Contacts of the strand formed by residues 205 - 210 (chain B) in PDB entry 1DE8
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 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B VAL* 3.4 15.0 - - + +
168B VAL* 3.6 31.9 - - + -
196B LEU* 3.7 34.1 - - + +
199B LEU* 4.8 6.7 - - + -
200B ALA* 3.7 28.9 - - + +
203B LYS 3.4 1.5 + - - +
204B PRO* 1.3 74.6 - - - +
206B VAL* 1.3 74.8 + - - +
207B LEU* 4.4 1.1 - - + +
247B VAL* 4.3 2.5 - - + -
249B LEU* 4.2 18.4 - - + -
287B LEU* 3.2 4.7 - - - +
288B SER* 2.6 43.7 + - - +
291B LEU* 3.6 2.1 - - - +
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 5.0 5.6 - - + -
165B PHE* 3.2 37.0 - - + -
166B VAL 2.9 8.3 + - - +
167B LEU* 3.1 16.2 - - + +
168B VAL 2.9 25.6 + - - -
205B LEU* 1.3 80.4 - - - +
207B LEU* 1.3 65.2 + - - +
285B PHE* 4.7 7.4 - - + -
286B LEU 3.4 7.0 - - - +
287B LEU* 4.1 5.8 - - + -
291B LEU* 3.7 16.6 - - + -
314B LEU* 4.3 20.9 - - + -
316B LEU* 4.5 10.8 - - + -
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Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B VAL* 3.3 37.7 - - + +
170B ALA* 4.2 7.0 - - + -
192B PHE* 4.0 23.3 - - + -
196B LEU* 3.9 28.7 - - + -
205B LEU* 4.2 2.1 - - + +
206B VAL* 1.3 74.0 - - - +
208B CYS* 1.3 64.4 + - - +
211B LEU* 4.3 24.0 - - + -
243B LEU* 4.6 7.0 - - + -
249B LEU* 4.0 16.2 - - + -
284B TYR 3.7 0.3 - - - +
285B PHE* 3.2 5.7 - - - -
286B LEU* 2.4 49.7 + - + +
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Residues in contact with CYS 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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64B ILE* 5.2 0.4 - - - -
66B SER* 3.6 13.5 - - - +
93B CYS* 3.5 33.2 - - - -
167B LEU* 3.6 17.9 - - + -
168B VAL 2.8 11.2 + - - -
169B THR* 2.9 11.9 + - - -
170B ALA* 2.7 31.9 + - - -
207B LEU* 1.3 82.9 - - - +
209B GLY* 1.3 53.1 + - - +
211B LEU* 5.2 3.4 - - - -
284B TYR 3.3 11.9 - - - +
285B PHE* 3.6 22.7 - - + -
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Residues in contact with GLY 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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66B SER* 3.5 6.4 + - - -
95B GLN* 3.1 24.0 - - - -
170B ALA 3.2 5.4 - - - -
208B CYS* 1.3 76.7 - - - +
210B ASP* 1.3 60.7 + - - -
211B LEU* 3.5 6.6 + - - +
283B ASP* 3.3 10.4 - - - +
284B TYR 3.1 28.9 + - - -
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Residues in contact with ASP 210 (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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68B ASN* 3.1 29.3 + - + +
95B GLN* 3.6 3.2 - - + +
170B ALA 3.1 6.8 + - - -
171B TYR* 3.7 9.1 - - + -
172B VAL* 3.2 23.0 + - - +
209B GLY* 1.3 69.4 - - - -
211B LEU* 1.3 58.1 + - - +
212B ASN* 3.0 18.4 + - - -
282B LEU* 3.4 16.7 - - - +
283B ASP* 3.1 15.6 + - - +
309B HIS* 3.2 11.4 + - - -
6X 3DR 2.9 32.3 + - - -
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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