Contacts of the strand formed by residues 192 - 198 (chain E) in PDB entry 6PI7
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 VAL 192 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150E LYS 3.9 0.7 - - - +
151E VAL* 3.4 6.2 - - - +
152E ASP* 2.8 51.8 + - - +
153E ASN 4.8 1.7 + - - +
191E LYS* 1.3 77.5 - - + +
193E TYR* 1.3 64.6 + - - +
194E ALA* 5.0 5.1 - - + +
209E SER* 4.2 20.2 - - - +
210E PHE 3.4 11.0 - - - +
211E ASN* 3.5 18.6 - - - +
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Residues in contact with TYR 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E ILE* 3.5 7.5 - - + +
133E VAL* 4.4 7.4 - - + -
149E TRP* 5.5 0.7 - - + -
150E LYS 3.8 2.0 - - - -
151E VAL* 3.7 28.9 - - + +
180E LEU* 4.4 9.9 - - + -
182E LEU* 3.6 23.2 - - + +
186E ASP 3.8 1.2 + - - -
187E TYR* 2.5 53.7 + + - -
190E HIS* 3.6 21.6 + - + +
191E LYS 3.3 21.1 - - - -
192E VAL* 1.3 70.0 - - - +
194E ALA* 1.3 61.1 + - - +
209E SER* 3.0 22.6 - - - -
210E PHE* 3.0 44.6 + + + -
212E ARG* 4.7 2.5 - - - -
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Residues in contact with ALA 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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118E ILE* 4.5 0.2 - - - -
149E TRP* 3.4 13.7 - - - -
150E LYS* 3.0 51.8 + - + +
192E VAL* 5.0 5.2 - - + -
193E TYR* 1.3 73.9 - - - +
195E CYS* 1.3 58.8 + - - +
196E GLU 4.1 0.4 - - - -
207E THR* 4.0 15.7 - - + -
208E LYS 3.3 4.9 - - - -
209E SER* 3.8 14.1 - - - -
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Residues in contact with CYS 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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116E VAL* 4.7 5.0 - - + +
118E ILE* 4.3 5.6 - - + +
135E CYS* 2.0 52.7 - - + -
137E LEU* 5.1 1.6 - - - -
147E VAL* 3.6 23.1 - - - -
148E GLN 3.8 2.9 - - - -
149E TRP* 4.2 13.2 - - + -
194E ALA* 1.3 71.9 - - - +
196E GLU* 1.3 60.0 + - - +
197E VAL* 5.2 1.1 - - - -
206E VAL 3.7 2.1 - - - +
207E THR* 3.2 5.5 - - - -
208E LYS* 2.8 36.4 + - + +
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Residues in contact with GLU 196 (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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146E LYS 3.6 1.4 - - - +
147E VAL* 3.4 4.4 - - - -
148E GLN* 2.8 63.9 + - - +
150E LYS* 3.1 33.7 + - - +
155E LEU* 5.5 0.3 - - - +
194E ALA 4.1 0.2 - - - -
195E CYS* 1.3 72.5 - - - +
197E VAL* 1.3 61.1 + - - +
198E THR* 4.2 4.9 + - - +
205E PRO* 3.9 32.0 - - + +
206E VAL 3.4 3.8 - - - +
207E THR* 3.7 18.3 + - + +
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Residues in contact with VAL 197 (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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114E PRO* 5.2 2.2 - - + -
116E VAL* 4.0 28.5 - - + -
137E LEU* 4.4 20.2 - - + -
146E LYS 3.3 7.6 - - - +
147E VAL* 4.8 2.0 - - + +
195E CYS* 4.2 1.8 - - - -
196E GLU* 1.3 73.1 - - - +
198E THR* 1.3 62.5 + - - +
199E HIS* 6.1 0.2 - - + -
202E LEU* 3.6 11.7 - - + +
205E PRO* 3.3 4.2 - - - +
206E VAL 2.8 36.9 + - - +
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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
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145E ALA* 3.6 5.9 - - - +
146E LYS* 3.0 44.9 + - + +
196E GLU* 4.2 7.0 + - - +
197E VAL* 1.3 71.0 - - - +
199E HIS* 1.3 67.1 + - - +
205E PRO* 3.5 27.4 - - + +
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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