Contacts of the helix formed by residues 254 - 261 (chain B) in PDB entry 3H8Q
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 GLY 254 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B ALA 3.3 4.3 + - - -
251B TYR 3.5 6.1 + - - -
252B GLN 3.3 3.8 + - - -
253B SER* 1.3 78.1 + - - +
255B LEU* 1.3 62.7 + - - +
256B LEU 3.3 3.1 + - - -
257B GLN* 3.4 10.7 + - - +
258B LYS* 3.2 30.7 + - - +
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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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241B VAL* 6.2 2.0 - - + -
250B ALA* 3.0 17.4 + - + +
253B SER* 3.1 15.7 + - - +
254B GLY* 1.3 77.8 - - - +
256B LEU* 1.3 57.7 + - - +
258B LYS* 3.3 10.0 + - + +
259B LEU* 3.0 55.4 + - + +
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Residues in contact with LEU 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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196B LEU* 4.1 19.5 - - + -
197B PHE* 4.2 19.3 - - + -
200B LEU* 4.3 12.8 - - + -
236B VAL* 3.9 29.2 - - + -
241B VAL* 4.5 12.3 - - + -
247B THR* 4.0 21.8 - - + +
250B ALA* 3.0 26.9 + - + +
251B TYR* 3.9 11.9 - - + +
255B LEU* 1.3 77.7 - - - +
257B GLN* 1.3 60.8 + - - +
259B LEU* 3.2 6.7 + - + +
260B LEU* 3.1 35.7 + - + +
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Residues in contact with GLN 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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251B TYR* 5.7 5.9 - - + +
254B GLY* 3.4 12.6 + - - +
255B LEU 3.3 0.4 - - - -
256B LEU* 1.3 78.8 - - - +
258B LYS* 1.3 59.9 + - + +
260B LEU* 3.4 11.2 + - - +
261B GLN* 3.0 32.5 + - - +
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Residues in contact with LYS 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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3B SO4 2.8 39.7 + - - -
254B GLY* 3.2 19.5 + - - +
255B LEU* 3.6 14.1 - - + +
257B GLN* 1.3 76.0 - - - +
259B LEU* 1.3 65.5 + - + +
261B GLN* 3.4 42.1 + - + +
263B ASP* 5.6 0.5 - - - +
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Residues in contact with LEU 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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236B VAL* 3.9 19.1 - - + +
237B ASN* 2.7 33.4 + - + +
239B VAL* 4.4 32.8 - - + -
241B VAL* 3.9 28.3 - - + -
255B LEU* 3.0 44.6 + - + +
256B LEU* 3.2 11.4 + - + +
258B LYS* 1.3 78.3 - - + +
260B LEU* 1.3 52.4 + - - +
261B GLN 3.7 3.3 + - - +
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Residues in contact with LEU 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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178B ARG* 3.0 51.9 + - + +
179B VAL* 3.9 19.1 - - + -
197B PHE* 4.6 4.0 - - + -
200B LEU* 4.4 12.3 - - + -
202B VAL* 4.0 23.1 - - + -
236B VAL* 3.8 22.0 - - + -
237B ASN* 4.0 5.7 + - - +
256B LEU* 3.1 34.6 + - + +
257B GLN* 3.8 7.9 - - - +
259B LEU* 1.3 77.6 - - - +
261B GLN* 1.3 63.1 + - - +
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Residues in contact with GLN 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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3B SO4 4.6 4.2 + - - -
237B ASN* 4.9 2.3 + - - -
257B GLN* 3.0 15.2 + - - +
258B LYS* 3.4 47.0 + - + +
259B LEU 4.2 3.5 - - - +
260B LEU* 1.3 81.8 - - - +
262B GLU* 1.3 76.9 + - - +
263B ASP* 3.5 10.2 - - - +
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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