Contacts of the strand formed by residues 202 - 209 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A SER* 3.5 5.9 - - - -
177A VAL* 2.9 46.2 + - + +
178A LYS 4.7 0.3 + - - -
195A THR* 3.0 28.8 + - - +
196A ASN 3.2 15.7 - - - +
197A THR* 4.1 7.4 + - - +
200A LYS 4.3 0.8 + - - -
201A ILE* 1.3 75.8 - - - +
203A PHE* 1.3 59.3 + - - +
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Residues in contact with PHE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A THR* 4.5 4.9 - - + -
131A THR* 3.7 32.3 - - + -
136A MET* 4.3 2.5 - - - -
169A ASN* 3.9 9.6 - - - -
171A HIS* 3.7 16.6 - + - -
174A SER* 3.6 26.5 - - - -
175A LEU 3.3 15.5 - - - +
176A SER* 4.2 1.1 - - - -
177A VAL* 3.9 5.8 - - - +
195A THR* 3.2 6.6 - - - -
196A ASN* 2.7 67.4 + - + -
197A THR 3.9 9.6 - - - -
198A ASP 4.0 0.7 - - - -
201A ILE* 3.7 14.4 - - + +
202A GLU* 1.3 75.5 - - - +
204A ILE* 1.3 75.4 + - - +
205A SER* 4.3 8.1 - - - -
218A GLN* 4.4 2.9 - - + -
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Residues in contact with ILE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 3.5 33.1 - - + -
175A LEU* 2.9 28.0 + - + +
176A SER 4.4 0.7 - - - +
177A VAL* 3.6 28.7 - - + -
180A PHE* 4.2 21.1 - - + -
192A VAL* 3.6 34.1 - - + -
194A THR 4.0 1.6 - - - -
195A THR* 4.2 0.7 - - + -
203A PHE* 1.3 82.4 - - - +
205A SER* 1.3 61.6 + - - +
206A THR 4.0 16.6 - - - +
207A MET* 4.0 15.9 - - + -
218A GLN* 3.8 5.7 - - - +
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Residues in contact with SER 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 4.5 2.7 - - - -
138A LEU* 4.4 0.2 - - - -
169A ASN* 5.8 1.1 - - - -
194A THR* 2.6 33.3 + - - -
195A THR 3.3 2.0 + - - -
196A ASN* 2.8 34.5 + - - -
203A PHE* 3.6 9.3 + - - -
204A ILE* 1.3 74.6 - - - +
206A THR* 1.3 63.2 + - - +
217A VAL* 3.3 1.1 - - - -
218A GLN* 2.9 31.5 + - - -
219A TRP* 3.2 16.8 + - - -
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Residues in contact with THR 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PHE* 4.9 0.2 - - - -
138A LEU* 4.3 1.2 - - - +
149A MET* 3.4 35.9 - - + -
150A PHE* 4.0 13.2 - - + -
192A VAL* 3.8 1.6 - - - -
193A LEU* 2.8 25.6 + - + -
194A THR* 2.7 36.9 + - - +
204A ILE* 3.8 2.3 - - - +
205A SER* 1.3 75.3 - - - +
207A MET* 1.3 66.2 + - - +
216A GLY 3.4 4.0 - - - -
217A VAL* 3.9 9.2 - - + -
219A TRP* 3.1 24.4 + - - -
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Residues in contact with MET 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PHE* 3.6 47.6 - - + +
116A LEU* 5.0 2.9 - - + -
117A SER* 4.8 6.7 - - - +
149A MET* 3.9 4.8 - - - +
175A LEU* 4.6 10.8 - - + -
180A PHE* 4.4 9.0 - - - -
186A LEU* 5.3 0.2 - - + -
190A PHE* 3.7 50.9 - - + -
191A ASN 3.4 13.2 - - - +
192A VAL* 4.2 7.2 - - - -
193A LEU* 4.2 4.0 - - - +
204A ILE* 4.0 12.1 - - + -
206A THR* 1.3 77.0 - - - +
208A GLU* 1.3 64.0 + - - +
215A TYR* 3.7 1.2 - - - -
216A GLY* 3.0 36.0 + - - +
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Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A HIS 4.9 0.3 - - - +
147A SER* 3.5 13.1 - - - -
148A ARG* 2.8 41.7 + - - +
149A MET* 2.9 33.0 + - + +
190A PHE* 3.6 5.6 - - - -
191A ASN* 2.7 45.2 + - + +
193A LEU* 4.0 11.4 - - + -
207A MET* 1.3 74.7 - - - +
209A GLY* 1.3 64.9 + - - +
210A TYR* 5.9 0.2 - - - -
214A VAL 3.4 6.1 - - - -
215A TYR* 3.4 24.5 - - + -
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Residues in contact with GLY 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ARG* 2.7 30.5 + - - +
189A PHE* 3.3 24.9 - - - -
190A PHE* 3.7 1.0 - - - -
208A GLU* 1.3 76.4 - - - +
210A TYR* 1.3 64.0 + - - -
211A LYS 3.2 2.2 - - - -
212A TYR 3.4 15.6 + - - -
214A VAL 2.9 15.4 + - - -
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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