Contacts of the helix formed by residues 264 - 272 (chain B) in PDB entry 1L9X
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 SER 264 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262B PHE* 3.2 7.1 - - - +
263B LYS* 1.3 83.9 - - - +
265B GLU* 1.3 63.4 + - - +
266B SER* 3.6 9.2 + - - -
267B GLU* 3.2 29.5 + - - +
268B GLU* 3.1 22.5 + - - +
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Residues in contact with GLU 265 (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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264B SER* 1.3 72.0 - - - +
266B SER* 1.3 57.3 + - - +
268B GLU* 3.6 11.3 - - - +
269B GLU* 2.8 32.6 + - - +
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Residues in contact with SER 266 (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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264B SER* 3.9 8.9 - - - -
265B GLU* 1.3 80.9 - - - +
267B GLU* 1.3 66.3 + - - +
269B GLU* 3.5 6.6 + - - +
270B LYS* 2.9 52.5 + - - +
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Residues in contact with GLU 267 (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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262B PHE* 3.9 15.7 - - + -
263B LYS* 3.4 37.0 + - + -
264B SER* 3.2 22.7 + - - +
266B SER* 1.3 82.8 + - - +
268B GLU* 1.3 63.1 + - - +
270B LYS* 3.5 12.6 + - - +
271B ALA* 3.2 23.7 + - - +
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Residues in contact with GLU 268 (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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11B ILE* 3.7 26.6 - - + +
46B ARG* 2.9 33.4 + - - +
261B HIS* 5.9 1.6 - - - +
262B PHE* 3.6 27.9 + - + +
264B SER 3.1 13.8 + - - +
265B GLU* 3.6 13.9 - - - +
267B GLU* 1.3 76.5 - - - +
269B GLU* 1.3 63.7 + - - +
271B ALA* 3.1 12.1 + - - +
272B LEU* 3.3 23.2 + - + +
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Residues in contact with GLU 269 (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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280A TYR* 2.7 46.1 + - + +
283A ASN* 3.7 18.9 + - - +
265B GLU 2.8 21.2 + - - +
266B SER* 3.8 7.7 - - - +
267B GLU 3.4 0.2 - - - -
268B GLU* 1.3 76.0 + - - +
270B LYS* 1.3 66.9 + - + +
271B ALA 3.4 0.5 + - - -
272B LEU* 3.6 16.4 + - + +
275B GLN* 3.2 23.8 + - - +
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Residues in contact with LYS 270 (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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266B SER* 2.9 39.7 + - - +
267B GLU* 4.0 13.0 - - - +
268B GLU 3.3 0.4 - - - -
269B GLU* 1.3 81.7 + - + +
271B ALA* 1.3 60.3 + - - +
272B LEU 3.5 0.2 - - - -
275B GLN* 3.8 19.9 - - - +
276B PHE* 4.5 7.8 - - - -
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Residues in contact with ALA 271 (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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48B VAL* 3.6 16.2 - - + +
49B PRO* 3.3 20.6 - - - +
62B LEU* 5.5 2.5 - - + -
262B PHE* 3.7 26.7 - - + -
267B GLU 3.2 15.8 + - - +
268B GLU 3.1 5.4 + - - +
270B LYS* 1.3 77.7 - - - +
272B LEU* 1.3 64.8 + - - +
276B PHE* 4.4 2.3 - - - -
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Residues in contact with LEU 272 (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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280A TYR* 6.1 1.3 - - + +
288A GLN* 5.5 1.6 - - - +
11B ILE* 4.0 23.1 - - + -
46B ARG* 3.8 34.1 - - + +
47B VAL 3.5 13.7 - - - +
48B VAL* 3.8 14.6 - - + -
49B PRO* 4.2 0.2 - - - -
268B GLU* 3.3 20.6 + - + +
269B GLU* 3.6 13.9 + - + +
270B LYS 3.5 1.2 - - - -
271B ALA* 1.3 81.1 - - - +
273B ILE* 1.3 65.1 + - + +
274B TYR* 3.0 36.8 + - + +
275B GLN* 3.0 19.1 + - - +
276B PHE* 3.6 4.5 - - - -
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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