Contacts of the helix formed by residues 252 - 260 (chain B) in PDB entry 1Q8Z
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 ASN 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251B GLU* 1.3 79.1 - - - +
253B LEU* 1.3 60.4 - - - +
254B LEU* 3.0 33.7 + - - +
255B ALA* 3.1 15.8 + - - +
256B LEU* 4.1 1.6 + - - +
297B PRO 3.7 1.1 - - - +
298B GLU* 3.5 40.2 + - - +
300B VAL 3.2 11.4 - - - +
301B LEU* 3.8 13.0 - - + +
302B MET* 5.2 1.3 - - - +
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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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252B ASN* 1.3 70.0 - - - +
254B LEU* 1.3 58.4 + - - +
255B ALA 3.2 0.2 - - - -
256B LEU* 3.2 10.2 + - + +
257B ILE* 2.9 34.6 + - - +
273B ILE* 3.9 31.9 - - + -
297B PRO* 3.3 18.2 + - + +
300B VAL* 3.0 51.7 + - + +
302B MET* 3.8 27.4 - - + -
546B ILE* 4.6 0.7 - - + -
593B LEU* 4.4 11.0 - - + -
597B LEU* 4.1 23.1 - - + -
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Residues in contact with LEU 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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252B ASN* 3.0 15.6 + - - +
253B LEU* 1.3 77.3 - - - +
255B ALA* 1.3 63.4 + - - +
257B ILE* 3.7 12.4 - - + +
258B LYS* 2.9 53.9 + - + +
262B HIS* 6.1 2.7 - - - +
297B PRO* 4.3 18.3 + - + -
298B GLU* 3.4 42.6 - - + +
596B GLU* 5.6 2.0 - - - +
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Residues in contact with ALA 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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251B GLU* 3.6 36.8 - - + +
252B ASN* 3.1 5.8 + - - +
254B LEU* 1.3 80.3 - - - +
256B LEU* 1.3 52.1 + - - +
258B LYS* 3.7 9.1 - - - +
259B LYS* 2.7 36.0 + - - +
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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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252B ASN 4.1 1.2 + - - +
253B LEU* 3.2 15.7 + - + +
255B ALA* 1.3 79.9 - - - +
257B ILE* 1.3 63.4 + - - +
259B LYS* 3.0 19.8 + - + +
260B TYR* 3.1 35.0 + - + -
265B ILE* 3.4 29.8 - - + -
269B TYR* 4.9 8.1 - - + -
273B ILE* 3.6 31.0 - - + -
302B MET* 4.0 22.7 - - + -
544B ILE* 5.3 1.1 - - + -
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Residues in contact with ILE 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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253B LEU 2.9 17.0 + - - +
254B LEU* 3.7 13.2 - - + +
256B LEU* 1.3 76.3 - - - +
258B LYS* 1.3 56.7 + - + +
260B TYR* 2.9 26.5 + - - +
262B HIS* 3.3 40.3 + - + +
265B ILE* 4.1 21.3 - - + -
297B PRO* 4.0 23.1 - - + -
593B LEU* 5.5 0.2 - - + -
596B GLU* 4.4 26.2 - - + +
597B LEU* 4.1 15.7 - - + -
600B GLY* 4.8 11.2 - - - +
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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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254B LEU* 2.9 47.4 + - + +
255B ALA* 3.8 6.7 - - - +
257B ILE* 1.3 70.5 - - + +
259B LYS* 1.3 56.4 + - - +
260B TYR 2.8 5.2 - - - -
261B GLU* 2.6 32.0 + - - +
262B HIS* 4.3 25.2 + - + -
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Residues in contact with LYS 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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255B ALA 2.7 19.2 + - - +
256B LEU* 3.0 22.0 + - + +
258B LYS* 1.3 73.2 - - - +
260B TYR* 1.3 83.9 + - + +
261B GLU* 3.7 4.5 + - - +
304B ILE* 5.7 7.1 - - - +
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Residues in contact with TYR 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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256B LEU* 3.1 35.6 + - + +
257B ILE 2.9 7.9 + - - +
258B LYS 2.8 0.8 - - - -
259B LYS* 1.3 105.3 + - + +
261B GLU* 1.3 53.7 + - - +
262B HIS* 2.7 3.4 + - - -
263B ARG* 2.6 38.3 + - + +
264B GLY 3.5 23.6 - - - +
265B ILE* 4.3 2.7 - - + -
266B PRO* 3.3 40.7 - - + +
269B TYR* 3.8 15.7 + + - -
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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