Contacts of the strand formed by residues 200 - 205 (chain E) in PDB entry 4XXD
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 200 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B GLN* 4.6 0.4 - - - +
108B SER 5.7 0.2 - - - -
110B SER* 3.1 22.8 + - - +
113E GLY* 3.7 6.5 - - - -
114E PRO* 4.1 28.5 - - + +
193E VAL* 4.0 1.2 - - - +
194E ASN* 3.6 5.8 + - - +
195E HIS* 2.9 34.5 + - - +
198E SER* 2.9 21.1 + - - -
199E ASN* 1.3 72.8 - - - +
201E LYS* 1.3 60.8 + - - +
202E VAL* 3.8 22.2 - - + -
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Residues in contact with LYS 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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13B GLN* 4.2 38.7 - - + +
192E ASN* 6.6 0.2 - - - -
193E VAL 3.6 4.0 - - - +
194E ASN* 3.4 33.7 - - - +
199E ASN 4.2 0.6 - - - -
200E THR* 1.3 74.1 - - - +
202E VAL* 1.3 64.6 + - - +
203E ASP* 4.2 15.9 + - - +
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Residues in contact with VAL 202 (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* 4.7 5.6 - - + +
115E SER* 6.3 0.2 - - - -
116E VAL* 3.8 36.3 - - + +
191E CYS 3.7 1.6 - - - +
193E VAL* 2.8 48.0 + - + +
200E THR* 3.8 22.4 - - + -
201E LYS* 1.3 77.2 - - - +
203E ASP* 1.3 66.5 + - - +
204E LYS* 3.8 9.0 + - + +
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Residues in contact with ASP 203 (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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190E ILE* 4.3 11.7 - - + +
191E CYS 3.5 4.3 - - - +
192E ASN* 2.7 40.1 + - - +
201E LYS* 4.2 17.7 + - - +
202E VAL* 1.3 75.7 - - - +
204E LYS* 1.3 61.7 + - - +
205E LYS* 4.0 3.1 + - - +
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Residues in contact with LYS 204 (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* 4.1 26.0 - - - +
116E VAL* 3.3 46.8 + - + +
117E PHE* 5.4 0.2 - - - -
118E PRO* 3.7 21.5 - - + +
135E CYS* 4.5 8.3 - - - -
190E ILE* 3.7 1.4 - - - +
191E CYS* 3.0 50.2 + - - -
202E VAL* 3.8 8.3 + - + -
203E ASP* 1.3 72.5 - - - +
205E LYS* 1.3 70.9 + - - +
206E VAL* 4.0 6.3 + - + +
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Residues in contact with LYS 205 (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* 5.1 2.1 - - - +
188E THR* 3.6 23.0 + - + +
189E TYR 3.0 27.8 - - - +
190E ILE* 3.1 37.5 - - + -
203E ASP 4.0 4.3 + - - +
204E LYS* 1.3 78.8 - - - +
206E VAL* 1.3 69.3 + - - +
207E GLU* 4.1 25.4 + - - +
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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