Contacts of the strand formed by residues 207 - 214 (chain A) in PDB entry 2L9N
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 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A ILE* 3.6 1.3 - - - -
178A LEU* 2.9 39.1 + - + +
179A PRO 3.4 3.3 - - - +
180A VAL 3.1 24.4 - - - +
183A GLY* 2.5 42.8 - - - +
184A LYS* 3.6 1.8 + - - +
187A LYS* 3.6 21.2 + - + +
200A GLU 3.3 5.4 - - - +
201A ASP* 3.3 28.7 - - + -
205A GLN 3.8 5.4 - - - +
206A LEU* 1.3 75.5 - - - +
208A ILE* 1.3 61.2 + - - +
209A VAL* 3.9 11.0 - - + -
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Residues in contact with ILE 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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175A ARG* 5.0 20.9 - - + +
176A PHE 3.6 3.8 - - - +
177A ILE* 3.5 37.7 - - + -
198A GLU* 2.9 13.1 - - - +
200A GLU* 2.8 67.3 + - + +
206A LEU* 4.6 8.5 - - + +
207A GLU* 1.3 70.8 - - - +
209A VAL* 1.3 61.2 + - - +
210A CYS* 6.1 0.2 - - - -
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Residues in contact with VAL 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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175A ARG* 5.2 0.4 - - - -
176A PHE* 2.7 43.2 + - - +
178A LEU* 5.0 4.9 - - + +
187A LYS* 4.3 24.5 - - + -
190A LEU* 5.0 8.1 - - + -
196A VAL* 3.0 37.9 - - + -
197A ILE 3.8 2.0 - - - +
198A GLU 3.3 2.9 - - - -
199A SER* 3.5 25.4 - - - -
200A GLU 4.4 2.2 - - - +
207A GLU* 3.9 7.3 + - + +
208A ILE* 1.3 81.3 - - - +
210A CYS* 1.3 64.3 + - - +
211A LEU* 3.7 7.6 - - + +
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Residues in contact with CYS 210 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A LEU 2.7 13.9 - - - +
175A ARG* 3.3 28.9 - - - -
197A ILE* 2.8 58.1 + - + +
198A GLU* 3.4 13.6 + - + -
208A ILE 6.1 0.4 - - - -
209A VAL* 1.3 73.2 - - - +
211A LEU* 1.3 68.4 + - - +
212A ILE* 4.9 0.9 - - + -
238A ASN* 3.0 26.2 - - - +
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Residues in contact with LEU 211 (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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174A LEU* 2.5 53.7 + - + +
176A PHE* 4.2 7.0 - - + -
190A LEU* 3.3 47.6 - - + -
194A ILE* 3.4 17.9 - - + -
195A LYS 3.7 0.7 - - - -
196A VAL* 3.5 23.6 - - + -
209A VAL 3.7 13.0 - - - +
210A CYS* 1.3 85.2 - - - +
212A ILE* 1.3 60.9 + - - +
221A ASP* 4.3 1.8 - - - +
225A LYS* 3.1 31.9 - - - +
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Residues in contact with ILE 212 (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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171A HIS* 6.0 2.2 - - + -
172A MET 3.8 9.2 - - - +
173A ARG* 3.2 50.0 - - + +
174A LEU 4.3 1.6 - - - +
194A ILE* 3.2 17.8 - - - +
195A LYS* 3.1 25.2 + - + +
197A ILE* 3.3 44.9 - - + -
210A CYS* 4.9 0.2 - - + -
211A LEU* 1.3 78.4 - - - +
213A ASP* 1.3 65.6 + - - +
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Residues in contact with ASP 213 (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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171A HIS* 4.9 1.1 - - - -
172A MET* 2.9 29.8 + - - +
174A LEU* 2.8 37.0 - - - +
194A ILE* 4.4 7.9 - - + -
212A ILE* 1.3 77.3 - - - +
214A PRO* 1.3 81.4 - - + +
217A PHE* 3.4 11.7 - - + -
218A ARG* 2.9 41.2 + - - +
221A ASP* 3.7 9.2 - - - +
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Residues in contact with PRO 214 (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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117A ASP 3.3 23.3 - - - +
118A LYS* 4.5 19.7 - - + -
170A ALA 3.3 13.9 - - - +
171A HIS* 4.1 7.2 - - + -
172A MET* 4.8 1.6 - - - +
194A ILE* 5.6 0.9 - - + -
213A ASP* 1.3 108.0 - - + +
215A GLY* 1.3 61.8 + - - +
216A CYS* 3.2 21.9 + - - -
217A PHE* 3.9 16.2 - - + -
218A ARG* 3.8 6.6 + - - +
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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