Contacts of the strand formed by residues 196 - 201 (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 SER 196 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E LYS 3.8 0.3 - - - +
155E ILE* 3.2 9.7 - - - +
156E ASP* 2.8 50.3 + - - -
157E GLY 4.1 3.1 + - - -
195E ASN* 1.3 77.0 - - - +
197E TYR* 1.3 62.3 + - - +
198E THR* 4.6 11.8 - - - +
213E SER* 5.1 0.4 - - - -
214E PHE 3.2 3.4 - - - -
215E ASN* 2.7 22.7 - - - -
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Residues in contact with TYR 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E ILE* 3.8 4.8 - - - +
137E VAL* 4.3 25.4 - - + -
153E TRP* 4.6 4.0 - - + -
154E LYS 3.5 2.7 - - - +
155E ILE* 3.6 37.9 - - + -
184E LEU* 4.2 10.3 - - + -
186E LEU* 4.1 9.4 - - + -
191E TYR* 2.5 66.2 + + - -
194E HIS* 3.3 27.6 - + + +
195E ASN 4.1 10.3 - - - -
196E SER* 1.3 73.4 - - - +
198E THR* 1.3 62.5 + - - +
213E SER* 3.5 0.5 - - - -
214E PHE* 2.7 54.4 + + + +
216E ARG* 4.5 2.5 - - - -
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Residues in contact with THR 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E ILE* 4.3 0.4 - - - -
153E TRP* 3.6 9.1 - - - -
154E LYS* 2.9 54.0 + - + +
157E GLY 6.0 2.0 - - - +
196E SER* 4.6 10.8 - - - +
197E TYR* 1.3 81.3 - - - +
199E CYS* 1.3 59.1 + - - +
200E GLU* 4.4 3.5 + - - +
211E VAL* 4.2 15.0 - - + +
212E LYS 3.4 11.7 - - - -
213E SER* 3.0 25.4 - - - +
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Residues in contact with CYS 199 (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* 4.3 6.0 - - - +
122E ILE* 3.7 20.5 - - - +
139E CYS* 2.0 52.5 - - + -
141E LEU* 5.6 0.2 - - + -
151E VAL* 4.0 15.9 - - + -
152E LYS 3.6 4.3 - - - +
153E TRP* 4.3 9.4 - - + -
198E THR* 1.3 73.7 - - - +
200E GLU* 1.3 60.8 + - - +
201E ALA 4.1 0.4 - - - -
210E ILE 3.5 2.4 - - - +
211E VAL* 3.5 4.2 - - - +
212E LYS 3.2 29.5 + - - +
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Residues in contact with GLU 200 (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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150E ASN 3.5 2.3 - - - +
151E VAL* 3.4 6.3 - - - -
152E LYS* 3.0 51.5 + - + +
154E LYS* 2.9 42.4 + - + +
198E THR* 4.4 8.0 + - - +
199E CYS* 1.3 72.3 - - - +
201E ALA* 1.3 60.8 + - - +
202E THR* 3.8 3.5 + - - +
209E PRO* 3.9 22.3 - - + +
210E ILE 3.5 5.2 - - - -
211E VAL* 3.7 28.1 - - + +
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Residues in contact with ALA 201 (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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118E PRO* 4.8 2.9 - - + -
120E VAL* 4.2 15.0 - - + +
141E LEU* 3.7 30.7 - - + -
149E ILE* 4.3 9.4 - - + -
150E ASN 3.7 4.7 - - - -
151E VAL* 4.7 1.8 - - + +
199E CYS 4.1 0.6 - - - -
200E GLU* 1.3 70.9 - - - +
202E THR* 1.3 61.1 + - - +
203E HIS 3.5 4.4 + - - +
208E SER 5.0 0.2 - - - +
209E PRO* 3.6 3.3 - - - +
210E ILE* 2.9 46.1 + - + +
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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
------------------------------------------------------------
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