Contacts of the strand formed by residues 210 - 215 (chain E) in PDB entry 3VI4
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 ILE 210 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117E ALA* 4.6 9.4 - - + -
118E PRO* 4.0 39.3 - - + +
120E VAL* 3.9 29.0 - - + +
199E CYS 3.5 2.4 - - - +
200E GLU* 3.5 1.2 - - - -
201E ALA* 2.9 42.5 + - + +
203E HIS* 5.7 2.7 - - + +
205E THR* 4.9 4.0 - - - +
206E SER* 4.9 11.4 - - - +
208E SER 4.6 4.7 - - - +
209E PRO* 1.3 74.8 - - - +
211E VAL* 1.3 62.0 + - - +
212E LYS* 4.1 9.7 + - + -
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Residues in contact with VAL 211 (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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198E THR* 4.2 16.6 - - + +
199E CYS 3.5 8.7 - - - +
200E GLU* 3.7 29.8 - - + +
209E PRO* 3.6 20.1 + - + +
210E ILE* 1.3 77.0 - - - +
212E LYS* 1.3 78.1 + - - +
213E SER* 4.8 5.8 - - - -
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Residues in contact with LYS 212 (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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120E VAL* 3.2 47.7 - - + +
121E SER* 5.3 0.7 - - - -
122E ILE* 4.0 21.3 - - + +
198E THR* 3.4 3.6 - - - -
199E CYS* 3.2 31.7 + - - +
210E ILE* 4.1 10.6 + - + -
211E VAL* 1.3 77.9 + - - +
213E SER* 1.3 63.3 + - - +
135F ALA* 5.1 20.5 + - + +
136F GLN 6.3 0.2 - - - -
137F THR* 4.9 12.1 + - - +
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Residues in contact with SER 213 (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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122E ILE* 3.7 12.2 - - - +
196E SER* 5.1 0.2 - - - -
197E TYR 3.5 4.4 - - - -
198E THR* 3.0 26.7 - - - +
211E VAL* 4.8 6.5 - - - -
212E LYS* 1.3 79.3 - - - +
214E PHE* 1.3 63.5 + - - +
215E ASN* 4.6 13.2 + - - -
133F SER* 5.4 3.8 + - - -
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Residues in contact with PHE 214 (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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122E ILE* 4.2 16.6 - - + +
124E PRO* 3.5 38.1 - - + -
125E PRO* 5.2 0.7 - - + -
137E VAL* 5.3 4.0 - - + -
191E TYR* 3.4 25.6 - + - -
195E ASN 3.7 0.7 - - - +
196E SER* 3.2 2.6 - - - -
197E TYR* 2.7 57.8 + + + +
213E SER* 1.3 74.4 + - - +
215E ASN* 1.3 78.1 + - - +
216E ARG* 3.9 20.9 - - + -
132F GLY* 4.2 23.3 - - - -
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Residues in contact with ASN 215 (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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195E ASN* 3.3 15.7 + - - +
196E SER* 2.7 35.2 - - - -
213E SER* 4.6 10.4 + - - -
214E PHE* 1.3 88.0 - - - +
216E ARG* 1.3 66.5 + - - +
217E ASN 3.2 1.4 + - - -
218E GLU* 3.2 45.7 + - + +
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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