Contacts of the strand formed by residues 200 - 205 (chain B) in PDB entry 1DWQ
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 LYS 200 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B GLY 3.4 4.0 - - - -
102B PHE* 3.9 19.3 - - + -
107B LEU* 4.5 4.3 - - + -
195B TYR* 3.0 50.8 + - - +
196B GLY 3.3 13.3 + - - -
198B ILE* 2.9 27.0 + - + +
199B LYS* 1.3 77.5 - - - +
201B VAL* 1.3 62.3 + - - +
223B TYR* 3.6 30.6 + - + -
224B LYS 5.9 0.2 - - - +
225B PRO* 3.5 17.9 - - + +
226B ASP* 2.8 44.9 + - - +
227B LYS 3.4 1.0 + - - -
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Residues in contact with VAL 201 (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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99B ALA* 5.4 0.9 - - + -
100B GLY 3.1 6.9 + - - +
101B VAL* 3.3 17.0 - - + +
102B PHE* 2.8 28.9 + - - -
200B LYS* 1.3 76.9 - - - +
202B TYR* 1.3 64.4 + - - +
203B ILE* 4.6 3.4 - - + -
227B LYS* 3.3 17.7 - - + +
229B TYR* 3.5 33.9 - - + -
249B ILE* 4.8 0.2 - - + -
253B VAL* 3.9 25.8 - - + -
257B TYR* 3.7 30.1 - - + +
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Residues in contact with TYR 202 (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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102B PHE* 3.5 17.0 - - + -
105B SER 3.5 19.8 + - - -
107B LEU* 3.8 34.1 - - + -
201B VAL* 1.3 73.5 - - - +
203B ILE* 1.3 57.3 + - - +
204B TRP* 3.8 24.5 - + + -
216B GLN* 2.7 39.0 + - + -
219B GLN* 2.9 22.7 + - + -
220B ILE* 3.9 25.4 - - + -
225B PRO* 3.7 20.4 - - + -
227B LYS 2.9 7.9 + - - +
228B VAL* 3.2 5.7 - - + +
229B TYR* 2.8 31.9 + - - +
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Residues in contact with ILE 203 (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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77B VAL* 5.7 0.4 - - + -
101B VAL* 3.6 26.5 - - + -
102B PHE 2.7 15.7 + - - +
103B HIS* 4.3 11.9 - - + -
104B ASN* 2.9 26.2 + - - -
201B VAL* 4.6 2.5 - - + -
202B TYR* 1.3 76.7 - - - +
204B TRP* 1.3 64.7 + - - +
229B TYR* 3.2 9.2 - - + +
231B VAL* 3.9 13.5 - - + -
238B LEU* 4.2 10.1 - - + -
246B VAL* 4.3 23.8 - - + -
249B ILE* 3.8 47.3 - - + -
250B LEU* 4.3 4.0 - - + -
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Residues in contact with TRP 204 (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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104B ASN* 3.3 9.9 - - - +
202B TYR* 3.8 12.8 - + + -
203B ILE* 1.3 74.1 - - - +
205B THR* 1.3 77.3 + - - +
206B ASP* 3.6 23.6 - - + -
213B PRO* 3.8 21.5 - - + -
216B GLN* 3.2 39.3 - - + +
217B ARG* 3.6 42.2 - - + -
220B ILE* 4.1 8.8 - - + +
228B VAL* 3.6 25.7 - - + +
229B TYR 3.2 12.1 + - - -
230B GLN* 3.4 34.6 - - + +
231B VAL* 2.9 27.2 + - - +
238B LEU* 4.0 6.3 - - - -
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Residues in contact with THR 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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104B ASN* 3.4 6.3 + - - +
204B TRP* 1.3 87.5 - - - +
206B ASP* 1.3 66.8 + - - +
207B GLN* 3.0 11.0 + - - +
208B ASP* 3.2 30.8 + - + +
211B PHE 4.8 0.3 - - - +
213B PRO* 5.6 0.5 - - - +
216B GLN* 3.9 0.5 + - - -
230B GLN* 4.6 0.7 - - - -
231B VAL 3.4 15.8 + - - -
233B GLY 2.6 25.8 + - - +
235B ASP 3.2 29.6 - - - +
238B LEU* 3.5 17.0 - - + -
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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