Contacts of the helix formed by residues 259 - 272 (chain B) in PDB entry 5WY5
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 SER 259 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B TRP* 4.3 4.3 - - - -
258B LEU* 1.3 81.4 - - - +
260B LYS* 1.3 62.3 + - - +
261B MET* 3.3 10.0 + - - +
262B LYS* 2.8 43.6 + - - +
263B VAL* 2.8 31.4 + - - +
288B ASP* 4.9 2.2 - - - -
292B ARG* 3.8 25.6 - - - +
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Residues in contact with LYS 260 (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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187B PHE* 3.2 32.7 - - + -
191B ASN* 4.2 15.5 - - - +
250B TRP* 4.0 23.7 - - + -
259B SER* 1.3 74.2 - - - +
261B MET* 1.3 61.9 + - - +
263B VAL 3.6 0.2 + - - -
264B LEU* 3.1 17.0 + - - +
284B GLU* 3.4 35.3 + - - +
285B ALA* 4.2 8.7 - - - -
288B ASP* 3.1 40.1 + - - +
292B ARG* 5.5 0.9 - - - +
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Residues in contact with MET 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TRP* 5.6 3.8 - - + -
35A ARG* 5.7 5.2 - - - +
259B SER* 3.1 9.6 + - - +
260B LYS* 1.3 77.1 - - - +
262B LYS* 1.3 54.6 + - + +
264B LEU* 2.8 14.5 + - + +
265B LYS* 2.7 49.5 + - + +
274B ASP* 6.0 0.2 - - - +
282B TYR* 4.5 14.1 - - - -
285B ALA* 3.5 38.8 + - - +
286B LEU* 3.6 35.2 - - + -
288B ASP* 5.3 0.6 + - - +
289B GLU* 3.6 24.7 - - + +
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Residues in contact with LYS 262 (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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166B GLU* 3.0 31.6 - - + +
180B MET* 4.7 0.2 - - - -
257B GLU 4.1 15.0 + - - -
258B LEU* 3.4 38.5 - - + +
259B SER* 2.8 34.6 + - - +
261B MET* 1.3 72.8 - - + +
263B VAL* 1.3 56.9 + - - +
265B LYS* 3.0 7.4 + - + -
266B PHE* 2.8 26.9 + - - +
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Residues in contact with VAL 263 (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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180B MET* 4.3 6.3 - - + +
183B LEU* 3.9 9.9 - - + +
184B GLY* 3.6 33.0 - - - +
187B PHE* 4.2 10.1 - - + -
250B TRP* 3.0 28.7 - - + -
258B LEU* 3.1 19.9 - - + +
259B SER 2.8 18.4 + - - +
260B LYS 3.7 5.2 - - - +
262B LYS* 1.3 75.8 - - - +
264B LEU* 1.3 57.3 + - - +
266B PHE* 3.2 7.5 - - + +
267B VAL* 2.9 29.5 + - + +
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PHE* 3.9 14.8 - - + -
260B LYS 3.1 10.2 + - - +
261B MET* 2.8 17.3 + - + +
263B VAL* 1.3 72.5 - - - +
265B LYS* 1.3 53.7 + - - +
266B PHE 2.9 1.5 + - - -
267B VAL* 3.0 19.2 - - + +
268B ALA* 2.6 36.9 + - - +
274B ASP* 4.7 13.5 - - + +
277B ASP* 4.7 3.1 - - - +
278B TRP* 3.5 30.5 - - + +
281B GLN* 4.6 5.6 - - - +
282B TYR* 3.6 40.4 - - + +
285B ALA* 3.9 14.4 - - + -
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Residues in contact with LYS 265 (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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35A ARG* 4.7 20.2 - - - +
166B GLU* 3.3 27.8 - - + +
261B MET* 2.7 33.5 + - + +
262B LYS* 3.4 5.2 - - + +
264B LEU* 1.3 71.5 - - - +
266B PHE* 1.3 51.7 + - - +
268B ALA* 3.0 9.2 - - - +
269B LYS* 2.8 45.9 + - - +
274B ASP* 5.5 5.5 + - - +
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Residues in contact with PHE 266 (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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166B GLU* 4.0 17.4 - - - +
167B MET* 5.0 6.1 - - + -
177B GLY* 4.4 8.7 - - - -
180B MET* 3.3 53.6 - - + -
181B ILE* 4.2 23.1 - - + -
262B LYS 2.8 12.2 + - - +
263B VAL* 3.2 12.6 - - + +
264B LEU 2.9 0.4 + - - -
265B LYS* 1.3 73.1 - - - +
267B VAL* 1.3 79.1 + - + +
268B ALA 3.0 0.9 - - - -
269B LYS* 2.9 16.7 + - + +
270B VAL* 3.1 33.6 + - + +
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Residues in contact with VAL 267 (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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181B ILE* 6.5 0.2 - - - -
184B GLY* 4.3 16.8 - - - -
187B PHE* 6.0 0.9 - - + -
188B MET* 3.6 38.4 - - + -
263B VAL* 2.9 24.1 + - + +
264B LEU* 3.0 37.7 - - + +
266B PHE* 1.3 85.3 - - + +
268B ALA* 1.3 66.9 + - - +
270B VAL* 3.3 14.8 + - - +
271B HIS* 3.4 22.5 + - - +
277B ASP* 4.8 7.4 - - - +
281B GLN* 5.3 0.7 - - - +
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Residues in contact with ALA 268 (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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264B LEU 2.6 17.7 + - - +
265B LYS* 3.0 14.8 - - - +
267B VAL* 1.3 80.2 - - - +
269B LYS* 1.3 53.5 + - + +
270B VAL 2.8 0.9 + - - -
271B HIS 2.9 1.0 + - - -
272B ASN 2.5 37.5 + - - +
273B GLN 2.7 25.6 - - - +
274B ASP* 3.2 19.5 - - + +
277B ASP* 4.9 5.4 - - - -
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Residues in contact with LYS 269 (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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166B GLU* 5.2 12.3 - - - +
265B LYS* 2.8 29.5 + - - +
266B PHE* 2.9 7.5 + - + +
268B ALA* 1.3 71.8 - - + +
270B VAL* 1.3 63.9 + - + +
271B HIS 4.0 0.2 - - - -
272B ASN* 3.2 15.0 + - - +
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Residues in contact with VAL 270 (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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266B PHE* 3.1 38.8 + - + +
267B VAL* 3.4 11.2 - - - +
268B ALA 2.8 5.5 + - - -
269B LYS* 1.3 76.0 - - - +
271B HIS* 1.3 73.9 + - + +
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Residues in contact with HIS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B MET* 5.7 4.0 - - - -
267B VAL* 3.4 20.4 + - - +
268B ALA 2.9 1.9 + - - -
270B VAL* 1.3 91.3 - - + +
272B ASN* 1.3 84.6 + - - +
273B GLN* 4.8 9.9 - - - +
276B LYS* 6.1 1.6 - - - -
277B ASP* 3.1 27.6 + - - -
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Residues in contact with ASN 272 (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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155A GLN* 2.9 33.6 + - - +
268B ALA* 2.5 26.3 + - - +
269B LYS* 3.2 17.2 + - - +
271B HIS* 1.3 90.7 + - - +
273B GLN* 1.3 82.7 + - - +
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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