Contacts of the strand formed by residues 212 - 220 (chain B) in PDB entry 5WY8
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 GLY 212 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B LYS* 3.6 4.3 - - - -
184B GLU* 3.1 12.1 - - - -
210B ASP 3.5 2.6 + - - -
211B ILE* 1.3 81.4 - - - +
213B ASN* 1.3 65.2 + - - -
214B TYR* 3.8 8.6 - - - -
230B GLU* 3.5 4.3 - - - +
231B LEU 2.9 29.3 + - - +
1G NAG 3.6 12.6 - - - -
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Residues in contact with ASN 213 (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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144B TYR* 3.4 22.0 + - + +
149B LYS* 3.3 19.9 + - - +
182B TYR 3.8 0.2 - - - +
183B LYS* 3.6 5.0 - - - +
184B GLU* 2.6 49.0 + - - +
212B GLY* 1.3 72.1 - - - -
214B TYR* 1.3 62.6 + - - +
215B THR* 3.9 2.5 + - - +
228B THR* 4.5 5.6 - - + -
229B THR 3.6 4.3 - - - +
230B GLU* 3.6 12.5 - - - +
1G NAG 1.4 62.1 + - - +
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Residues in contact with TYR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ILE* 4.0 21.5 - - + -
181B TRP* 4.4 16.4 - + + -
182B TYR 3.4 5.4 - - - +
183B LYS* 3.9 17.4 - - + -
190B TRP* 3.7 31.1 - + - -
194B ILE* 6.0 0.2 - - - +
201B LEU* 3.8 26.7 - - + -
203B ILE* 3.9 15.8 - - + +
210B ASP* 2.9 34.8 + - - +
212B GLY 3.8 10.5 - - - -
213B ASN* 1.3 74.2 - - - +
215B THR* 1.3 60.6 + - - +
216B CYS 3.9 0.3 + - - -
227B ARG 3.8 1.7 - - - +
228B THR* 3.3 3.0 - - - -
229B THR* 2.8 47.2 + - - +
231B LEU* 3.8 19.8 - - + +
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Residues in contact with THR 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B CYS* 3.3 40.6 - - - +
144B TYR* 4.1 3.1 - - - -
181B TRP* 3.5 4.6 - - - -
182B TYR* 2.9 54.0 + - + -
185B CYS* 4.3 5.7 + - - -
213B ASN 3.9 2.8 + - - -
214B TYR* 1.3 72.5 - - - +
216B CYS* 1.3 63.3 + - - +
226B ARG* 4.2 18.6 - - + -
227B ARG 3.7 2.2 - - - +
228B THR* 3.3 26.5 + - - +
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Residues in contact with CYS 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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164B CYS* 2.0 51.1 - - - -
179B ILE* 3.5 20.9 - - - -
180B LEU 3.6 4.0 - - - -
181B TRP* 3.5 25.6 - - + -
214B TYR 3.9 0.6 + - - -
215B THR* 1.3 72.3 - - - +
217B GLU* 1.3 63.5 + - - +
218B LEU* 5.1 1.8 - - - -
225B VAL 4.0 0.4 - - - +
226B ARG* 3.1 7.3 - - - +
227B ARG 2.8 38.0 + - - +
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Residues in contact with GLU 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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178B GLU 4.3 1.2 - - - +
179B ILE* 3.5 4.6 - - - -
180B LEU* 2.9 40.8 + - + +
182B TYR* 3.0 42.6 + - + -
215B THR* 4.0 0.4 + - + -
216B CYS* 1.3 74.1 - - - +
218B LEU* 1.3 64.0 + - - +
219B LYS* 4.4 19.7 + - - -
224B VAL* 3.9 23.7 - - + +
225B VAL 3.6 4.3 - - - -
226B ARG* 3.3 26.8 + - + -
2F NAG 4.7 8.5 - - - +
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Residues in contact with LEU 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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164B CYS* 5.8 0.4 - - - -
167B ILE* 4.3 20.9 - - + -
170B PHE* 3.9 30.5 - - + +
171B LEU* 4.8 6.3 - - + -
177B PRO* 3.9 35.4 - - + +
178B GLU 4.9 1.3 - - - +
179B ILE* 4.3 12.8 - - + +
216B CYS* 4.3 3.6 - - - -
217B GLU* 1.3 76.5 - - - +
219B LYS* 1.3 84.0 + - - +
220B TYR* 4.9 1.3 - - + -
224B VAL* 3.6 2.3 - - - +
225B VAL* 2.9 54.2 + - + +
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Residues in contact with LYS 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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178B GLU 5.0 5.0 + - - +
180B LEU* 6.4 2.2 - - - -
217B GLU* 4.4 15.8 + - + -
218B LEU* 1.3 88.5 - - - +
220B TYR* 1.3 62.2 + - - +
221B GLY 4.3 0.2 - - - -
222B GLY* 5.9 4.5 - - - +
223B PHE 3.9 3.6 - - - +
224B VAL* 3.8 27.5 - - + +
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Residues in contact with TYR 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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48B PRO* 4.2 15.0 - - + -
104B TRP* 4.9 11.0 - + - -
106B ARG* 5.7 5.3 + - - -
169B ASP 3.9 9.3 + - - -
170B PHE* 3.7 66.4 - + + -
172B LEU* 5.7 7.4 - - + -
218B LEU* 4.9 2.7 - - + -
219B LYS* 1.3 75.9 - - - +
221B GLY* 1.3 66.2 + - - +
222B GLY 3.2 1.9 - - - +
223B PHE* 2.9 38.7 + + - +
225B VAL* 4.6 7.9 - - + -
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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