E GLY* 1.3 63.3 + - - +
164E PRO* 3.2 23.2 - - + +
165E PHE* 3.5 3.1 - - - -
166E VAL* 3.3 12.4 - - - +
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Residues in contact with GLY 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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80E LEU* 3.4 7.3 - - - +
81E MET* 2.8 34.0 + - - +
134E ILE* 1.3 82.6 - - - +
136E TRP* 1.3 61.6 + - - -
165E PHE* 3.5 12.6 - - - -
166E VAL* 3.5 22.4 - - - -
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Residues in contact with TRP 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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78E MET* 3.6 21.5 - - + -
79E GLY 3.9 13.7 - - - +
80E LEU* 4.0 9.9 - - + -
81E MET* 4.1 2.9 - - - +
103E THR* 3.8 23.3 - - + -
110E GLN* 3.5 26.1 - - - +
135E GLY* 1.3 76.3 - - - +
137E TYR* 1.3 59.5 + - - +
138E HIS* 3.4 28.0 - + - -
151E ASP* 3.5 27.8 - - + -
154E THR* 5.8 2.0 - - - -
155E GLN* 4.1 45.3 - - + +
158E ASN* 4.9 4.9 - - - +
165E PHE* 4.2 23.7 - + + +
166E VAL 2.9 22.7 + - - +
167E ALA* 3.5 14.5 - - + -
168E VAL 3.5 0.9 + - - -
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Residues in contact with TYR 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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64E LYS* 4.2 5.4 + - - +
65E MET* 3.7 50.0 - - + -
68E HIS* 3.5 30.4 + - - +
69E ALA* 5.9 1.8 - - + -
78E MET* 3.5 4.6 - - - +
79E GLY* 2.9 34.3 + - - -
80E LEU 3.5 25.1 - - - -
81E MET* 3.6 29.6 - - + -
95E SER* 4.5 5.0 - - - -
96E PHE 3.7 15.5 + - - -
97E ALA* 4.0 4.7 + - - -
136E TRP* 1.3 75.1 - - - +
138E HIS* 1.3 66.8 + - - +
168E VAL* 3.4 18.2 - - + +
170E ILE* 3.9 8.1 - - + -
116F PHE* 5.4 0.7 - - - -
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Residues in contact with HIS 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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69E ALA* 5.3 1.1 - - - +
77E VAL* 3.4 16.8 - - - +
78E MET* 3.8 14.4 - - + +
102E GLY* 6.0 0.2 - - - -
103E THR* 4.5 4.0 - - - +
136E TRP* 3.4 26.2 - + + -
137E TYR* 1.3 81.3 - - - +
139E SER* 1.3 74.7 + - - +
140E HIS* 3.5 37.7 + + - -
147E LEU* 3.8 16.5 - - + +
151E ASP* 4.4 4.6 + - - -
167E ALA* 4.4 5.6 - - + -
168E VAL 3.1 10.9 + - - -
169E VAL* 3.5 33.1 - - + +
170E ILE* 3.5 25.0 + - - +
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Residues in contact with SER 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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69E ALA* 3.7 19.2 - - - +
75E LEU 4.7 1.6 + - - -
76E GLU* 3.7 14.0 - - - +
77E VAL* 3.2 34.6 + - - +
138E HIS* 1.3 83.4 - - - +
140E HIS* 1.3 72.5 + - - +
141E PRO* 3.4 11.5 - - - +
170E ILE 3.4 18.8 - - - +
172E PRO* 4.6 3.6 - - - -
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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