Contacts of the strand formed by residues 209 - 215 (chain E) in PDB entry 6IAP
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 THR 209 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122E GLY* 4.4 7.6 - - - -
123E PRO* 3.5 12.7 - - - +
202E VAL 4.5 0.4 - - - -
203E ASN* 3.4 7.9 - - - +
204E HIS* 2.9 41.8 + - - +
207E SER* 2.7 30.1 + - - +
208E ASN* 1.3 78.5 - - - +
210E LYS* 1.3 60.1 + - - +
211E VAL* 4.2 10.5 - - + -
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Residues in contact with LYS 210 (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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201E ASN* 6.5 0.4 - - + -
202E VAL 3.4 8.1 - - - +
203E ASN* 4.5 9.0 - - + +
209E THR* 1.3 75.1 - - - +
211E VAL* 1.3 60.9 + - - +
212E ASP* 3.8 27.2 + - - +
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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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123E PRO* 4.6 14.6 - - + +
125E VAL* 3.8 36.5 - - + +
200E CYS 3.6 2.3 - - - +
202E VAL* 2.8 40.2 + - + +
209E THR* 4.7 11.0 - - - +
210E LYS* 1.3 79.6 - - - +
212E ASP* 1.4 64.6 + - - +
213E LYS* 3.8 12.8 - - + +
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Residues in contact with ASP 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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199E ILE* 3.5 19.0 - - + +
200E CYS 3.5 4.9 - - - -
201E ASN* 3.3 30.2 + - - +
210E LYS* 3.8 30.1 + - - +
211E VAL* 1.4 77.0 - - - +
213E LYS* 1.3 61.4 + - - +
214E ARG* 3.6 5.9 + - - +
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Residues in contact with LYS 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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123D GLU* 3.2 36.4 - - - +
125E VAL* 3.2 46.4 + - + +
126E PHE* 4.8 0.2 - - - -
127E PRO* 3.5 28.9 - - + +
144E CYS* 4.6 1.8 - - - -
199E ILE* 3.4 2.1 - - - +
200E CYS* 3.1 35.9 + - - +
211E VAL* 3.8 9.6 - - + +
212E ASP* 1.3 73.6 - - - +
214E ARG* 1.3 65.4 + - - +
215E VAL* 3.7 2.1 + - - +
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Residues in contact with ARG 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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127E PRO* 3.9 13.5 - - - +
197E THR* 5.5 11.9 - - - -
198E TYR 3.5 7.0 - - - +
199E ILE* 3.8 27.8 - - + +
212E ASP 3.6 5.1 + - - +
213E LYS* 1.3 75.5 - - - +
215E VAL* 1.4 62.3 + - - +
216E GLU* 3.7 29.5 + - + +
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Residues in contact with VAL 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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127E PRO* 3.8 16.2 - - + -
128E LEU 4.0 2.9 - - - +
129E ALA* 3.8 28.5 - - - +
130E PRO* 4.4 3.1 - - + +
142E LEU* 4.1 21.5 - - + +
143E GLY 3.6 21.8 - - - +
144E CYS* 3.7 21.8 - - - -
158E TRP* 3.8 14.8 - - + -
197E THR* 5.6 0.3 - - - -
198E TYR* 2.7 34.9 + - - +
213E LYS 4.2 2.0 - - - +
214E ARG* 1.4 71.5 - - - +
216E GLU* 1.3 60.5 + - - +
217E PRO* 4.9 0.9 - - - +
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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