Contacts of the strand formed by residues 199 - 204 (chain A) in PDB entry 4LIR
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 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A LEU* 3.8 25.4 - - + +
193A PHE 3.9 4.0 - - - -
194A ALA* 3.7 33.6 - - + +
197A GLY 3.5 4.6 + - - +
198A ASN* 1.3 73.3 - - - +
200A LEU* 1.4 59.9 + - - +
201A LYS 3.5 29.4 - - - +
202A HIS* 4.1 14.4 - - + -
213A ILE* 3.7 26.5 - - + -
214A ARG 3.5 3.8 - - - -
215A TYR* 3.9 9.6 - - + -
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ASN* 4.6 3.1 - - + +
199A ILE* 1.4 75.2 - - - +
201A LYS* 1.3 62.6 + - - +
214A ARG* 2.8 40.3 + - - +
215A TYR 3.7 15.9 - - - +
216A GLN* 3.8 42.4 - - + +
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Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A TRP* 3.9 30.0 - - + -
199A ILE* 3.5 8.7 - - - +
200A LEU* 1.3 79.5 - - - +
202A HIS* 1.3 69.2 + - - +
203A VAL* 4.2 15.0 - - + +
212A HIS 4.5 0.2 - - - -
214A ARG* 2.8 37.0 + - + +
248A VAL 5.3 4.5 - - - +
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Residues in contact with HIS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A LEU* 3.5 48.5 - - + +
199A ILE* 4.1 10.8 - - + -
201A LYS* 1.3 80.5 - - - +
203A VAL* 1.3 68.6 + - - +
204A MSE 4.8 9.4 + - + +
211A MSE 5.2 5.8 - - - -
212A HIS 3.1 10.5 - - - +
213A ILE* 4.3 4.7 - - + -
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A TRP* 4.7 1.8 - - + -
201A LYS* 4.2 22.7 - - + +
202A HIS* 1.3 78.8 - - - +
204A MSE 1.3 71.1 + - - +
205A SER* 5.8 0.2 - - - -
211A MSE 3.2 6.6 - - - -
212A HIS* 2.8 49.3 + - + -
248A VAL* 3.8 35.9 - - + +
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Residues in contact with MSE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PHE* 3.7 29.2 - - + +
183A GLN* 3.5 36.8 - - + +
186A ALA* 4.4 12.3 - - + -
202A HIS* 4.2 10.0 + - + +
203A VAL* 1.3 83.1 - - - +
205A SER* 1.3 67.5 - - - +
206A ASN* 3.6 1.9 + - - -
208A GLY 3.6 17.3 - - - +
209A ASN* 5.1 0.4 - - - -
210A TRP 3.5 13.7 - - - +
211A MSE 4.0 16.8 - - + -
212A HIS* 5.9 0.2 - - - -
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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