Contacts of the strand formed by residues 220 - 225 (chain E) in PDB entry 3CQ6
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 LEU 220 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187E ILE* 4.0 18.8 - - + -
194E VAL* 3.6 12.8 - - + +
196E VAL* 3.5 32.3 - - + -
209E ALA* 3.3 28.3 - - + +
212E LEU* 3.6 29.2 - - + +
213E LEU* 3.7 25.1 - - + +
216E TYR* 3.1 19.4 + - + +
217E PRO* 4.5 3.5 - - - +
219E LYS* 1.3 76.8 - - - +
221E VAL* 1.3 69.3 + - - +
222E VAL* 4.1 5.4 - - + -
242E ALA* 4.0 4.2 - - - +
243E ASN 4.9 0.3 + - - -
246E PHE* 3.9 8.5 - - - -
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Residues in contact with VAL 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E LEU* 3.9 24.5 - - + -
193E ILE* 4.9 5.6 - - + -
194E VAL 3.1 9.1 + - - +
195E ILE* 3.4 11.7 - - + -
196E VAL 3.0 23.9 + - - -
219E LYS 4.9 1.3 - - - +
220E LEU* 1.3 80.3 - - - +
222E VAL* 1.3 66.7 + - - +
223E SER 3.9 1.4 + - - +
240E PHE* 3.7 35.0 - - + -
241E VAL 4.1 3.8 - - - -
242E ALA* 4.2 1.8 - - + -
246E PHE* 3.6 41.3 - - + -
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Residues in contact with VAL 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E VAL* 3.5 4.3 - - + +
198E GLU* 3.6 38.6 - - + +
209E ALA* 3.8 36.3 - - + +
210E THR* 4.0 15.3 - - + +
213E LEU* 4.2 9.0 - - + -
220E LEU* 4.1 11.4 - - + -
221E VAL* 1.3 74.6 - - - +
223E SER* 1.3 60.3 + - - +
224E ARG* 3.9 12.8 + - + +
240E PHE* 3.2 5.5 - - - -
241E VAL* 2.9 39.6 + - + +
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Residues in contact with SER 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E SER* 4.0 16.3 + - - -
101E ILE* 4.7 8.3 - - - +
102E LEU* 3.9 17.1 - - - +
195E ILE* 4.1 16.8 - - - -
196E VAL 3.0 11.2 + - - -
197E ASP* 4.1 17.1 + - - -
198E GLU* 2.8 35.5 + - - +
199E ALA 4.1 0.2 + - - -
221E VAL* 3.9 2.7 + - - -
222E VAL* 1.3 72.2 - - - +
224E ARG* 1.3 59.5 + - - +
239E TYR 3.5 6.8 + - - -
240E PHE* 4.2 4.0 - - - +
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Residues in contact with ARG 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E TYR* 4.3 0.2 + - - -
79E ILE* 4.1 15.4 - - + +
82E GLN* 4.0 22.0 - - - +
83E THR* 4.0 6.7 - - - +
98E SER* 3.4 11.6 + - - -
198E GLU* 2.7 48.8 + - - -
199E ALA* 5.2 0.4 - - - -
201E ALA* 3.6 16.1 - - - +
202E GLU* 3.4 31.5 + - - +
208E SER* 3.4 16.4 + - - -
210E THR* 4.7 1.8 - - - +
222E VAL* 4.2 11.9 - - + +
223E SER* 1.3 83.6 + - - +
225E THR* 1.3 62.8 + - - +
239E TYR* 2.6 70.4 + - + +
241E VAL* 4.5 4.7 - - + -
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Residues in contact with THR 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E SER* 3.6 4.9 - - - -
198E GLU 5.0 0.6 + - - -
199E ALA* 3.7 37.9 + - + +
202E GLU* 4.6 10.7 - - - +
224E ARG* 1.3 77.6 - - - +
226E MET* 1.3 70.7 + - - +
227E SER* 3.0 18.3 + - - +
228E LLP 2.7 46.1 + - + +
230E PHE* 4.3 9.9 + - - +
237E LEU 3.7 7.5 + - - -
238E GLY* 4.2 0.4 - - - -
239E TYR* 4.3 6.0 - - - -
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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