Contacts of the strand formed by residues 198 - 206 (chain B) in PDB entry 2DW1
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 ARG 198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195B ASN 4.9 3.4 + - - -
196B PRO 3.5 19.0 + - - -
197B PHE* 1.3 77.8 + - - +
199B PHE* 1.3 67.3 + - - +
240B TYR 3.4 9.0 + - - +
241B ILE* 4.5 10.1 - - + -
242B HIS* 2.9 24.9 + - - +
378B TRP* 4.0 27.4 - - + -
381B ILE* 3.7 26.9 - - + +
382B MET* 4.9 8.1 - - - +
385B ASN* 6.0 1.4 - - - +
386B PRO* 4.9 2.0 - - - +
389B ILE* 3.4 41.2 - - + +
390B LEU* 3.6 28.5 - - - +
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Residues in contact with PHE 199 (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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195B ASN* 3.9 17.5 - - - -
197B PHE* 3.7 22.7 - - + -
198B ARG* 1.3 76.9 - - - +
200B VAL* 1.3 63.2 + - - +
201B GLU* 3.9 1.8 - - + +
242B HIS* 3.4 41.1 - + + -
244B ALA* 6.0 2.0 - - + -
285B ASP* 3.1 7.3 - - - +
389B ILE* 2.6 35.3 + - - +
390B LEU 4.0 8.3 - - - -
391B ASN 3.4 15.7 - - - +
392B GLU* 3.8 43.5 - - + -
393B PRO* 3.6 22.4 - - + -
407B GLU 5.2 1.1 - - - -
408B LEU* 3.9 13.7 - - + -
711B CA 4.2 1.2 - - - -
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Residues in contact with VAL 200 (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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199B PHE* 1.3 76.9 - - - +
201B GLU* 1.3 60.9 + - - +
202B LEU* 3.1 8.2 + - + +
241B ILE* 3.8 24.0 - - + -
242B HIS 2.7 13.7 + - - +
243B VAL* 3.7 4.0 - - + -
244B ALA* 3.0 25.2 + - - -
285B ASP* 3.6 4.0 - - + -
286B ASN* 3.7 22.7 - - + -
307B MET* 4.5 11.4 - - - -
335B MET* 3.3 34.3 - - + -
339B LEU* 5.0 7.4 - - + -
389B ILE* 4.2 12.6 - - + -
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Residues in contact with GLU 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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199B PHE 5.0 2.0 - - - +
200B VAL* 1.3 69.6 - - - +
202B LEU* 1.3 59.0 + - - +
244B ALA 3.4 6.5 - - - +
246B VAL* 3.6 28.5 - - + +
283B LYS* 3.2 28.9 - - - +
284B HIS* 3.4 7.1 - - - +
285B ASP* 2.8 38.1 + - - +
286B ASN 3.3 6.8 + - - -
391B ASN* 3.2 13.9 - - - +
393B PRO* 3.6 32.0 - - + +
397B ASP* 4.8 8.1 - - - +
711B CA 2.4 28.4 - - - -
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Residues in contact with LEU 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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200B VAL* 3.1 10.0 + - + +
201B GLU* 1.3 74.0 - - - +
203B VAL* 1.3 81.2 + - - +
204B LEU* 4.4 4.0 - - + -
229B VAL* 4.3 16.8 - - + -
243B VAL* 3.9 23.3 - - + -
244B ALA 2.8 14.8 + - - +
245B LEU* 3.3 9.3 - - + +
246B VAL 2.8 28.6 + - - -
247B GLY 3.5 0.3 + - - -
286B ASN* 3.4 32.8 - - + +
288B GLN* 3.7 16.2 - - + -
331B MET* 4.2 20.0 - - - -
335B MET* 4.1 10.3 - - - -
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Residues in contact with VAL 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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202B LEU* 1.3 79.1 - - - +
204B LEU* 1.3 73.5 + - - +
205B VAL* 4.6 3.5 - - + +
246B VAL* 3.8 8.5 - - + -
247B GLY* 3.6 19.7 - - - -
248B LEU* 4.2 1.3 - - - +
249B GLU* 4.9 4.3 - - + +
278B LEU* 3.9 25.8 - - + -
282B LYS* 4.4 7.9 - - + -
284B HIS* 3.3 44.9 - - + +
286B ASN 2.9 6.9 + - - -
287B ALA* 3.1 5.0 - - + +
288B GLN 3.1 23.6 + - - -
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Residues in contact with LEU 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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202B LEU* 4.4 7.4 - - + -
203B VAL* 1.3 77.0 - - - +
205B VAL* 1.3 62.5 + - - +
225B MET* 3.3 37.0 - - + -
229B VAL* 3.7 24.9 - - + -
245B LEU* 3.8 14.1 - - + +
247B GLY 3.3 5.7 + - - -
248B LEU* 3.2 18.1 - - + +
249B GLU 2.9 24.8 + - - -
288B GLN* 3.6 31.9 - - + +
290B LEU* 4.5 6.7 - - + -
331B MET* 3.9 23.1 - - + -
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Residues in contact with VAL 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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203B VAL* 4.6 5.6 - - + +
204B LEU* 1.3 79.8 - - - +
206B VAL* 1.3 60.8 + - - +
249B GLU* 3.2 13.2 - - + +
251B TRP* 3.5 39.7 - - + +
270B PHE* 3.7 30.7 - - + -
273B TRP* 4.0 15.0 - - + -
278B LEU* 4.5 10.8 - - + -
288B GLN 3.0 6.4 + - - +
289B LEU* 3.3 13.3 - - + +
290B LEU* 2.6 34.3 + - - +
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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
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205B VAL* 1.3 77.1 - - - +
207B ASP* 1.3 62.4 + - - +
210B MET* 3.2 33.7 - - + -
211B VAL* 4.7 2.9 - - + +
221B ILE* 3.9 24.2 - - + -
225B MET* 3.6 30.7 - - + -
248B LEU* 4.2 13.2 - - + -
249B GLU 2.8 11.5 + - - +
250B ILE* 4.1 16.1 - - + +
251B TRP* 2.8 31.4 + - - +
290B LEU* 3.7 6.1 - - + -
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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