Contacts of the strand formed by residues 204 - 209 (chain B) in PDB entry 1EF1
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 ASN 204 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B LYS 4.8 9.0 + - - +
85B TYR* 5.8 5.1 - - - -
202B GLY 4.2 7.2 + - - -
203B VAL* 1.3 71.4 - - - +
205B TYR* 1.3 61.1 + - - +
206B PHE* 3.6 21.8 - - + -
218B LEU 3.4 1.6 - - - +
219B GLY* 3.2 3.3 - - - -
220B VAL* 2.7 58.7 + - + +
221B ASP* 4.5 0.6 - - - +
283B LEU* 3.4 31.9 - - + +
287B ASN* 4.4 8.3 - - - +
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Residues in contact with TYR 205 (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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114B ASP 5.7 0.2 - - - -
199B GLU 4.2 0.7 + - - -
200B MSE 3.3 42.9 - - + +
203B VAL* 3.5 33.5 + - + +
204B ASN* 1.3 73.7 - - - +
206B PHE* 1.3 68.8 + - - +
217B TRP* 4.0 21.9 - - + -
218B LEU 3.2 4.5 - - - -
228B TYR* 3.7 32.2 + + - -
233B ARG* 2.8 68.5 + - + +
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Residues in contact with PHE 206 (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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204B ASN* 3.6 30.5 - - + -
205B TYR* 1.3 80.0 - - - +
207B SER* 1.3 64.4 + - - +
208B ILE* 3.8 7.0 - - + +
217B TRP* 3.3 7.7 - - - -
218B LEU* 2.7 44.2 + - + +
220B VAL* 3.9 15.5 - - + -
276B ILE* 3.7 28.7 - - + -
279B ARG* 4.1 23.8 - - + -
280B ILE* 3.7 38.4 - - + -
283B LEU* 3.6 24.0 - - + -
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Residues in contact with SER 207 (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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206B PHE* 1.3 72.7 - - - +
208B ILE* 1.3 62.8 + - - +
215B GLU* 3.1 31.6 + - - -
216B LEU 3.7 5.7 + - - -
217B TRP* 3.6 23.6 - - - -
271B ALA* 4.3 0.5 - - - +
272B PRO* 3.2 32.3 - - - +
276B ILE* 4.8 2.5 - - - +
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Residues in contact with ILE 208 (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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206B PHE* 3.8 13.9 - - + +
207B SER* 1.3 80.4 + - - +
209B LYS* 1.3 63.3 + - - +
214B SER 3.5 0.5 - - - +
215B GLU* 3.6 5.0 - - - +
216B LEU* 2.8 46.5 + - + +
217B TRP 4.6 0.7 - - - -
218B LEU* 3.8 32.8 - - + +
227B ILE* 4.2 9.2 - - + -
269B PHE* 3.6 55.4 - - + -
270B TYR 3.5 6.7 - - - +
271B ALA* 4.8 2.9 - - + -
272B PRO* 5.1 0.4 - - - -
280B ILE* 4.7 2.0 - - + -
574D PHE* 4.0 20.0 - - + -
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Residues in contact with LYS 209 (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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208B ILE* 1.3 78.0 - - - +
210B ASN* 1.3 68.6 + - - +
213B GLY* 2.8 32.6 + - - +
214B SER 3.0 13.9 - - - +
215B GLU* 3.7 23.8 - - - +
216B LEU* 5.5 0.2 - - - -
269B PHE* 3.5 7.3 - - - +
270B TYR* 3.0 43.8 + - + +
574D PHE* 4.5 3.4 - - - -
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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