Contacts of the strand formed by residues 214 - 224 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B ASP* 4.4 1.2 + - - -
150B GLY 4.3 13.0 + - - +
151B ASP* 4.9 3.4 + - - +
152B GLN* 3.2 41.0 - - - +
210B ILE* 3.7 3.3 - - - +
211B VAL* 2.9 34.1 + - - +
212B ASN 3.1 3.1 + - - +
213B ASN* 1.3 74.8 - - - +
215B ALA* 1.3 77.3 + - - +
216B HIS* 3.3 10.8 + - + +
245B TYR* 3.6 9.6 + - - +
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Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B LEU* 4.0 30.1 - - + -
208B VAL* 5.0 2.0 - - + -
209B LEU 3.7 7.6 - - - +
210B ILE* 3.9 16.5 - - + +
213B ASN 4.3 0.2 + - - -
214B LYS* 1.3 87.4 - - - +
216B HIS* 1.3 57.3 + - - +
245B TYR* 4.1 6.9 + - - -
246B PRO* 3.9 22.1 - - + +
248B CYS* 6.0 0.2 - - - -
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Residues in contact with HIS 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B PRO* 6.2 1.1 - - + -
147B ASP* 3.3 50.4 + - + -
148B CYS* 5.4 0.7 - - - -
150B GLY* 4.7 8.4 - - - -
209B LEU* 2.9 18.0 + - + +
211B VAL* 3.7 33.4 - - + -
214B LYS* 4.0 9.4 - - + +
215B ALA* 1.3 73.0 - - - +
217B MET* 1.4 74.2 + - + +
245B TYR* 3.4 22.6 - + - -
246B PRO* 3.6 6.7 - - - -
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Residues in contact with MET 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A TYR* 3.7 12.3 - - - +
7A THR* 3.6 30.5 - - + -
146B PRO* 5.5 11.9 - - + -
207B SER 3.6 0.3 - - - +
208B VAL* 3.6 2.1 - - - +
209B LEU* 2.8 46.4 + - + +
216B HIS* 1.4 93.1 - - + +
218B VAL* 1.3 72.8 + - - +
219B THR* 3.5 22.9 - - - +
243B SER* 3.8 12.3 - - - +
244B TYR 3.4 14.8 - - - +
246B PRO* 3.6 3.0 - - - +
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Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B TYR* 4.5 17.5 - - + -
182B ILE* 4.7 7.9 - - + -
183B LEU* 4.3 14.6 - - + -
188B ALA* 5.1 2.0 - - + -
206B THR* 4.6 8.5 - - + -
207B SER 3.3 6.3 - - - +
208B VAL* 4.4 8.7 - - + -
217B MET* 1.3 79.1 - - - +
219B THR* 1.3 63.0 + - - +
220B LEU* 3.8 23.3 - - + -
243B SER* 3.4 1.7 - - - -
244B TYR* 2.7 48.8 + - + +
246B PRO* 3.8 24.5 - - + -
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Residues in contact with THR 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A TYR* 2.9 27.5 + - + +
205B THR 3.6 2.4 - - - +
207B SER* 2.9 41.3 + - - -
217B MET* 3.5 7.6 - - - -
218B VAL* 1.3 73.6 - - - +
220B LEU* 1.3 63.9 + - - +
221B ASP* 4.1 7.0 + - - +
241B ARG* 3.2 45.1 - - + +
242B LEU 3.7 3.6 - - - +
243B SER* 2.7 19.0 + - - +
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Residues in contact with LEU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ARG* 4.4 9.4 - - - +
188B ALA* 4.0 20.0 - - + +
204B VAL* 4.0 9.4 - - + -
205B THR 3.4 3.1 - - - +
206B THR* 3.9 22.4 - - + +
218B VAL* 3.8 19.3 - - + -
219B THR* 1.3 81.2 - - - +
221B ASP* 1.3 61.6 + - - +
222B TYR* 3.5 38.3 + - + +
240B PHE 3.9 0.7 - - - +
241B ARG* 3.4 4.0 - - - +
242B LEU 2.9 32.4 + - - +
244B TYR* 3.9 27.6 - - + -
2001B CIT 4.6 0.9 - - - +
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Residues in contact with ASP 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B ASP 3.9 0.7 - - - +
204B VAL* 3.6 2.5 - - - -
205B THR* 2.8 50.5 + - - +
207B SER* 4.8 6.8 + - - -
219B THR* 4.2 6.4 - - - +
220B LEU* 1.3 73.0 - - - +
222B TYR* 1.3 61.1 + - - +
223B THR* 4.9 2.0 + - - -
240B PHE 3.6 5.0 - - - +
241B ARG* 3.1 49.3 + - - +
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Residues in contact with TYR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B TYR* 3.6 11.2 + + - -
177B ARG* 4.9 1.9 + - - -
188B ALA 5.5 0.5 + - - -
190B PRO* 4.8 5.0 - - + +
202B LYS* 4.2 26.0 - - + -
203B ASP 3.4 4.0 - - - -
204B VAL* 3.2 28.7 - - + +
220B LEU* 3.5 41.5 - - + +
221B ASP* 1.3 72.3 - - - +
223B THR* 1.3 61.2 + - - +
224B VAL* 4.2 2.9 - - + -
238B SER 3.6 0.4 - - - +
239B LYS* 3.2 25.5 - - - +
240B PHE* 3.0 54.4 + + + +
242B LEU* 4.5 15.5 - - + -
244B TYR* 5.1 0.2 - - - -
2001B CIT 2.8 25.7 + - - -
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Residues in contact with THR 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B LYS* 3.5 3.3 - - - -
203B ASP* 2.9 48.6 + - + +
221B ASP 4.0 1.9 + - - -
222B TYR* 1.3 73.3 + - - +
224B VAL* 1.3 63.6 + - - +
225B GLN 4.5 0.2 + - - -
237B LEU* 3.8 33.2 - - + -
238B SER 3.3 6.5 - - - +
239B LYS* 2.6 34.9 + - + +
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Residues in contact with VAL 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B VAL* 3.5 31.4 - - + +
32B LEU* 5.9 4.7 - - + -
33B TYR* 5.6 0.4 - - + -
200B LEU* 4.8 17.9 - - + -
201B THR 3.9 6.5 - - - +
202B LYS* 3.9 25.8 - - + -
222B TYR* 4.5 1.6 - - + -
223B THR* 1.3 80.3 - - - +
225B GLN* 1.3 61.8 + - - +
236B GLY 3.1 5.5 - - - +
237B LEU* 3.4 4.5 - - - -
238B SER* 2.8 36.1 + - - +
240B PHE* 4.0 20.6 - - + -
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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