Contacts of the strand formed by residues 214 - 223 (chain A) in PDB entry 1R74
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 LYS 214 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ASP* 4.7 1.4 + - - +
150A GLY 4.5 12.0 + - - +
151A ASP* 5.1 3.6 + - - +
152A GLN* 3.1 33.1 - - - +
210A ILE* 3.6 2.7 - - - +
211A VAL 2.9 38.2 + - - +
212A ASN 3.2 4.0 - - - +
213A ASN* 1.3 74.7 - - - +
215A ALA* 1.3 79.0 + - - +
216A HIS* 3.9 8.2 - - + +
245A TYR* 3.5 16.7 + - - +
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Residues in contact with ALA 215 (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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183A LEU* 3.9 32.1 - - + -
208A VAL* 5.0 1.3 - - + -
209A LEU 3.9 5.8 - - - +
210A ILE* 3.9 14.6 - - + +
213A ASN 4.1 0.6 + - - -
214A LYS* 1.3 87.9 - - - +
216A HIS* 1.3 59.5 + - - +
245A TYR* 4.1 7.4 + - - -
246A PRO* 3.8 22.7 - - + +
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Residues in contact with HIS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PRO* 5.9 0.8 - - - +
147A ASP* 3.2 53.2 + - + +
150A GLY* 5.0 6.7 + - - -
209A LEU* 2.9 13.0 + - + +
211A VAL* 3.7 35.0 - - + +
214A LYS* 3.9 8.8 - - + +
215A ALA* 1.3 77.5 - - - +
217A MET* 1.3 76.9 + - + +
245A TYR* 3.5 22.4 + + - -
246A PRO* 3.6 6.9 - - - +
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Residues in contact with MET 217 (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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146A PRO* 5.4 12.3 - - + -
207A SER 3.6 0.7 - - - +
208A VAL* 3.5 4.7 - - - +
209A LEU* 2.9 47.1 + - + +
216A HIS* 1.3 95.6 - - + +
218A VAL* 1.3 70.5 - - - +
219A THR* 3.4 24.0 - - - +
243A SER* 3.5 13.7 - - - +
244A TYR 3.6 12.8 - - - +
246A PRO* 3.6 2.1 - - - +
5B TYR* 3.8 13.0 - - - +
7B THR* 3.7 29.6 - - + -
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Residues in contact with VAL 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A TYR* 4.5 18.2 - - + -
182A ILE* 4.5 7.0 - - + -
183A LEU* 4.2 15.3 - - + -
188A ALA* 5.0 1.8 - - + -
206A THR* 4.3 10.5 - - + -
207A SER 3.3 6.1 - - - +
208A VAL* 4.3 10.3 - - + -
217A MET* 1.3 79.6 - - - +
219A THR* 1.3 61.4 + - - +
220A LEU* 3.7 24.7 - - + -
243A SER* 3.4 1.7 - - - -
244A TYR* 2.8 48.0 + - + +
246A PRO* 3.9 24.0 - - + -
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Residues in contact with THR 219 (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 THR 3.5 3.1 - - - +
207A SER* 2.9 45.8 + - - -
217A MET* 3.4 7.3 - - - +
218A VAL* 1.3 71.2 - - - +
220A LEU* 1.3 63.3 + - - +
221A ASP* 4.0 7.4 + - - +
241A ARG* 3.3 43.1 - - - +
242A LEU 3.6 3.4 - - - +
243A SER* 2.4 24.4 + - - +
5B TYR* 3.3 25.3 + - + +
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Residues in contact with LEU 220 (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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177A ARG* 4.3 9.2 - - - +
188A ALA* 3.9 21.5 - - + +
204A VAL* 3.8 11.4 - - + -
205A THR 3.4 2.7 - - - -
206A THR* 3.8 22.9 - - + +
218A VAL* 3.7 21.1 - - + -
219A THR* 1.3 79.7 - - - +
221A ASP* 1.3 61.0 + - - +
222A TYR* 3.5 38.6 + - + +
241A ARG* 3.3 6.8 - - - +
242A LEU 2.9 32.3 + - - +
244A TYR* 3.7 26.9 - - + -
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Residues in contact with ASP 221 (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 ASP 3.8 0.7 - - - +
204A VAL* 3.5 2.4 - - - -
205A THR* 2.9 46.3 + - + +
207A SER* 4.7 8.0 + - - -
219A THR* 4.0 5.2 + - - +
220A LEU* 1.3 71.4 - - - +
222A TYR* 1.3 63.9 + - - +
223A THR* 5.0 0.9 + - - -
239A LYS* 6.1 1.4 - - - +
240A PHE 3.6 4.6 - - - +
241A ARG* 3.0 50.2 + - - +
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Residues in contact with TYR 222 (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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33A TYR* 3.6 22.4 + + - -
177A ARG* 5.1 2.4 + - - -
190A PRO* 5.0 3.2 - - + +
202A LYS* 4.2 25.4 - - + -
203A ASP 3.5 3.1 - - - -
204A VAL* 3.3 28.2 - - + +
220A LEU* 3.5 47.0 - - + +
221A ASP* 1.3 75.2 - - - +
223A THR* 1.3 63.5 + - - +
224A VAL* 4.5 1.8 - - + -
238A SER 4.5 0.7 - - - -
239A LYS* 3.4 9.0 - - - +
240A PHE* 3.0 71.3 + + + +
242A LEU* 4.4 15.3 - - + -
244A TYR* 4.3 5.2 + - - -
1001A CIT 3.9 8.0 + - - +
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Residues in contact with THR 223 (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 LYS* 3.4 4.7 - - - -
203A ASP* 2.9 51.4 + - + +
221A ASP 5.0 1.2 + - - -
222A TYR* 1.3 75.5 + - - +
224A VAL* 1.3 64.5 + - - +
237A LEU* 3.8 35.4 - - + -
238A SER 3.6 8.2 + - - +
239A LYS* 4.9 5.0 - - - +
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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