Contacts of the helix formed by residues 251 - 262 (chain B) in PDB entry 6VWW
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 LEU 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236B ILE* 4.3 6.2 + - + -
237B VAL* 4.3 17.5 - - + +
249B LEU 3.7 0.4 - - - -
250B HIS* 1.3 87.7 - - + +
252B LEU* 1.3 61.4 + - - +
253B ILE* 3.2 13.5 - - + -
254B GLY* 2.9 20.4 + - - -
255B LEU* 3.2 14.5 + - - +
296B ILE* 3.6 15.3 - - + +
298B LEU* 4.9 10.8 - - + +
300B LEU* 3.7 25.1 - - + -
303B PHE* 3.6 61.9 - - + -
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Residues in contact with LEU 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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199B ARG 3.2 32.1 - - - +
200B ASN* 4.4 2.5 - - - +
201B LEU* 3.7 28.0 - - + +
204B PHE* 4.1 13.0 - - + -
251B LEU* 1.3 72.0 - - - +
253B ILE* 1.3 57.1 + - - +
255B LEU* 3.0 15.4 + - + +
256B ALA* 2.9 25.5 + - - +
279B TYR* 5.9 3.8 - - + +
295B VAL* 3.8 16.8 - - + +
296B ILE 3.3 8.2 + - - +
297B ASP* 3.5 39.0 - - + +
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Residues in contact with ILE 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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199B ARG* 5.5 1.1 - - - +
204B PHE* 3.6 31.4 - - + -
211B GLU* 3.7 49.1 - - + +
214B PHE* 3.4 34.2 - - + -
215B LEU* 4.0 6.2 - - + +
237B VAL* 4.5 2.2 - - + -
251B LEU* 4.2 17.3 - - + -
252B LEU* 1.3 78.6 - - - +
254B GLY* 1.3 65.0 + - - +
256B ALA* 3.3 3.1 + - - +
257B LYS* 3.1 18.5 + - - +
297B ASP* 5.1 1.2 + - - +
298B LEU 5.4 4.7 + - - +
300B LEU* 4.2 20.6 - - + -
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Residues in contact with GLY 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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214B PHE* 3.9 14.1 - - - -
237B VAL* 3.4 21.0 - - - +
238B TYR* 5.0 2.4 - - - +
249B LEU* 3.9 9.9 - - - +
251B LEU 2.9 10.1 + - - -
253B ILE* 1.3 84.4 - - - +
255B LEU* 1.3 59.7 + - - +
257B LYS* 3.5 3.1 + - - +
258B ARG* 3.3 21.7 + - - +
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Residues in contact with LEU 255 (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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201B LEU* 3.6 16.2 - - + -
249B LEU* 3.7 37.7 - - + +
251B LEU 3.2 29.6 - - - +
252B LEU* 3.0 13.7 + - + +
254B GLY* 1.3 74.4 - - - +
256B ALA* 1.3 59.6 + - - +
258B ARG* 3.3 2.6 + - - +
259B PHE* 2.9 30.8 + - - +
264B PHE* 3.5 15.3 - - + -
266B LEU* 4.2 27.1 - - + -
279B TYR* 5.3 2.2 - - + -
281B ILE* 4.4 9.9 - - + -
295B VAL* 3.9 24.9 - - + -
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Residues in contact with ALA 256 (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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201B LEU* 3.4 16.3 - - + +
204B PHE* 3.7 41.5 - - + -
215B LEU* 5.0 4.5 - - + -
252B LEU 2.9 13.4 + - - +
253B ILE 3.3 5.6 + - - +
255B LEU* 1.3 75.8 - - - +
257B LYS* 1.3 61.6 + - - +
259B PHE* 3.9 3.5 - - - +
260B LYS* 3.4 27.7 + - - +
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Residues in contact with LYS 257 (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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214B PHE* 3.0 41.3 + - + +
215B LEU* 2.8 41.6 + - + +
216B GLU 4.6 0.6 + - - -
217B LEU 3.3 14.9 + - - -
218B ALA* 5.4 2.2 - - - +
219B MET 5.5 0.4 - - - +
238B TYR* 4.2 18.4 - - + -
253B ILE 3.1 16.3 + - - +
254B GLY 3.8 5.2 - - - +
255B LEU 3.2 0.2 - - - -
256B ALA* 1.3 79.6 - - - +
258B ARG* 1.3 61.1 + - - +
259B PHE 3.4 0.2 + - - -
260B LYS* 3.7 7.4 + - - +
261B GLU* 3.3 34.9 + - - +
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Residues in contact with ARG 258 (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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238B TYR 5.6 1.6 - - - +
241B PHE* 3.7 45.3 - - + +
249B LEU* 5.3 3.6 - - + -
254B GLY 3.3 14.2 + - - +
255B LEU* 3.8 5.6 - - - +
257B LYS* 1.3 78.7 - - - +
259B PHE* 1.3 61.7 + - - +
261B GLU* 3.2 20.2 + - - +
262B SER* 2.9 41.9 + - - +
264B PHE* 3.7 20.0 - - + -
283B ASP* 2.8 39.6 + - - +
285B GLN* 4.2 5.3 - - - +
286B THR* 3.7 15.6 - - - +
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Residues in contact with PHE 259 (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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201B LEU* 4.1 25.1 - - + +
202B GLN* 5.1 11.7 - - + -
255B LEU 2.9 17.5 + - - +
256B ALA* 3.9 5.2 - - - +
257B LYS 3.3 0.4 - - - -
258B ARG* 1.3 78.5 - - - +
260B LYS* 1.3 81.7 + - - +
261B GLU 3.2 0.9 + - - -
262B SER 3.6 12.9 - - - +
263B PRO* 4.1 20.2 - - + +
264B PHE* 3.5 44.4 - + + -
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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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201B LEU 4.6 3.6 + - - -
202B GLN* 3.8 20.8 + - - +
256B ALA 3.4 14.9 + - - +
257B LYS* 4.2 6.1 - - - +
258B ARG 3.4 0.4 - - - -
259B PHE* 1.3 98.2 - - - +
261B GLU* 1.3 64.1 + - + +
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Residues in contact with GLU 261 (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 LYS* 3.3 37.2 + - - +
258B ARG* 3.6 26.1 + - - +
259B PHE 3.1 0.8 - - - -
260B LYS* 1.3 84.1 - - + +
262B SER* 1.3 61.6 + - - +
263B PRO* 4.6 2.1 - - - +
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Residues in contact with SER 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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258B ARG* 2.9 44.8 + - - +
259B PHE 3.6 4.0 - - - +
261B GLU* 1.3 80.7 - - - +
263B PRO* 1.3 74.6 - - - +
264B PHE* 3.5 8.7 - - - -
283B ASP* 4.2 2.1 + - - -
285B GLN* 4.1 30.4 - - - +
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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