Contacts of the strand formed by residues 205 - 214 (chain A) in PDB entry 3CB4
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 205 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A PHE* 3.6 18.7 - - - -
201A ASP* 2.6 45.5 + - - +
203A TYR 3.3 3.0 + - - -
204A LEU* 1.3 76.8 - - - +
206A VAL* 1.3 60.3 + - - -
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Residues in contact with VAL 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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198A SER* 4.8 2.5 - - - -
199A TRP 3.4 8.5 - - - +
200A PHE* 3.9 17.0 - - + -
204A LEU 3.9 2.9 + - - +
205A GLY* 1.3 70.7 - - - -
207A VAL* 1.3 69.8 + - - +
208A SER* 4.7 7.4 - - - +
258A LEU 4.0 6.4 - - - +
259A VAL* 4.3 5.5 - - - +
260A CYS 3.8 15.4 + - - +
261A ALA* 6.0 0.8 - - - +
262A ILE* 3.2 43.5 + - + +
263A LYS 4.1 1.6 - - - +
264A ASP* 3.7 25.8 - - - +
265A ILE* 3.9 21.5 - - + +
268A ALA* 4.9 2.9 - - + -
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Residues in contact with VAL 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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198A SER* 3.4 1.8 - - - -
199A TRP* 3.0 66.4 + - + +
201A ASP* 3.7 29.8 - - + +
204A LEU* 4.1 17.5 - - + -
205A GLY 3.8 0.9 - - - +
206A VAL* 1.3 79.0 - - - +
208A SER* 1.3 65.2 + - - +
240A PHE* 5.3 1.1 - - + -
244A GLN* 5.5 2.5 - - - +
257A TRP* 3.9 21.5 - - + -
258A LEU 3.6 11.0 - - - +
259A VAL* 4.0 11.4 - - + -
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Residues in contact with SER 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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195A ILE* 4.5 7.1 - - - +
197A ASP 3.3 6.1 - - - -
198A SER* 2.6 22.5 + - - -
199A TRP* 4.1 3.6 - - - -
206A VAL* 4.7 2.8 - - - +
207A VAL* 1.3 73.5 - - - +
209A LEU* 1.3 62.1 + - - +
210A ILE* 3.8 18.2 + - - -
256A GLY 3.7 0.2 - - - +
257A TRP* 3.1 5.8 - - - -
258A LEU* 2.9 39.5 + - - +
262A ILE* 5.2 3.1 - - - +
268A ALA* 3.5 15.4 - - - +
274A LEU* 5.6 1.7 - - - +
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Residues in contact with LEU 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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57A GLN* 4.3 16.8 - - - +
58A SER* 3.4 36.8 - - - +
76A ILE* 4.6 5.6 - - + -
195A ILE* 3.8 2.9 - - - -
196A ILE* 2.8 58.4 + - + -
197A ASP* 2.8 18.9 + - + +
199A TRP* 3.7 17.6 - - + -
208A SER* 1.3 72.1 - - - +
210A ILE* 1.3 55.5 + - - +
240A PHE* 4.2 12.6 - - + -
255A VAL* 3.8 15.7 - - + -
256A GLY* 3.4 21.8 - - - +
257A TRP* 4.5 0.7 - - - +
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Residues in contact with ILE 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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193A ALA* 3.7 10.8 - - + -
194A LEU 3.4 7.9 - - - +
195A ILE* 4.6 4.7 - - + -
196A ILE* 3.8 4.5 - - - -
208A SER* 4.5 9.9 - - - +
209A LEU* 1.3 79.1 - - - +
211A ARG* 1.3 61.9 + - - +
212A ILE* 3.6 30.5 - - + -
217A LEU* 4.5 6.1 - - + -
250A LEU* 4.6 7.4 - - + -
254A GLU 3.7 0.2 - - - +
255A VAL* 3.1 8.0 - - - +
256A GLY 2.7 38.1 + - - +
258A LEU* 3.6 26.2 - - + -
274A LEU* 3.0 36.8 - - + -
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Residues in contact with ARG 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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6A ASN* 3.1 22.0 - - - +
94A ALA* 3.3 43.3 + - + +
96A GLU* 2.5 31.3 + - - -
183A PRO* 3.2 15.9 - - - +
184A GLU 4.4 5.5 + - - +
193A ALA* 3.1 2.9 - - - -
194A LEU* 2.7 47.3 + - + +
196A ILE* 3.7 4.0 - - + +
210A ILE* 1.3 74.8 - - - +
212A ILE* 1.3 81.4 + - - +
213A LYS* 3.2 38.6 + - - +
253A GLY* 3.7 8.3 - - - -
254A GLU 3.4 5.6 - - - -
255A VAL* 3.9 14.4 - - + -
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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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191A LEU* 4.1 4.5 - - + -
192A GLN 4.1 2.0 - - - -
193A ALA* 3.9 10.1 - - + -
210A ILE* 3.6 22.9 - - + -
211A ARG* 1.3 76.1 + - - +
213A LYS* 1.3 59.0 + - - +
214A ASN 3.8 12.1 - - - +
215A GLY 3.4 27.6 - - - +
217A LEU* 4.1 18.6 - - + -
250A LEU* 3.6 26.9 - - + +
251A LYS 3.2 26.0 - - - +
252A CYS* 3.7 2.5 - - - -
253A GLY* 2.8 28.4 + - - -
254A GLU 2.9 14.4 + - - +
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Residues in contact with LYS 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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93A ALA* 2.7 32.5 + - - +
94A ALA* 4.6 4.4 - - - +
95A CYS 5.3 0.6 + - - -
96A GLU* 4.8 4.6 + - - -
184A GLU 3.0 25.6 - - - +
192A GLN 2.9 13.0 + - - +
194A LEU* 4.4 13.0 - - + -
211A ARG* 3.2 31.8 + - - +
212A ILE* 1.3 72.6 - - - +
214A ASN* 1.3 63.9 + - + +
252A CYS* 3.6 6.9 - - - -
285A LEU* 3.7 36.6 - - + -
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Residues in contact with ASN 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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185A GLY* 3.4 9.2 - - - -
186A ASP* 3.2 31.0 + - - +
189A GLY* 4.0 10.7 - - - -
190A PRO* 3.3 21.7 + - - +
191A LEU* 3.2 10.4 - - - +
192A GLN* 2.9 53.8 + - + +
212A ILE* 3.4 2.4 - - - +
213A LYS* 1.3 80.1 - - + +
215A GLY* 1.3 62.7 + - - +
252A CYS* 3.8 4.7 - - - -
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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