Contacts of the strand formed by residues 211 - 215 (chain B) in PDB entry 1ECX
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 211 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B PHE* 3.5 9.4 - - - -
67B THR* 2.8 47.5 + - - +
69B CYS* 3.4 14.8 - - - +
199B PHE 3.6 7.9 - - - -
210B VAL* 1.3 75.4 - - - +
212B ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B VAL* 4.0 35.0 - - + -
57B LEU* 4.7 1.1 - - + -
64B ILE* 4.3 13.0 - - + -
65B PHE 3.7 2.2 - - - -
66B PHE* 4.1 14.1 - - + -
73B SER* 4.1 1.5 + - - -
198B SER* 3.7 2.3 - - - -
199B PHE* 3.0 57.3 + - + +
201B ALA* 5.2 3.1 - - + +
204B PHE* 4.5 9.9 - - + -
210B VAL* 4.9 4.9 - - + -
211B GLY* 1.3 78.6 - - - +
213B THR* 1.3 67.9 + - - +
247B ALA* 4.4 18.8 - - + +
251B MET* 3.6 25.1 - - + -
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Residues in contact with THR 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B GLU 3.4 0.7 - - - +
64B ILE* 3.3 10.9 - - - +
65B PHE* 2.7 44.8 + - + -
67B THR* 3.7 8.5 - - - +
73B SER* 2.7 31.7 + - - -
76B TRP* 3.9 17.1 - - + -
77B ILE* 3.8 20.6 - - + -
197B ALA 3.6 2.7 - - - -
199B PHE* 5.6 0.2 - - - -
212B ILE* 1.3 74.1 - - - +
214B TYR* 1.3 62.9 + - - +
215B ILE* 3.5 26.5 - - + -
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Residues in contact with TYR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B VAL* 3.5 35.7 - - + +
63B GLU* 3.2 32.7 + - + -
64B ILE* 4.4 6.7 - - + -
189B LEU* 3.6 23.4 + - + -
194B VAL* 3.7 24.2 + - + -
195B ASP 3.8 11.2 - - - -
196B TYR* 3.2 10.3 - - - +
197B ALA* 3.0 51.4 + - + +
199B PHE* 5.0 4.0 - - + -
213B THR* 1.3 74.4 - - - +
215B ILE* 1.3 66.2 + - - +
216B ARG* 3.4 40.0 + - - +
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Residues in contact with ILE 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B SER 4.9 0.2 - - - +
63B GLU* 3.0 27.8 + - - +
65B PHE* 4.0 22.9 - - + -
76B TRP* 3.7 26.9 - - + -
77B ILE* 5.0 0.9 - - + -
195B ASP 3.7 2.9 - - - -
196B TYR* 4.2 11.2 - - + -
213B THR* 3.5 15.5 - - + -
214B TYR* 1.3 77.6 - - - +
216B ARG* 1.3 68.4 + - - +
217B LYS* 3.4 2.6 + - - -
219B VAL* 3.5 25.8 - - + +
221B ILE* 3.7 41.3 - - + -
234B LEU* 4.9 0.9 - - + -
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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