Contacts of the strand formed by residues 202 - 208 (chain E) in PDB entry 3WBR
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 GLN 202 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100E GLY 3.5 1.2 - - - +
101E MET* 3.4 7.0 - - - -
102E GLN 2.8 26.8 + - - +
107E SER* 4.2 4.3 + - - -
139E SER* 2.7 35.3 + - - +
141E PHE* 3.6 20.4 - - + +
182E ILE* 3.5 21.4 - - + +
196E ILE* 3.7 24.2 - - + -
200E VAL* 3.4 1.1 + - + +
201E PRO* 1.3 85.9 - - - +
203E LYS* 1.3 71.6 + - - +
101H MET* 3.4 8.2 - - - +
200H VAL* 3.7 4.9 - - - +
201H PRO* 2.9 28.3 - - - +
202H GLN* 3.6 1.7 - - - +
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Residues in contact with LYS 203 (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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98E SER 3.4 7.4 - - - +
99E THR* 3.1 44.2 + - - +
100E GLY 3.3 9.0 - - - +
101E MET* 4.1 8.3 - - + +
135E LYS* 4.8 8.9 - - - +
137E ASN* 5.1 0.4 + - - -
138E SER* 3.3 35.2 + - - -
139E SER 3.2 12.7 + - - +
140E TYR* 3.2 20.0 - - + -
141E PHE* 2.7 27.4 + - - +
202E GLN* 1.3 80.3 - - - +
204E SER* 1.3 56.3 + - - +
99H THR 4.6 4.9 + - - -
101H MET* 4.1 10.2 - - - +
203H LYS* 4.0 27.5 - - - +
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Residues in contact with SER 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E ILE* 3.8 1.9 - - - -
98E SER* 2.9 45.5 + - - +
100E GLY 4.4 1.4 + - - -
107E SER* 3.6 36.0 + - - -
110E ASN* 4.9 1.0 + - - -
111E CYS* 5.1 2.1 - - - -
118E LEU* 3.7 12.0 - - - +
140E TYR* 3.9 4.3 - - - -
141E PHE* 3.9 10.1 - - - +
203E LYS* 1.3 79.9 - - - +
205E ILE* 1.3 69.2 + - - +
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Residues in contact with ILE 205 (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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95E TYR* 5.0 5.4 - - + -
96E PHE 3.4 10.1 - - - +
97E ILE* 3.8 19.1 - - + -
111E CYS* 4.2 0.2 - - - -
118E LEU* 3.3 8.8 - - - +
119E VAL* 2.8 56.2 + - + +
130E ILE* 4.0 17.0 - - + -
134E LEU* 3.7 20.9 - - + -
140E TYR* 3.8 12.3 - - + -
141E PHE 3.7 6.4 + - - +
142E LEU* 4.6 0.2 - - + -
183E ILE* 3.8 27.1 - - + -
204E SER* 1.3 83.8 - - - +
206E CYS* 1.3 69.3 + - - +
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Residues in contact with CYS 206 (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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87E TRP* 4.1 3.4 - - + -
95E TYR* 3.4 4.5 - - - +
96E PHE* 2.7 51.3 + - + +
98E SER* 4.0 20.2 - - - -
110E ASN* 4.6 2.0 - - - -
111E CYS* 2.0 54.7 - - + -
114E MET* 5.2 1.8 - - - -
116E ALA* 4.0 9.4 - - + -
117E ASP 3.3 3.8 - - - -
204E SER* 5.2 0.9 - - - -
205E ILE* 1.3 80.6 - - - +
207E LYS* 1.3 64.1 + - - +
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Residues in contact with LYS 207 (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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157D ASP* 5.7 2.5 - - - -
87E TRP* 4.7 0.2 - - - -
93E SER* 3.9 21.7 + - - +
94E CYS 3.3 10.5 - - - +
95E TYR* 3.7 16.6 - - + +
116E ALA* 3.8 2.2 - - - +
117E ASP* 2.8 36.6 + - + +
119E VAL* 4.0 16.2 - - + -
120E VAL* 2.8 29.2 + - - +
122E ASN* 3.4 19.4 - - - +
126E GLU* 2.6 30.1 + - - +
206E CYS* 1.3 77.5 - - - +
208E MET* 1.3 66.0 + - - +
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Residues in contact with MET 208 (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 PRO* 3.9 23.8 - - + -
87E TRP* 3.7 47.3 - - + -
92E SER 4.5 2.6 - - - +
93E SER* 3.8 15.1 + - - -
94E CYS* 3.3 39.3 + - + +
114E MET 3.9 11.7 - - - +
115E GLY* 3.4 27.6 - - - +
116E ALA* 3.8 2.2 - - - +
207E LYS* 1.3 78.2 - - - +
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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