Contacts of the strand formed by residues 204 - 209 (chain F) in PDB entry 4LOU
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 204 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111F ALA* 5.4 5.2 - - + -
112F PRO* 3.5 39.3 - - + +
114F VAL* 4.0 27.2 - - + +
193F CYS 3.9 0.9 - - - +
194F GLU* 3.4 1.2 - - - -
195F ALA* 2.6 44.6 + - + +
199F THR* 5.9 0.7 - - - +
200F SER* 5.4 9.0 - - - +
202F SER 5.0 2.2 - - - +
203F PRO* 1.3 73.9 - - - +
205F VAL* 1.3 65.6 + - - +
206F LYS* 4.3 11.9 - - + +
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Residues in contact with VAL 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F THR* 3.6 25.4 - - + +
193F CYS 3.4 4.0 - - - -
194F GLU* 3.7 28.5 - - + +
203F PRO* 3.9 16.6 - - + +
204F ILE* 1.3 79.8 - - - +
206F LYS* 1.3 69.1 + - - +
207F SER* 4.4 4.6 + - - +
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Residues in contact with LYS 206 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F VAL* 3.4 48.8 + - + +
115F SER* 5.4 0.7 - - - +
116F ILE* 4.0 26.5 - - + +
192F THR* 3.3 2.6 - - - -
193F CYS* 3.1 31.9 + - - -
204F ILE* 4.3 11.1 - - + +
205F VAL* 1.3 77.6 + - - +
207F SER* 1.3 62.0 + - - +
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Residues in contact with SER 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F ILE* 4.2 9.9 - - - +
190F SER* 4.9 4.7 - - - -
191F TYR 3.1 13.2 - - - -
192F THR* 3.4 19.3 - - - -
205F VAL* 5.1 5.5 + - - +
206F LYS* 1.3 76.1 - - - +
208F PHE* 1.3 63.5 + - - +
209F ASN* 6.4 0.2 - - - -
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Residues in contact with PHE 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E GLY* 6.0 3.4 - - - -
116F ILE* 3.8 23.3 - - + -
118F PRO* 3.5 44.2 - - + -
119F PRO* 4.1 9.2 - - + -
131F VAL* 3.6 19.7 - - + -
185F TYR* 3.8 14.6 - + - -
189F ASN 3.9 0.2 - - - +
190F SER* 3.7 1.8 + - - -
191F TYR* 2.8 71.4 + + + +
207F SER* 1.3 75.3 - - - +
209F ASN* 1.3 71.0 + - - +
210F ARG* 4.4 9.0 - - - -
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Residues in contact with ASN 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F ASN* 3.5 16.2 + - - +
190F SER* 2.8 36.2 + - - -
208F PHE* 1.3 80.0 - - - +
210F ARG* 1.3 65.8 + - - +
211F ALA* 3.2 16.0 + - + +
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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