Contacts of the helix formed by residues 245 - 254 (chain B) in PDB entry 6VSU
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 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241B TYR* 5.3 0.2 - - - -
242B GLU* 3.1 14.8 + - + +
243B MET 3.0 0.8 - - - -
244B ARG* 1.3 103.4 - - + +
246B PHE* 1.3 61.3 + - - -
247B SER* 3.4 3.6 - - - -
248B LYS* 3.3 35.4 + - - +
249B ASP* 2.7 42.0 + - - +
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Residues in contact with PHE 246 (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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220B VAL* 5.3 2.0 - - + -
242B GLU 3.7 3.9 + - - -
243B MET* 3.1 45.1 + - + +
244B ARG 3.7 0.2 - - - -
245B THR* 1.3 74.9 - - - +
247B SER* 1.3 67.2 + - - +
249B ASP* 4.3 2.9 - - - +
250B ARG* 2.9 78.9 + - + +
253B LEU* 3.9 31.9 - - + -
254B GLU* 5.3 2.0 - - + -
290B LEU* 3.5 26.9 - - + -
294B ASP* 4.0 9.0 - - + -
298B ILE* 4.9 8.5 - - + -
293C ARG* 5.4 4.5 - - + -
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Residues in contact with SER 247 (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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245B THR* 5.1 1.3 - - - -
246B PHE* 1.3 78.9 - - - +
248B LYS* 1.3 59.1 - - - +
250B ARG* 4.1 13.1 + - - +
251B PRO* 4.2 4.0 - - - +
250C ARG* 5.6 0.7 + - - -
254C GLU* 4.3 7.1 + - - -
297C ASN* 3.3 27.7 + - - -
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Residues in contact with LYS 248 (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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245B THR* 3.3 36.0 + - - +
246B PHE 3.1 0.4 - - - -
247B SER* 1.3 77.2 - - - +
249B ASP* 1.3 75.7 + - - +
250B ARG 3.3 0.2 - - - -
251B PRO* 3.3 17.2 - - - +
252B MET* 5.2 1.0 + - - +
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Residues in contact with ASP 249 (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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241B TYR* 3.6 28.5 - - + +
242B GLU 4.3 2.9 - - - +
245B THR* 2.7 35.7 + - - +
246B PHE* 3.1 4.2 + - - +
248B LYS* 1.3 95.1 - - - +
250B ARG* 1.3 54.1 - - - +
251B PRO* 3.4 1.3 - - - -
252B MET* 3.3 10.9 + - - +
253B LEU* 2.8 52.7 + - + +
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Residues in contact with ARG 250 (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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247A SER* 5.5 0.8 + - - -
246B PHE* 2.9 55.7 + - + +
247B SER* 4.1 7.3 - - - +
249B ASP* 1.3 72.5 - - - +
251B PRO* 1.3 74.1 - - + +
253B LEU* 3.1 2.5 + - - -
254B GLU* 2.8 68.8 + - + +
294B ASP* 3.1 32.5 + - - -
297B ASN* 4.3 4.6 - - - +
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Residues in contact with PRO 251 (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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247B SER 4.2 4.5 - - - +
248B LYS 3.3 18.8 - - - +
249B ASP 3.5 1.1 - - - -
250B ARG* 1.3 98.5 - - + +
252B MET* 1.3 59.5 + - - +
254B GLU* 3.5 7.1 + - + +
255B ASN* 3.3 26.8 + - - +
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Residues in contact with MET 252 (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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216B ARG* 5.2 12.1 - - - +
218B LEU* 5.4 0.9 - - + -
239B GLU* 5.2 0.4 - - - +
241B TYR* 3.0 42.4 - - + +
248B LYS 5.7 0.7 - - - +
249B ASP* 3.3 10.0 + - - +
251B PRO* 1.3 79.8 - - - +
253B LEU* 1.3 63.5 + - - +
255B ASN* 3.1 24.3 + - - -
256B LEU* 3.5 22.8 + - + +
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Residues in contact with LEU 253 (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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218B LEU* 5.4 0.2 - - + -
220B VAL* 3.7 35.9 - - + -
241B TYR* 4.0 34.3 - - + -
246B PHE* 3.9 24.9 - - + -
249B ASP* 2.8 37.2 + - + +
250B ARG* 3.1 4.9 + - - +
252B MET* 1.3 71.9 - - - +
254B GLU* 1.3 56.5 + - + +
255B ASN 3.1 8.6 + - - -
256B LEU* 3.4 30.1 + - + +
298B ILE* 3.5 30.7 - - + +
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Residues in contact with GLU 254 (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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247A SER* 4.0 11.1 + - - -
246B PHE* 5.3 2.4 - - + -
250B ARG* 2.8 61.1 + - + +
251B PRO* 4.2 5.0 - - + +
252B MET 3.3 0.6 - - - -
253B LEU* 1.3 74.4 - - + +
255B ASN* 1.3 70.2 + - - +
294B ASP* 4.6 2.9 - - - +
297B ASN* 3.0 45.6 + - + +
298B ILE* 4.5 7.6 - - + +
301B ASN* 3.1 28.5 - - - +
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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