Contacts of the strand formed by residues 205 - 211 (chain B) in PDB entry 3DLX
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 205 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B THR* 3.8 17.7 - - - -
60B LEU* 4.2 15.0 - - - +
204B THR* 1.3 78.3 - - - +
206B ASP* 1.3 63.4 + - - -
207B PHE 3.4 1.3 - - - -
237B ALA 2.9 9.3 + - - +
238B ALA* 3.2 3.7 - - - -
239B GLU* 3.1 21.7 + - - +
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Residues in contact with ASP 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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54B PRO* 5.7 3.4 - - + -
57B ALA* 3.5 10.6 - - + -
58B THR* 2.9 37.3 + - - +
205B GLY* 1.3 72.5 - - - -
207B PHE* 1.3 83.9 + - + +
239B GLU* 3.5 13.1 + - - +
240B THR* 3.0 22.2 + - - -
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Residues in contact with PHE 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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49B ALA 5.5 0.9 - - - -
50B VAL* 6.0 0.4 - - + -
52B ASP* 4.0 13.9 - - - -
53B ILE* 3.7 61.9 - - + -
54B PRO* 3.9 10.5 - - + -
57B ALA* 4.6 2.2 - - + -
58B THR 3.3 3.0 + - - +
59B VAL* 3.3 12.5 - - + -
60B LEU* 2.8 29.9 + - - +
206B ASP* 1.3 94.8 + - + +
208B ALA* 1.3 55.6 + - - +
209B LEU* 5.2 1.3 - - + -
238B ALA* 3.4 10.2 - - - +
240B THR* 3.1 33.2 - - + +
242B VAL* 4.6 9.6 - - + -
268B ARG* 4.1 18.6 - - - -
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Residues in contact with ALA 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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60B LEU* 3.3 12.1 - - + +
207B PHE* 1.3 73.5 - - - +
209B LEU* 1.3 62.2 + - - +
210B VAL* 3.8 14.1 - - + -
234B MET 3.3 28.3 - - - +
238B ALA* 3.4 10.5 - - + +
240B THR 2.9 7.3 + - - +
241B THR* 4.1 9.0 - - - -
242B VAL* 2.8 34.8 + - - +
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Residues in contact with LEU 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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50B VAL* 3.9 26.9 - - + -
53B ILE* 4.5 6.1 - - + -
59B VAL* 3.6 23.3 - - + -
60B LEU 2.7 11.4 + - - +
61B VAL* 4.6 9.4 - - + -
62B GLY 3.0 25.8 + - - -
70B PRO* 3.5 16.6 - - + +
73B LEU* 4.2 23.1 - - + -
74B ILE* 4.5 11.4 - - + +
77B LEU* 3.8 29.2 - - + -
102B LEU* 5.7 0.4 - - + -
207B PHE* 5.2 1.6 - - + -
208B ALA* 1.3 76.1 - - - +
210B VAL* 1.3 60.6 + - - +
242B VAL* 3.6 10.3 - - + -
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Residues in contact with VAL 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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70B PRO* 3.9 3.6 - - - -
73B LEU* 4.0 1.7 - - - +
208B ALA* 3.9 23.3 - - + +
209B LEU* 1.3 79.5 - - - +
211B LYS* 1.3 67.4 + - - +
223B PHE* 4.1 5.6 - - + -
231B ASN* 3.5 42.2 - - + +
234B MET* 4.4 5.6 - - + -
235B CYS* 3.8 22.9 - - - +
241B THR* 5.1 1.3 - - - -
242B VAL 2.8 15.0 + - - +
243B VAL* 3.1 16.3 - - + -
244B GLU* 2.8 28.9 + - - +
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Residues in contact with LYS 211 (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 GLY* 3.8 20.7 - - - +
69B ILE 3.5 35.1 + - - +
70B PRO* 3.7 5.1 - - + +
210B VAL* 1.3 75.0 - - - +
212B ALA* 1.3 82.5 + - - +
223B PHE* 3.6 8.1 - - - -
227B ALA* 4.7 2.3 - - + +
231B ASN* 3.0 25.5 + - - -
244B GLU* 3.5 11.7 - - + +
246B GLU* 2.8 35.8 + - - +
275B TYR* 4.0 25.7 - - + -
277B LYS* 3.4 18.6 - - - +
362B ASP* 5.3 1.6 + - - -
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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