Contacts of the strand formed by residues 207 - 217 (chain A) in PDB entry 5CH3
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 GLY 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A LYS* 3.6 8.3 - - - -
127A ARG 3.6 8.3 - - - -
129A VAL* 3.6 14.4 - - - -
159A VAL* 3.8 8.2 - - - +
202A CYS* 2.9 16.5 + - - -
203A ALA* 3.4 11.8 - - - +
205A PHE 3.5 1.8 - - - -
206A GLY* 1.4 80.5 - - - +
208A ASN* 1.3 61.6 + - - -
209A PRO* 3.3 11.3 - - - +
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Residues in contact with ASN 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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126A LYS* 3.7 23.9 + - + +
127A ARG 2.8 23.1 + - - +
129A VAL* 3.8 2.5 - - - +
202A CYS* 4.1 1.6 - - - -
207A GLY* 1.3 71.8 - - - -
209A PRO* 1.4 68.4 - - - +
210A ASP* 2.8 32.4 + - - +
211A ASN* 3.0 40.4 + - + +
212A ILE* 4.0 4.0 - - - +
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Residues in contact with PRO 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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126A LYS* 5.0 5.6 - - + -
199A LYS* 3.2 50.2 + - + +
202A CYS* 3.7 12.5 - - - -
203A ALA* 4.3 18.8 - - + -
207A GLY 3.3 11.4 - - - +
208A ASN* 1.4 86.7 - - - +
210A ASP* 1.3 63.5 + - - +
211A ASN 3.4 0.4 - - - -
212A ILE* 3.7 5.6 - - + +
238A HIS* 3.3 9.2 - - - -
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Residues in contact with ASP 210 (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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199A LYS* 3.9 11.1 + - - -
208A ASN* 2.8 21.4 + - - +
209A PRO* 1.3 79.9 - - - +
211A ASN* 1.3 60.5 + - - +
238A HIS* 3.3 29.4 + - - +
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Residues in contact with ASN 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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128A PRO* 3.6 24.7 - - + +
129A VAL 3.0 23.7 + - - +
208A ASN* 3.0 29.2 + - + +
209A PRO 3.4 0.4 - - - -
210A ASP* 1.3 79.9 - - - +
212A ILE* 1.3 60.9 + - - +
213A THR* 5.1 0.6 + - - -
238A HIS* 3.7 1.6 - - - -
239A ARG* 3.1 22.8 + - - -
508A ALA 3.1 25.4 + - - +
509A THR* 3.4 17.3 + - - +
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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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129A VAL* 3.3 19.1 - - + +
131A VAL* 3.8 23.3 - - + -
195A LEU* 5.8 1.6 - - + +
198A ILE* 4.4 10.5 - - + -
199A LYS* 4.1 22.7 - - + -
202A CYS* 4.5 1.6 - - - -
208A ASN 4.0 6.7 - - - +
209A PRO* 3.7 24.9 - - + +
211A ASN* 1.3 77.0 + - - +
213A THR* 1.3 65.8 + - - +
214A VAL* 4.7 2.0 - - + -
236A LEU 3.5 17.7 - - - +
237A PHE* 3.6 18.0 - - + +
238A HIS* 2.8 35.6 + - + +
239A ARG* 3.3 4.7 + - - -
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Residues in contact with THR 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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129A VAL 2.8 10.9 + - - +
130A LEU* 3.3 7.9 - - + -
131A VAL* 2.7 32.9 + - - +
211A ASN 5.1 0.5 + - - -
212A ILE* 1.3 75.4 - - - +
214A VAL* 1.3 68.5 + - - +
215A PHE* 4.2 2.4 + - + -
239A ARG* 3.4 29.4 - - + +
241A ILE* 4.0 25.6 - - + -
507A PHE* 4.9 0.2 - - + -
508A ALA* 3.2 37.3 + - + +
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Residues in contact with VAL 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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131A VAL* 3.5 15.3 - - + +
133A ILE* 3.7 23.6 - - + -
195A LEU* 3.8 27.1 - - + -
212A ILE* 4.7 0.9 - - + -
213A THR* 1.3 77.2 - - - +
215A PHE* 1.3 64.0 + - - +
224A THR* 3.4 24.6 - - + +
227A MET* 5.1 0.7 - - + -
237A PHE* 3.7 40.1 - - + -
239A ARG 3.1 5.9 + - - -
240A GLY* 3.2 6.6 - - - -
241A ILE 2.9 23.9 + - - -
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Residues in contact with PHE 215 (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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130A LEU* 3.9 23.6 - - + -
131A VAL 2.9 32.1 + - - +
132A TYR* 3.3 41.8 - + + -
133A ILE* 2.9 23.6 + - - +
153A PHE* 3.8 31.0 - + - -
160A LEU* 4.2 6.1 - - + -
213A THR* 4.6 3.1 - - + -
214A VAL* 1.3 78.6 - - - +
216A GLY* 1.3 58.2 + - - +
224A THR* 3.3 7.5 + - - -
241A ILE* 3.3 29.4 - - + +
243A MET* 3.8 11.9 - - - -
478A PHE* 4.8 2.5 - + - -
479A PHE* 4.1 6.5 - + - -
504A TRP* 3.6 31.2 - + - -
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Residues in contact with GLY 216 (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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132A TYR* 3.6 9.0 - - - -
133A ILE 3.2 17.7 - - - -
215A PHE* 1.3 77.1 - - - +
217A GLU* 1.3 59.5 + - - -
220A GLY 3.4 9.2 - - - -
221A ALA* 3.3 11.0 - - - +
224A THR* 3.3 4.4 + - - -
241A ILE 3.4 2.2 + - - +
243A MET* 3.0 29.6 + - - +
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Residues in contact with GLU 217 (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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132A TYR* 3.4 21.0 + - - +
133A ILE 3.8 0.6 + - - -
135A GLY* 3.2 17.2 + - - -
148A TYR* 5.3 0.7 + - - -
216A GLY* 1.3 74.8 - - - -
218A SER* 1.3 79.6 + - - +
220A GLY 2.8 19.9 + - - -
221A ALA 3.5 0.2 - - - -
243A MET* 3.1 15.9 - - + +
244A SER* 4.4 0.8 - - - -
457A TYR* 5.4 1.0 - - - -
471A HIS* 3.4 17.0 + - - -
472A THR* 3.4 30.3 + - - +
474A GLU* 3.3 26.8 - - - +
475A LEU* 3.7 27.7 - - + +
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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