Contacts of the strand formed by residues 201 - 207 (chain A) in PDB entry 1R1H
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 ASN 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A LYS* 3.5 34.0 + - + +
199A LEU 4.3 0.4 - - - -
200A ILE* 1.3 70.4 - - - +
202A LEU* 1.3 60.1 + - - +
203A PHE* 3.7 20.2 - - - -
217A HIS 3.7 0.9 - - - +
218A ILE* 3.4 2.8 - - - -
219A ASP* 2.6 59.0 + - - +
220A GLN 3.4 20.1 + - - +
221A PRO* 4.0 8.9 - - + +
222A ARG* 5.3 5.1 - - - +
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Residues in contact with LEU 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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191A ASN* 2.9 31.4 + - - +
197A LYS* 3.6 5.4 - - - -
200A ILE 3.4 4.0 + - - -
201A ASN* 1.3 73.7 + - - +
203A PHE* 1.3 68.2 + - - +
204A VAL* 4.8 0.9 - - + +
216A ILE* 2.7 37.2 - - + -
217A HIS 2.5 26.7 - - - +
218A ILE* 3.2 23.3 - - + +
325A PHE* 4.1 23.3 - - + -
326A THR* 5.1 8.7 - - + +
329A ILE* 4.0 28.9 - - + -
330A MET* 5.4 2.5 - - - -
518A GLN* 5.1 0.5 + - - -
522A LEU* 5.4 4.4 - - + +
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Residues in contact with PHE 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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197A LYS* 4.4 16.2 - - - +
201A ASN* 3.7 22.2 - - - -
202A LEU* 1.3 79.9 - - - +
204A VAL* 1.3 73.6 + - - +
205A GLY* 4.0 4.7 - - - -
216A ILE* 4.5 0.2 - - - -
217A HIS* 2.8 73.1 + + + +
219A ASP* 4.1 23.1 - - + -
346A TYR* 4.0 12.6 - + - -
518A GLN* 5.9 0.9 - - - +
521A GLN* 6.0 2.2 - - + -
522A LEU* 5.6 2.9 - - - -
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Residues in contact with VAL 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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202A LEU* 5.6 0.9 - - + -
203A PHE* 1.3 79.3 - - - +
205A GLY* 1.3 61.2 + - - +
214A HIS* 3.8 26.7 - - + -
215A VAL 3.6 3.8 - - - +
216A ILE* 4.4 6.3 - - + -
330A MET* 4.3 11.2 - - - -
521A GLN* 2.8 48.5 + - - +
522A LEU* 3.9 36.8 - - + +
524A LYS 4.3 0.7 - - - -
525A LEU* 3.9 28.9 - - + +
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Residues in contact with GLY 205 (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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203A PHE* 3.6 10.8 + - - -
204A VAL* 1.3 73.8 - - - +
206A THR* 1.3 65.2 + - - -
214A HIS* 3.2 11.2 - - - +
215A VAL 2.9 33.0 + - - +
217A HIS* 3.7 9.2 + - - -
521A GLN* 4.3 7.2 - - - -
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Residues in contact with THR 206 (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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205A GLY* 1.3 71.3 - - - -
207A ASP* 1.3 73.8 + - - +
208A ASP* 3.4 9.1 + - - +
211A SER* 3.8 28.3 - - - +
213A ASN 3.6 9.2 - - - +
214A HIS* 4.0 6.8 + - - -
217A HIS* 3.2 19.4 + - - -
529A VAL* 4.0 16.0 - - + +
548A GLY* 5.1 12.3 - - - +
549A ARG* 5.8 1.4 + - - -
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Residues in contact with ASP 207 (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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205A GLY 3.7 1.0 + - - -
206A THR* 1.3 71.0 - - - +
208A ASP* 1.3 66.3 + - - +
209A LYS* 3.1 7.5 + - - -
210A ASN* 2.9 48.1 + - + +
211A SER* 3.6 5.7 + - - -
213A ASN* 3.0 15.9 + - + +
215A VAL* 3.2 32.2 - - + +
217A HIS* 4.9 2.5 - - - -
299A TYR* 2.6 30.6 + - - -
301A LYS* 5.0 6.2 + - - +
344A VAL* 5.0 2.4 - - - +
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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