Contacts of the helix formed by residues 263 - 273 (chain B) in PDB entry 5VSW
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 THR 263 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262B LEU* 1.3 75.2 - - - +
264B VAL* 1.3 64.6 + - - +
265B ARG* 4.0 8.8 + - + +
266B SER* 3.0 33.6 + - - +
267B ALA* 2.6 35.7 + - - +
298B LYS 6.1 0.7 - - - +
299B SER* 6.3 0.7 - - - -
302B GLU* 3.6 22.0 + - + +
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Residues in contact with VAL 264 (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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262B LEU 5.5 0.7 - - - +
263B THR* 1.3 78.3 + - - +
265B ARG* 1.3 64.1 + - - +
267B ALA* 3.9 7.9 - - + -
268B ASN* 3.0 41.3 + - - +
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Residues in contact with ARG 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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263B THR* 3.3 9.5 + - + +
264B VAL* 1.3 78.3 - - - +
266B SER* 1.3 57.5 + - - +
268B ASN* 5.0 1.5 - - - +
269B CYS* 3.1 24.8 + - - +
294B ASN* 3.5 50.2 + - + +
295B LEU* 6.0 0.2 - - - +
299B SER* 3.7 25.8 - - - +
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Residues in contact with SER 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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262B LEU* 4.3 8.2 - - - +
263B THR* 3.0 26.3 + - - +
265B ARG* 1.3 78.5 - - - +
267B ALA* 1.3 64.1 + - - +
269B CYS* 3.8 6.6 - - - +
270B LEU* 3.6 23.2 + - - +
295B LEU* 5.7 2.2 - - - -
299B SER* 3.0 27.8 + - - -
302B GLU* 3.6 6.7 - - - +
303B ILE* 3.7 22.2 - - - +
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Residues in contact with ALA 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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257B VAL* 4.9 7.1 - - - +
258B ASP* 6.0 3.8 - - - +
262B LEU* 3.8 25.6 - - + +
263B THR 2.6 20.9 + - - +
264B VAL* 3.0 11.6 + - + +
266B SER* 1.3 73.2 - - - +
268B ASN* 1.3 67.2 + - - +
270B LEU* 3.7 2.8 + - - +
271B LYS* 3.4 19.2 + - - +
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Residues in contact with ASN 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 VAL* 3.0 31.7 + - - +
265B ARG* 5.0 1.3 - - - +
267B ALA* 1.3 78.9 - - - +
269B CYS* 1.3 54.6 + - - +
270B LEU 3.2 0.2 - - - -
271B LYS* 3.0 36.8 - - - +
272B ALA* 2.6 36.1 + - - +
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Residues in contact with CYS 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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265B ARG 3.1 23.3 + - - +
266B SER* 4.1 7.2 - - - +
267B ALA 3.2 1.0 - - - -
268B ASN* 1.3 80.2 - - - +
270B LEU* 1.3 60.4 + - + +
272B ALA* 3.5 6.6 - - - +
273B GLU* 3.5 22.0 + - - +
292B THR* 3.7 10.9 - - - +
293B PRO 3.0 28.9 - - - -
294B ASN* 4.5 4.9 - - + -
295B LEU* 3.5 34.3 - - + +
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Residues in contact with LEU 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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257B VAL* 3.7 20.6 - - + -
262B LEU* 4.5 10.1 - - + -
266B SER 3.6 16.4 + - - +
267B ALA* 4.3 3.6 - - - +
268B ASN 3.2 0.4 - - - -
269B CYS* 1.3 76.8 - - + +
271B LYS* 1.3 59.2 + - - +
273B GLU 4.4 0.9 - - - +
274B ALA 4.0 1.4 + - - -
275B ILE* 2.7 78.9 + - + +
281B LEU* 3.5 43.1 - - + -
289B LEU* 5.6 7.4 - - + -
295B LEU* 6.0 4.7 - - + -
303B ILE* 4.6 9.4 - - + -
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Residues in contact with LYS 271 (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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95B LYS* 4.0 16.4 - - - +
118B ASP* 4.1 7.3 - - - +
119B GLY* 3.1 53.3 - - - +
120B ASP* 3.4 26.0 + - - +
257B VAL* 5.1 2.8 - - + +
267B ALA 3.4 8.7 + - - +
268B ASN* 3.0 50.3 - - + +
270B LEU* 1.3 79.0 - - - +
272B ALA* 1.3 62.9 + - - +
274B ALA* 3.5 8.1 + - - -
275B ILE 4.4 3.9 + - - -
276B HIS* 4.6 4.0 - - - -
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Residues in contact with ALA 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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119B GLY* 6.0 1.3 - - - -
268B ASN 2.6 18.0 + - - +
269B CYS* 3.5 12.6 - - - +
270B LEU 3.4 0.2 - - - -
271B LYS* 1.3 74.1 - - - +
273B GLU* 1.3 59.9 + - - +
274B ALA* 2.8 13.9 + - - +
293B PRO* 5.2 13.7 - - + +
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Residues in contact with GLU 273 (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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269B CYS 3.5 7.2 + - - +
270B LEU 4.2 0.2 + - - -
271B LYS 3.6 0.4 - - - -
272B ALA* 1.3 75.9 - - - +
274B ALA* 1.3 69.9 + - - +
275B ILE* 3.7 18.0 - - + +
284B ARG* 4.6 23.0 + - - +
288B GLU 5.0 0.2 - - - +
291B LYS 4.2 4.2 - - - +
292B THR* 3.2 43.7 + - + +
293B PRO* 3.0 27.5 - - - +
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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