Contacts of the strand formed by residues 202 - 209 (chain B) in PDB entry 1L9X
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 GLU 202 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B SER* 3.4 6.1 - - - -
177B VAL* 2.9 45.1 + - + +
178B LYS 4.8 0.2 + - - -
195B THR* 3.4 25.1 + - - +
196B ASN 3.3 12.3 - - - +
197B THR* 3.9 13.9 - - + +
200B LYS 4.1 1.6 + - - -
201B ILE* 1.3 76.1 - - - +
203B PHE* 1.3 61.8 + - - +
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Residues in contact with PHE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B THR* 4.4 5.8 - - + -
131B THR* 3.6 32.5 - - + -
136B MET* 4.4 2.7 - - - -
169B ASN* 3.9 9.4 - - - -
171B HIS* 3.7 17.0 - + - -
174B SER* 3.6 27.4 - - - -
175B LEU 3.4 15.3 - - - +
176B SER* 3.9 2.2 - - - +
177B VAL* 4.0 4.0 - - - +
195B THR* 3.2 6.8 - - - -
196B ASN* 2.8 67.0 + - + -
197B THR 4.0 9.4 - - - -
198B ASP* 4.2 1.1 - - + -
201B ILE* 3.8 12.1 - - + -
202B GLU* 1.3 74.2 - - - +
204B ILE* 1.3 77.3 + - - +
205B SER* 4.3 8.1 - - - -
218B GLN* 4.4 2.9 - - + -
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Residues in contact with ILE 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PHE* 3.6 33.6 - - + -
175B LEU* 2.9 27.3 + - + +
177B VAL* 4.6 11.9 - - + -
180B PHE* 3.2 51.4 - - + -
192B VAL* 3.7 23.6 - - + -
194B THR 4.0 3.6 - - - -
195B THR* 4.4 0.4 - - - +
203B PHE* 1.3 83.5 - - - +
205B SER* 1.3 61.9 + - - +
206B THR 4.0 19.1 - - - +
207B MET* 4.2 7.9 - - - -
218B GLN* 3.8 5.5 - - - +
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Residues in contact with SER 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PHE* 4.5 1.6 - - - -
138B LEU* 4.1 0.6 - - - +
169B ASN* 5.8 1.3 - - - -
194B THR* 2.7 32.3 + - - -
195B THR 3.3 2.8 + - - -
196B ASN* 2.8 30.5 + - - -
203B PHE* 3.7 10.7 + - - -
204B ILE* 1.3 76.0 - - - +
206B THR* 1.3 64.4 + - - +
217B VAL* 3.3 0.9 - - - -
218B GLN* 2.8 30.7 + - - -
219B TRP* 3.2 18.3 + - - -
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Residues in contact with THR 206 (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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138B LEU* 4.4 0.7 - - - +
149B MET* 3.4 35.9 - - + -
150B PHE* 4.0 14.1 - - + -
192B VAL* 3.7 2.4 - - - +
193B LEU* 2.8 27.1 + - + -
194B THR* 2.7 37.7 + - - +
204B ILE* 3.8 2.2 - - - +
205B SER* 1.3 81.4 + - - +
207B MET* 1.3 65.9 + - - +
216B GLY 3.4 7.6 - - - +
217B VAL* 4.0 5.2 - - + -
219B TRP* 3.1 17.8 + - - -
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Residues in contact with MET 207 (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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113B PHE* 3.6 50.3 - - + +
116B LEU* 4.6 6.3 - - + -
117B SER* 4.7 4.9 - - - +
149B MET* 3.9 5.6 - - - +
175B LEU* 4.8 7.9 - - + -
180B PHE* 4.6 9.4 - - - -
186B LEU* 5.2 0.4 - - + -
190B PHE* 3.7 50.3 - - + -
191B ASN 3.4 14.6 - - - +
192B VAL* 4.1 7.9 - - + -
193B LEU* 4.1 2.5 - - - +
204B ILE* 4.2 11.4 - - + -
206B THR* 1.3 77.0 - - - +
208B GLU* 1.3 62.6 + - - +
214B VAL 4.3 0.2 - - - +
215B TYR* 3.7 0.5 - - - -
216B GLY 2.9 34.7 + - - +
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Residues in contact with GLU 208 (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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147B SER* 3.7 6.3 - - - -
148B ARG* 2.9 44.6 + - - +
149B MET* 2.9 34.6 + - + +
190B PHE* 3.7 5.6 - - - -
191B ASN* 2.8 35.3 + - + +
193B LEU* 3.8 20.0 - - + -
207B MET* 1.3 76.0 - - - +
209B GLY* 1.3 63.5 + - - +
214B VAL 3.3 6.7 - - - -
215B TYR* 3.4 24.7 - - + -
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Residues in contact with GLY 209 (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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148B ARG* 2.8 27.5 + - - -
189B PHE* 3.3 24.7 - - - -
190B PHE* 3.8 1.4 - - - -
208B GLU* 1.3 75.9 - - - +
210B TYR* 1.3 63.2 + - - -
211B LYS 3.2 3.1 - - - -
212B TYR 3.4 14.6 + - - -
214B VAL 2.9 15.2 + - - -
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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