Contacts of the strand formed by residues 187 - 195 (chain B) in PDB entry 1A07
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 TYR 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B ILE* 3.6 18.9 - - + +
152B TYR* 3.6 35.0 + + - -
177B VAL* 4.1 6.5 - - + -
178B ARG 3.4 14.1 - - - +
179B GLU* 3.9 14.7 + - + +
180B SER* 3.2 9.3 + - - -
185B GLY* 4.2 13.2 - - - -
186B ALA* 1.3 78.8 - - - +
188B CYS* 1.3 62.8 + - - +
206B LYS* 3.8 2.3 - - - -
207B ILE* 3.0 45.2 + - + +
209B LYS* 5.8 1.8 - - + -
215B PHE* 3.7 35.7 - + - -
226B LEU* 4.1 10.8 - - + -
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Residues in contact with CYS 188 (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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176B LEU 3.9 0.2 - - - +
177B VAL* 3.3 5.7 - - - -
178B ARG* 2.9 75.0 + - + +
180B SER* 3.3 14.4 - - - +
187B TYR* 1.3 79.1 - - - +
189B LEU* 1.3 64.1 + - - +
190B SER* 4.0 2.7 - - - -
204B HIS* 3.7 13.7 - - - -
205B TYR 3.3 13.2 - - - +
207B ILE* 4.4 2.7 - - - +
101D PTR 3.7 18.4 - - + -
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Residues in contact with LEU 189 (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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175B PHE* 4.1 10.3 - - + -
176B LEU 3.7 13.0 - - - +
177B VAL* 4.0 15.3 - - + +
188B CYS* 1.3 71.8 - - - +
190B SER* 1.3 60.1 + - - +
191B VAL* 4.1 9.4 - - + -
203B LYS 3.8 0.7 - - - +
204B HIS* 3.4 3.3 - - - -
205B TYR* 2.7 47.6 + - + +
207B ILE* 4.1 14.8 - - + +
217B ILE* 3.8 23.3 - - + -
229B LEU* 4.7 6.3 - - + -
230B VAL* 5.3 2.5 - - + -
233B TYR* 5.2 0.7 - - + -
240B LEU* 3.9 26.0 - - + -
244B LEU* 4.1 27.1 - - + -
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Residues in contact with SER 190 (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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161B SER* 4.2 2.0 - - - -
165B LEU* 3.5 21.4 - - - +
175B PHE* 3.1 24.8 - - - +
176B LEU* 3.1 24.3 + - - +
178B ARG* 3.4 14.7 + - - +
188B CYS* 3.9 0.9 + - - -
189B LEU* 1.3 71.2 - - - +
191B VAL* 1.3 58.2 + - - +
202B VAL* 4.2 0.4 - - - -
203B LYS 3.4 5.2 - - - -
204B HIS* 2.7 32.6 + - - -
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Residues in contact with VAL 191 (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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165B LEU* 4.1 0.6 - - - +
173B GLY* 3.7 20.9 - - - -
174B THR 3.4 5.2 - - - +
175B PHE* 4.3 0.9 - - + -
189B LEU* 4.1 14.6 - - + -
190B SER* 1.3 75.1 - - - +
192B SER* 1.3 74.1 + - - +
202B VAL* 3.3 5.0 - - - +
203B LYS* 2.9 32.4 + - - +
205B TYR* 4.3 15.7 - - + -
240B LEU* 4.9 2.5 - - + -
241B CYS* 3.8 21.1 - - - -
242B HIS* 4.3 11.2 - - + +
244B LEU* 3.8 24.7 - - + -
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Residues in contact with SER 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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165B LEU* 4.5 24.6 + - - +
166B LEU* 5.1 5.6 - - - -
170B ASN* 5.1 2.0 + - - +
171B PRO 3.2 24.1 + - - -
172B ARG* 4.1 1.8 - - - -
173B GLY 3.1 20.0 + - - -
174B THR* 2.9 19.0 + - - -
191B VAL* 1.3 82.1 - - - +
193B ASP* 1.3 62.2 + - - +
200B LEU* 5.1 7.5 - - - +
201B ASN 3.2 11.0 - - - -
202B VAL* 4.2 4.9 - - - +
241B CYS* 4.4 0.7 - - - -
242B HIS* 4.8 1.4 - - - +
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Residues in contact with ASP 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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172B ARG* 2.6 39.9 + - - +
192B SER* 1.3 78.0 - - - +
194B PHE* 1.3 66.9 + - - +
195B ASP* 5.5 2.1 - - - +
200B LEU* 3.3 8.7 - - - +
201B ASN* 2.8 39.2 + - - +
203B LYS* 2.7 33.6 + - + +
241B CYS* 3.5 26.7 - - - +
242B HIS* 4.6 1.0 - - - +
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Residues in contact with PHE 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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172B ARG* 3.5 48.0 + - + +
193B ASP* 1.3 84.9 + - - +
195B ASP* 1.3 66.6 + - - +
196B ASN* 4.0 23.6 - - - -
199B GLY* 3.4 31.4 - - - -
200B LEU* 3.7 17.5 - - + -
201B ASN* 4.6 0.2 - - - -
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Residues in contact with ASP 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 ASP* 5.5 2.7 - - - +
194B PHE* 1.3 78.0 - - - +
196B ASN* 1.4 58.8 + - - +
197B ALA* 3.0 3.3 + - + +
198B LYS* 4.1 18.2 - - + +
199B GLY* 2.6 41.8 + - - +
201B ASN* 4.3 5.6 - - - +
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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