Contacts of the strand formed by residues 202 - 209 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139C ASN* 6.1 0.4 - - - +
176C SER* 3.5 8.0 - - - -
177C VAL* 2.9 47.6 + - + +
178C LYS 4.8 0.2 + - - -
195C THR* 2.8 31.0 + - - +
196C ASN 3.2 13.0 - - - +
197C THR* 4.3 4.0 - - - +
201C ILE* 1.3 75.9 - - - +
203C PHE* 1.3 61.0 + - - +
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Residues in contact with PHE 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C THR* 4.5 7.6 - - + -
131C THR* 3.7 32.3 - - + -
136C MET* 4.3 2.2 - - + -
169C ASN* 3.9 10.3 - - - -
171C HIS* 3.7 16.6 - + - -
174C SER* 3.6 27.4 - - - -
175C LEU 3.4 15.0 - - - +
176C SER* 4.2 1.6 - - - -
177C VAL* 4.0 4.7 - - - +
195C THR* 3.1 5.9 - - - -
196C ASN* 2.7 62.8 + - + -
197C THR 3.8 15.0 - - - -
198C ASP 4.0 1.6 - - - -
201C ILE* 4.2 11.2 - - + -
202C GLU* 1.3 76.2 - - - +
204C ILE* 1.3 76.4 + - - +
205C SER* 4.4 7.4 - - - -
218C GLN* 4.4 2.9 - - + -
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Residues in contact with ILE 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C PHE* 3.6 33.1 - - + -
175C LEU* 2.9 29.0 + - + +
177C VAL* 4.5 11.4 - - + -
180C PHE* 3.1 54.3 - - + -
192C VAL* 4.0 26.2 - - + -
194C THR 4.0 3.1 - - - -
195C THR* 4.4 1.3 - - - +
203C PHE* 1.3 84.3 - - - +
205C SER* 1.3 62.1 + - - +
206C THR 4.0 9.6 - - - +
207C MET* 4.1 9.6 - - + -
218C GLN* 3.8 5.9 - - - +
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Residues in contact with SER 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C PHE* 4.5 2.7 - - - -
138C LEU* 4.0 0.4 - - - +
169C ASN* 5.8 1.1 - - - -
194C THR* 2.6 32.8 + - - -
195C THR 3.3 3.5 + - - -
196C ASN* 2.8 30.4 + - - -
203C PHE* 3.6 9.3 + - - -
204C ILE* 1.3 75.1 - - - +
206C THR* 1.3 64.0 + - - +
217C VAL* 3.3 1.1 - - - -
218C GLN* 2.9 31.8 + - - -
219C TRP* 3.2 17.9 + - - -
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Residues in contact with THR 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C PHE* 4.9 0.2 - - - -
138C LEU* 4.3 0.9 - - - +
149C MET* 3.4 33.2 - - + -
150C PHE* 4.0 13.9 - - + -
192C VAL* 3.8 1.9 - - - +
193C LEU* 2.8 25.8 + - + -
194C THR* 2.6 38.4 + - - +
204C ILE* 3.8 1.6 - - - +
205C SER* 1.3 74.9 - - - +
207C MET* 1.3 67.9 + - - +
216C GLY 3.4 9.4 - - - +
217C VAL* 3.9 6.3 - - + -
219C TRP* 3.1 25.0 + - + -
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Residues in contact with MET 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C PHE* 3.7 48.0 - - + +
116C LEU* 4.7 7.0 - - + -
117C SER* 4.8 5.6 - - - +
149C MET* 3.9 6.2 - - - +
175C LEU* 4.9 6.5 - - + -
180C PHE* 4.4 9.9 - - - -
186C LEU* 5.2 0.4 - - + -
190C PHE* 3.6 52.3 - - + -
191C ASN 3.3 14.1 - - - +
192C VAL* 4.1 7.0 - - - -
193C LEU* 4.2 2.7 - - - +
204C ILE* 4.1 11.7 - - + -
206C THR* 1.3 77.5 - - - +
208C GLU* 1.3 62.5 + - - +
214C VAL 4.3 0.2 - - - +
215C TYR* 3.7 1.2 - - - -
216C GLY 3.0 35.8 + - - +
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Residues in contact with GLU 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C SER* 3.5 13.4 - - - -
148C ARG* 2.9 43.7 + - - +
149C MET* 2.9 34.5 + - + +
190C PHE* 3.7 5.2 - - - -
191C ASN* 2.7 48.2 + - + +
193C LEU* 3.9 10.1 - - + -
207C MET* 1.3 74.4 - - - +
209C GLY* 1.3 66.0 + - - +
210C TYR* 5.9 0.2 - - - -
214C VAL 3.5 6.3 - - - -
215C TYR* 3.4 22.1 - - + -
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Residues in contact with GLY 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ARG* 2.7 31.2 + - - +
189C PHE* 3.3 19.5 - - - -
190C PHE* 3.7 6.9 - - - -
208C GLU* 1.3 75.2 - - - +
210C TYR* 1.3 62.9 + - - -
211C LYS 3.2 2.2 - - - -
212C TYR 3.4 14.9 + - - -
214C VAL 2.9 15.8 + - - -
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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