Contacts of the strand formed by residues 187 - 195 (chain E) in PDB entry 3RBQ
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 LYS 187 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123C PRO* 4.3 15.6 - - - +
89E VAL* 5.1 13.5 - - + -
148E GLU* 2.9 32.7 + - + +
149E PHE 3.3 13.9 - - - +
150E THR* 4.0 20.2 - - + +
186E SER* 1.3 75.9 - - - +
188E ASN* 1.3 69.3 + - - +
189E THR* 4.7 5.4 + - - -
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Residues in contact with ASN 188 (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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123C PRO* 5.2 4.5 - - - +
124C ASN* 5.1 0.9 + - - -
148E GLU* 3.1 6.9 - - - +
149E PHE* 2.5 62.2 + - + +
151E VAL* 3.6 13.9 - - - +
181E PHE 3.9 4.0 - - - +
182E CYS* 3.6 5.6 - - - -
183E ILE* 3.0 56.4 + - - +
186E SER* 3.3 13.7 + - - -
187E LYS* 1.3 74.4 - - - +
189E THR* 1.3 67.0 + - - +
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Residues in contact with THR 189 (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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123C PRO* 4.8 18.4 - - - +
124C ASN* 5.9 1.0 + - - -
146E THR* 4.3 15.7 - - + -
147E VAL 3.4 11.0 - - - +
148E GLU* 3.7 23.2 - - + +
149E PHE* 4.4 3.9 - - - -
187E LYS* 4.7 6.4 + - - -
188E ASN* 1.3 80.4 + - - +
190E CYS* 1.3 68.8 - - - +
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Residues in contact with CYS 190 (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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145E ALA 3.8 0.2 - - - +
146E THR* 3.6 4.6 - - - +
147E VAL* 2.9 35.5 + - + +
149E PHE* 4.6 0.7 - - + -
178E HIS 4.7 3.4 - - - -
179E PHE* 3.7 44.0 - - + -
180E GLY 4.5 5.2 - - - +
189E THR* 1.3 80.8 - - - +
191E GLU* 1.3 72.0 + - - +
192E HIS* 3.7 27.8 - - - +
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Residues in contact with GLU 191 (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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94E ARG* 2.5 43.4 + - - -
96E MET* 5.7 0.2 - - - +
144E GLY* 4.0 2.9 - - - -
145E ALA 3.2 12.3 - - - +
146E THR* 3.8 17.5 - - + +
190E CYS* 1.3 79.2 - - - +
192E HIS* 1.3 67.6 + - - +
193E ILE* 3.8 27.3 + - + +
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Residues in contact with HIS 192 (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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91E PHE* 6.0 0.4 - - - -
143E VAL 3.6 0.9 - - - +
144E GLY* 3.3 4.9 - - - -
145E ALA* 2.7 38.7 + - + +
147E VAL* 4.0 20.2 - - + +
161E MET* 3.9 24.9 - - + +
177E PHE* 3.6 42.8 - + + +
178E HIS 5.7 0.4 - - - -
179E PHE* 3.5 32.7 - + - -
190E CYS* 3.7 20.9 - - - -
191E GLU* 1.3 81.3 - - - +
193E ILE* 1.3 63.3 + - - +
194E TYR* 4.0 12.9 + - + -
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Residues in contact with ILE 193 (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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96E MET* 4.3 15.0 - - + -
142E GLN* 3.5 37.7 - - + +
143E VAL 3.6 1.3 - - - +
144E GLY* 4.0 8.1 - - - -
175E PHE* 4.9 1.6 - - - -
177E PHE* 3.4 18.2 - - - -
191E GLU* 3.8 31.8 + - - +
192E HIS* 1.3 82.1 - - - +
194E TYR* 1.3 61.7 + - - +
195E ASP* 3.7 10.4 + - - +
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Residues in contact with TYR 194 (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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91E PHE* 5.3 1.7 - - - -
142E GLN* 3.3 5.8 - - - +
143E VAL* 2.8 57.8 + - + +
145E ALA* 3.8 24.9 - - + +
161E MET* 3.5 12.5 - - - +
163E GLU* 2.9 34.8 + - - -
175E PHE* 3.6 44.2 - + + -
177E PHE* 3.8 13.2 - + - -
192E HIS* 4.0 14.7 + - + -
193E ILE* 1.3 73.5 - - - +
195E ASP* 1.3 62.2 - - - +
196E PHE* 3.8 2.6 + - + -
500K DAO 3.7 35.1 - - + +
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Residues in contact with ASP 195 (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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141E ARG* 3.8 8.8 + - - +
142E GLN* 2.8 34.7 + - - +
173E LYS* 2.7 40.3 + - - +
175E PHE* 3.3 8.9 - - - -
193E ILE* 3.7 8.3 + - - +
194E TYR* 1.3 72.5 - - - +
196E PHE* 1.3 59.3 + - - +
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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