Contacts of the strand formed by residues 80 - 87 (chain E) in PDB entry 1VQM
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 TRP 80 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27820 G 5.7 0.4 - - - -
71E ASN* 3.1 52.6 + - + -
74E HIS* 3.5 35.9 - + + -
75E GLY* 3.4 12.8 - - - -
79E GLY* 1.3 71.3 - - - -
81E GLU* 1.3 66.2 + - - +
82E TYR* 4.9 2.5 - - + -
134E SER* 2.9 24.8 - - - -
135E GLY 2.8 20.4 + - - +
136E PRO 3.4 21.9 + - - -
138E ILE* 3.5 43.2 - - + +
141E VAL* 4.5 12.8 - - + -
172E PRO* 3.5 39.7 - - + -
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Residues in contact with GLU 81 (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 GLU 6.1 0.4 - - - +
79E GLY 4.4 2.4 + - - -
80E TRP* 1.3 82.4 - - - +
82E TYR* 1.3 66.2 + - - +
132E THR* 3.7 16.3 + - - +
133E VAL 3.0 6.5 - - - +
134E SER* 3.2 23.0 + - - -
170E ARG* 4.4 10.5 + - - +
171E LYS 4.4 0.2 - - - -
172E PRO* 3.1 29.9 - - - +
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Residues in contact with TYR 82 (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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27800 C 5.0 0.2 - - - -
27810 U 2.7 36.8 + - - -
80E TRP* 4.9 2.0 - - + -
81E GLU* 1.3 79.7 - - - +
83E GLY* 1.3 61.2 + - - +
84E MET* 4.8 0.4 - - + -
131E LEU 3.9 0.2 - - - +
132E THR* 3.3 4.2 + - - -
133E VAL* 2.7 36.2 + - + +
138E ILE* 3.9 13.1 - - + +
141E VAL* 3.6 28.0 - - + -
142E GLY* 3.5 22.4 - - - -
145E ALA* 4.0 25.1 - - + -
168E ILE* 4.3 12.1 - - + -
170E ARG* 3.4 14.1 - - - +
171E LYS* 4.2 10.1 - - + -
172E PRO* 3.5 34.5 - - + +
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Residues in contact with GLY 83 (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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82E TYR* 1.3 71.1 - - - +
84E MET* 1.3 61.1 + - - +
131E LEU 3.3 6.5 - - - -
168E ILE* 3.4 2.3 - - - +
169E THR* 2.5 36.4 + - - -
170E ARG* 3.0 40.2 + - - +
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Residues in contact with MET 84 (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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82E TYR 4.8 0.7 - - - -
83E GLY* 1.3 81.8 - - - +
85E GLU* 1.3 60.2 + - - +
86E VAL 4.1 0.2 - - - -
130E GLU* 3.4 2.8 - - - +
131E LEU* 2.6 59.9 + - + +
133E VAL* 3.2 20.6 - - + -
145E ALA* 3.7 15.0 - - + +
148E ILE* 3.2 44.0 - - + -
149E GLU 5.0 1.6 - - - -
166E VAL* 3.6 14.4 - - + -
167E TYR 3.0 16.6 - - - +
168E ILE* 3.5 27.8 - - + -
169E THR* 3.5 3.8 + - - -
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Residues in contact with GLU 85 (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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84E MET* 1.3 74.6 - - - +
86E VAL* 1.3 63.7 + - - +
87E PHE* 3.5 5.6 + - + +
129E GLU* 3.4 11.0 - - + +
130E GLU* 4.7 16.7 - - + +
165E GLY 4.0 0.5 - - - +
166E VAL* 4.1 2.2 - - - -
167E TYR* 3.1 29.0 + - + +
169E THR* 3.0 38.6 + - + +
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Residues in contact with VAL 86 (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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84E MET 4.1 0.8 + - - -
85E GLU* 1.3 71.2 - - - +
87E PHE* 1.3 59.6 + - - +
88E TYR* 4.4 6.7 - - + -
93E MET* 3.7 40.2 - - + +
95E VAL* 3.9 19.1 - - + -
126E ILE* 5.4 3.1 - - + -
128E GLY 4.1 5.4 - - - +
129E GLU* 2.9 63.4 + - - +
130E GLU 5.6 0.4 - - - -
131E LEU* 5.7 3.8 - - + -
166E VAL* 4.1 19.4 - - + +
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Residues in contact with PHE 87 (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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85E GLU* 3.5 5.9 + - + +
86E VAL* 1.3 74.5 - - - +
88E TYR* 1.3 88.5 + - - +
89E SER* 4.5 10.5 - - - -
93E MET* 3.4 3.3 - - - +
163E GLN* 3.7 46.9 - - + -
164E ASP* 3.4 1.4 - - - -
165E GLY 2.9 37.6 + - - +
167E TYR* 4.7 7.9 - + + -
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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