Contacts of the helix formed by residues 291 - 295 (chain B) in PDB entry 1O9S
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 291 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B PRO* 6.4 1.1 - - + -
212B GLU* 3.0 25.5 + - + +
213B SER* 6.4 0.2 - - - -
216B VAL* 4.1 25.8 - - + +
217B TYR* 5.3 1.6 - - - -
218B VAL* 4.1 25.8 - - + -
230B LEU* 4.0 15.5 - - + +
243B SER* 3.3 6.4 + - - +
284B VAL* 4.4 11.4 - - + -
288B CYS* 4.2 26.9 - - + +
290B SER* 1.3 81.1 - - - +
292B GLY* 1.3 66.6 + - - +
293B HIS* 3.2 12.1 - - + -
294B LYS* 2.9 20.4 + - + +
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Residues in contact with GLY 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LEU* 4.7 0.9 - - - -
243B SER* 3.0 13.3 + - - -
244B PHE 2.8 21.7 + - - -
245B TYR* 3.6 16.5 - - - -
290B SER 3.8 0.6 - - - -
291B LEU* 1.3 77.4 - - - +
293B HIS* 1.3 58.1 + - - +
294B LYS 3.1 4.7 + - - -
295B ALA* 3.2 19.9 + - - +
305B TYR* 4.8 0.9 - - - -
319B ILE* 3.8 16.0 - - - +
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Residues in contact with HIS 293 (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 TYR* 3.6 33.7 - - + +
246B ASN 5.0 0.8 + - - -
265B ASN* 4.1 13.0 - - - +
277B VAL* 3.6 32.3 - - + +
281B TYR 3.8 11.9 + - - -
282B ASN* 4.3 3.5 - - - -
283B HIS 5.9 0.2 - - - -
284B VAL* 5.8 0.8 - - - +
287B TYR* 4.0 19.5 + + - -
290B SER* 3.2 28.9 + - - -
291B LEU* 3.7 15.8 - - + +
292B GLY* 1.3 75.9 + - - +
294B LYS* 1.3 82.4 + - + +
295B ALA 3.3 0.4 - - - -
1367B SAH 3.2 28.9 - - - +
4L MLZ 3.9 4.1 - - - -
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Residues in contact with LYS 294 (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 VAL* 4.0 30.3 - - + -
228B GLU* 2.7 32.5 + - + +
229B GLY* 3.3 25.0 - - - -
230B LEU* 4.0 8.7 - - + -
282B ASN* 2.8 32.6 + - - -
283B HIS* 4.6 4.0 + - - +
284B VAL* 4.4 12.8 - - + -
291B LEU* 2.9 15.8 + - + +
293B HIS* 1.3 93.9 - - + +
295B ALA* 1.3 62.8 + - - +
296B ASN 3.3 0.9 + - - -
1367B SAH 3.5 37.3 + - + +
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Residues in contact with ALA 295 (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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230B LEU* 3.9 20.8 - - + +
292B GLY 3.2 15.2 + - - +
294B LYS* 1.3 77.2 - - - +
296B ASN* 1.3 55.2 + - - +
305B TYR* 4.3 2.2 + - - +
319B ILE* 4.0 18.4 - - + -
331B LEU* 3.8 16.6 - - + +
333B VAL* 4.3 11.0 - - + -
335B TYR* 2.7 28.3 + - - -
1367B SAH 3.9 1.8 - - - +
4L MLZ 4.1 4.7 - - - -
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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