Contacts of the strand formed by residues 187 - 195 (chain B) in PDB entry 5YDJ
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 187 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B THR* 4.7 4.9 - - + -
180B VAL 3.7 8.5 - - - +
181B ASP* 4.6 8.7 - - - +
185B GLY 3.9 2.2 + - - +
186B LYS* 1.3 75.6 - - - +
188B VAL* 1.3 65.7 + - - +
264B ARG* 3.6 64.4 + - + +
265B PRO* 6.0 0.2 - - - +
298B SER* 4.9 1.7 - - - -
809B SO4 2.7 32.9 + - - -
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Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ILE 3.9 0.2 - - - +
179B THR* 3.4 4.9 - - - +
180B VAL* 3.0 53.2 + - + +
182B ALA* 4.5 4.9 - - + +
187B LYS* 1.3 79.9 - - - +
189B ASP* 1.3 66.2 + - - +
190B VAL* 3.9 9.9 - - + -
261B VAL* 4.3 5.4 - - + -
262B ALA 3.5 14.4 - - - +
263B PRO* 4.2 5.8 - - + -
264B ARG* 4.4 3.8 - - - -
294B ARG* 3.9 27.8 - - + +
298B SER* 3.7 28.5 - - - +
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Residues in contact with ASP 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 4.6 9.3 - - + +
178B ILE 3.7 5.6 - - - +
179B THR* 3.3 21.3 + - - -
188B VAL* 1.3 72.2 - - - +
190B VAL* 1.3 60.8 + - - +
191B TRP* 3.5 23.6 - - + -
261B VAL* 3.5 1.7 - - - +
262B ALA* 2.8 40.8 + - + +
263B PRO 5.2 0.5 - - - +
264B ARG* 3.4 31.7 + - - +
266B ARG* 3.0 31.5 + - - +
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Residues in contact with VAL 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B GLY* 3.2 4.3 - - - -
178B ILE* 2.9 59.8 + - + +
180B VAL* 3.6 27.8 - - + -
188B VAL* 3.9 4.7 - - + -
189B ASP* 1.3 79.3 - - - +
191B TRP* 1.3 65.1 + - - +
192B LEU* 3.7 30.5 - - + +
221B THR 4.3 0.2 - - - +
260B VAL 3.5 5.8 - - - +
261B VAL* 3.8 23.1 - - + -
294B ARG* 4.7 7.0 - - + +
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Residues in contact with TRP 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 2.9 28.4 + - + -
168B VAL* 4.2 9.6 - - + +
175B ILE* 4.0 6.7 + - + -
176B ARG 4.1 0.4 - - - -
177B GLY* 3.4 23.6 - - - +
189B ASP* 3.5 28.9 - - + -
190B VAL* 1.3 75.8 - - - +
192B LEU* 1.3 61.1 + - - +
194B ILE* 3.8 17.2 - - + +
221B THR* 3.5 24.5 - - + -
259B ASN* 3.5 3.5 - - - -
260B VAL* 2.6 51.5 + - + +
262B ALA* 3.7 17.9 - - + -
266B ARG* 3.4 38.6 - - - -
347B PHE* 3.6 38.8 - + + -
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Residues in contact with LEU 192 (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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190B VAL* 3.7 32.7 - - + -
191B TRP* 1.3 79.1 - - - +
193B GLY* 1.3 57.5 + - - +
221B THR* 2.8 39.0 + - - -
222B THR* 3.2 19.4 + - - +
223B THR 3.1 21.2 + - - +
224B PRO* 3.9 24.7 - - + -
259B ASN* 3.9 15.5 - - + +
260B VAL 4.3 3.1 - - - +
261B VAL* 4.5 9.0 - - + -
293B HIS* 6.0 1.1 - - + -
294B ARG* 6.0 3.6 - - - +
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Residues in contact with GLY 193 (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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192B LEU* 1.3 73.1 - - - +
194B ILE* 1.3 63.7 + - - +
195B PRO* 3.3 9.7 - - - +
219B LEU* 4.8 2.6 - - - +
221B THR* 3.3 7.9 + - - -
223B THR 3.7 7.5 + - - -
225B PRO* 3.9 11.1 - - - +
257B TYR* 3.4 26.7 - - - -
258B ILE 3.6 0.8 + - - -
259B ASN* 3.4 12.5 + - - -
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Residues in contact with ILE 194 (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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170B THR* 5.3 0.7 - - + -
175B ILE* 3.8 28.5 - - + -
191B TRP* 3.8 23.6 - - + +
193B GLY* 1.3 73.7 - - - +
195B PRO* 1.4 78.1 - - + +
196B TYR 3.5 0.5 + - - -
215B TRP* 5.0 4.7 - - + -
221B THR* 3.2 17.5 - - - +
257B TYR* 3.3 1.4 - - - -
258B ILE* 2.7 45.7 + - + +
260B VAL* 3.8 15.9 - - + -
339B TRP* 3.6 41.3 - - + +
347B PHE* 4.2 1.3 - - + -
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Residues in contact with PRO 195 (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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193B GLY 3.3 10.5 - - - +
194B ILE* 1.4 94.5 - - + +
196B TYR* 1.3 59.8 + - - +
197B ALA 3.7 10.8 - - - +
212B ALA* 4.3 11.2 - - + +
215B TRP* 3.9 23.2 - - + -
219B LEU* 3.5 28.5 - - + -
256B LEU 3.9 3.6 - - - +
257B TYR* 3.4 26.2 - - + +
339B TRP* 4.5 4.7 + - - -
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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