Contacts of the strand formed by residues 207 - 212 (chain J) in PDB entry 5ANC
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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176J PHE 2.9 17.5 - - - +
177J ILE* 3.8 0.9 - - - -
178J LEU* 2.8 34.6 + - + +
179J PRO 4.1 0.2 - - - -
180J VAL 2.9 26.5 - - - +
183J GLY* 3.3 14.4 - - - +
184J LYS* 3.1 29.1 + - - +
187J LYS* 5.5 1.6 - - - +
200J GLU* 3.6 26.6 - - - +
201J ASP* 4.6 0.9 - - - +
202J TYR* 3.4 26.0 - - + +
205J GLN 4.3 0.2 - - - +
206J LEU* 1.3 76.2 - - - +
208J ILE* 1.3 61.1 + - - +
209J VAL* 3.2 11.2 + - + +
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Residues in contact with ILE 208 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175J ARG* 4.7 8.5 - - + -
176J PHE 3.9 3.4 - - - -
198J GLU 3.0 21.7 - - - +
199J SER* 4.3 2.8 - - - -
200J GLU* 3.1 31.4 + - - +
206J LEU* 4.0 11.4 - - + -
207J GLU* 1.3 67.9 - - - +
209J VAL* 1.3 59.5 + - - +
210J CYS* 3.6 1.1 + - + +
932K ASP* 3.4 33.0 - - + +
933K GLY 3.7 32.5 - - - +
934K CYS* 3.4 26.7 - - - +
938K PHE* 4.5 5.6 - - + -
953K CYS* 4.3 16.6 - - + -
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Residues in contact with VAL 209 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175J ARG* 3.5 1.3 - - - -
176J PHE* 2.8 34.7 + - + +
178J LEU* 3.7 27.4 - - + -
187J LYS* 4.2 35.9 - - + -
196J VAL* 4.4 7.2 - - + -
197J ILE 5.0 0.2 - - - -
198J GLU 4.7 1.3 - - - -
199J SER* 4.6 3.6 - - - +
200J GLU 5.0 4.9 - - - +
207J GLU* 3.2 21.6 + - + +
208J ILE* 1.3 72.9 - - - +
210J CYS* 1.3 59.3 + - - +
211J LEU* 3.3 34.5 - - + +
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Residues in contact with CYS 210 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173J ARG* 4.0 32.8 - - - -
174J LEU 3.5 4.0 - - - -
175J ARG* 4.1 20.2 - - + +
197J ILE* 2.9 55.1 + - - +
198J GLU* 4.1 28.5 - - + +
208J ILE* 3.6 4.1 + - + +
209J VAL* 1.3 70.5 - - - +
211J LEU* 1.3 64.9 + - - +
212J ILE* 5.2 0.4 - - - -
934K CYS* 5.6 3.6 - - - -
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Residues in contact with LEU 211 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173J ARG* 3.3 7.8 - - - -
174J LEU* 2.8 40.1 + - + +
176J PHE* 4.2 17.5 - - + -
178J LEU* 6.2 0.2 - - + -
187J LYS* 6.0 0.9 - - + -
190J LEU* 5.6 12.6 - - + -
194J ILE* 3.7 25.8 - - + -
195J LYS 3.5 15.7 - - - +
196J VAL* 3.8 17.7 - - + -
209J VAL* 3.3 44.0 - - + +
210J CYS* 1.3 75.8 - - - +
212J ILE* 1.3 68.7 + - - +
213J ASP 3.8 1.8 - - - +
225J LYS* 4.9 7.0 - - - +
235J GLU* 5.5 0.4 - - - +
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Residues in contact with ILE 212 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171J HIS* 3.7 32.5 + - + +
172J MET 3.1 24.7 - - - +
173J ARG* 3.9 16.2 - - + -
194J ILE* 3.6 19.7 - - - +
195J LYS* 3.5 38.6 + - + +
197J ILE* 4.5 23.6 - - + -
210J CYS* 5.2 0.9 - - - -
211J LEU* 1.3 81.4 - - - +
213J ASP* 1.3 58.4 + - - +
250J GLU* 4.5 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