Contacts of the strand formed by residues 208 - 214 (chain A) in PDB entry 2CMG
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 LYS 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A GLN* 4.5 23.0 + - - +
50A LEU* 6.0 3.4 - - - +
58A GLU* 2.8 36.6 + - - +
62A LEU* 6.0 0.2 - - - +
146A LEU* 5.0 5.6 + - - +
170A VAL* 3.6 39.4 - - + +
171A ALA 4.0 3.4 - - - +
173A HIS* 3.8 17.5 - - - +
199A VAL* 4.7 4.2 - - - +
200A ALA 5.2 0.9 + - - -
203A ARG* 6.0 2.7 - - - +
206A SER* 3.0 22.6 + - - +
207A ASN* 1.3 78.9 - - - +
209A GLY* 1.3 62.6 + - - +
210A TYR* 3.8 16.1 - - - +
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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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170A VAL* 3.3 4.3 - - - +
171A ALA* 2.9 30.6 + - - -
172A LYS 3.7 17.0 - - - -
173A HIS* 4.6 2.5 - - - -
181A MET* 4.5 3.6 - - - -
198A PHE 4.0 4.3 - - - -
199A VAL* 4.7 4.5 - - - -
208A LYS* 1.3 73.7 - - - +
210A TYR* 1.3 78.5 + - - -
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Residues in contact with TYR 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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58A GLU* 2.6 40.1 + - + +
61A LEU* 5.2 2.2 - - + -
62A LEU* 3.6 22.9 - - + -
169A SER 3.2 9.4 - - - +
170A VAL* 4.0 15.5 - - + +
171A ALA* 4.3 0.9 - - - +
181A MET* 3.7 5.8 - - - +
197A PRO* 3.3 3.3 - - - +
198A PHE* 2.9 71.5 + + + +
199A VAL* 4.0 2.0 - - - -
200A ALA* 4.1 27.3 - - + +
203A ARG* 5.0 5.4 + - - -
206A SER* 5.5 1.4 + - - -
208A LYS* 3.8 29.4 - - + +
209A GLY* 1.3 86.2 - - - -
211A ILE* 1.3 72.0 + - - +
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Residues in contact with ILE 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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167A PHE 3.6 1.9 - - - +
168A ILE* 3.3 5.5 - - - +
169A SER* 2.7 45.5 + - - +
170A VAL 5.1 1.6 - - - +
171A ALA* 4.1 11.2 - - + -
181A MET* 4.0 9.0 - - - -
184A ALA* 3.4 46.2 - - + +
185A LEU* 3.9 22.9 - - + +
188A MET* 4.1 25.4 - - + -
195A ALA* 4.6 1.8 - - - -
196A MET 3.4 10.8 - - - +
197A PRO* 4.6 0.2 - - + -
198A PHE* 3.9 4.0 - - - -
210A TYR* 1.3 80.3 - - - +
212A TYR* 1.3 71.2 + - - +
213A ALA 4.6 0.2 - - - +
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Residues in contact with TYR 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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65A MET* 3.6 30.1 - - + -
69A THR* 2.8 41.0 + - + +
166A VAL* 3.4 23.4 - - + +
167A PHE 3.9 1.8 - - - -
168A ILE* 3.7 13.7 - - + -
194A VAL* 3.8 4.3 - - + +
195A ALA* 3.5 1.6 + - - -
196A MET* 2.7 41.8 + - + +
198A PHE* 3.8 13.4 - - + -
211A ILE* 1.3 72.9 - - - +
213A ALA* 1.3 65.8 + - - +
214A SER* 4.8 0.7 - - - -
217A THR* 3.4 24.1 - - - +
219A PRO* 3.3 41.5 - - + +
246A PHE* 4.0 7.0 - - + -
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Residues in contact with ALA 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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166A VAL* 3.5 4.0 - - - +
167A PHE* 2.7 48.4 + - + +
188A MET* 3.9 17.0 - - + -
192A PHE* 3.8 25.4 - - + -
194A VAL 3.0 12.8 - - - +
195A ALA* 4.5 4.5 - - + -
211A ILE* 3.9 2.0 + - + -
212A TYR* 1.3 76.7 - - - +
214A SER* 1.3 63.6 + - - +
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Residues in contact with SER 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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161A LEU* 4.8 2.0 - - - -
165A GLY 3.6 20.0 - - - -
166A VAL* 4.5 4.0 - - - -
192A PHE* 3.3 16.6 - - - +
193A SER 3.2 6.4 + - - -
194A VAL* 2.9 37.5 + - - +
212A TYR* 4.8 0.7 - - - -
213A ALA* 1.3 76.9 - - - +
215A PHE* 1.3 59.5 + - - +
216A LYS 3.1 11.0 + - - -
217A THR* 2.6 31.9 + - - -
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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