Contacts of the helix formed by residues 263 - 268 (chain K) in PDB entry 6LTJ
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 GLN 263 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223K PHE* 5.3 19.1 - - + -
259K GLU* 2.5 29.7 + - - +
260K ALA* 3.1 9.7 - - - -
262K PHE* 1.3 91.2 - - + +
264K PRO* 1.3 66.6 - - - +
265K SER* 3.3 11.9 + - - -
266K PHE* 3.1 28.5 + - + +
267K LEU 3.1 7.8 + - - -
275K HIS* 4.9 3.8 + - - -
312K ARG* 6.2 0.9 - - - +
316K GLU* 5.0 2.8 - - - +
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Residues in contact with PRO 264 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180K LEU* 3.8 12.8 - - + -
260K ALA 3.4 12.1 - - - +
261K LEU 4.6 0.7 - - - +
262K PHE 3.5 8.7 - - - +
263K GLN* 1.3 87.3 - - - +
265K SER* 1.3 50.5 + - - +
267K LEU* 2.9 8.7 + - + +
268K GLY 2.7 28.4 + - - -
269K MET* 2.7 31.6 + - + +
271K SER 3.3 26.0 - - - +
272K CYS* 3.5 17.0 - - - +
273K GLY* 3.8 10.1 - - - +
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Residues in contact with SER 265 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263K GLN* 3.3 10.8 + - - -
264K PRO* 1.3 77.7 - - - +
266K PHE* 1.3 64.1 + - - +
268K GLY* 3.1 15.1 + - - -
269K MET 3.3 12.0 + - - -
270K GLU* 5.7 6.5 - - - -
271K SER 5.0 1.0 + - - -
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Residues in contact with PHE 266 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188K TYR* 2.7 46.5 + + - -
192K ILE* 4.2 6.1 - - + -
227K MET* 4.9 8.7 - - + -
256K ARG* 3.4 54.1 - - + -
259K GLU* 4.4 16.8 - - + -
260K ALA 4.8 2.7 - - - -
263K GLN* 3.1 25.8 + - + +
265K SER* 1.3 79.5 + - - +
267K LEU* 1.3 62.6 + - - +
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Residues in contact with LEU 267 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180K LEU* 5.2 9.9 - - + -
184K ASP* 4.3 20.0 - - + +
185K LEU* 4.6 9.2 - - + +
188K TYR* 3.2 50.8 - - + -
191K LYS* 5.5 2.3 - - - +
260K ALA* 3.7 28.5 - - + +
263K GLN 3.1 5.3 + - - -
264K PRO* 2.9 15.6 + - + +
266K PHE* 1.3 78.1 - - - +
268K GLY* 1.3 55.2 + - - -
269K MET* 3.4 33.0 - - + +
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Residues in contact with GLY 268 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264K PRO 2.7 6.4 + - - -
265K SER 3.1 13.1 + - - -
267K LEU* 1.3 78.3 - - - +
269K MET* 1.3 64.6 + - - +
270K GLU* 3.9 6.7 + - - +
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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