Contacts of the helix formed by residues 264 - 271 (chain A) in PDB entry 1SEK
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 ALA 264 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A GLU* 3.9 5.5 - - - +
225A LEU* 4.1 22.8 - - + +
258A LYS* 3.6 23.8 - - + +
259A LEU* 4.3 8.1 - - + -
261A ASP* 3.1 8.6 + - + +
263A LYS* 1.3 75.9 - - - +
265A LEU* 1.3 58.9 + - - +
267A ARG* 3.1 24.5 + - - +
268A ALA* 3.0 28.8 + - - +
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Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A MET* 3.8 12.3 - - + -
242A ILE* 5.2 4.3 - - + -
244A ILE* 3.6 31.2 - - + -
259A LEU* 4.3 14.7 - - + +
261A ASP 4.7 0.8 + - - -
262A PRO 5.2 6.1 - - - +
263A LYS 3.2 0.6 - - - +
264A ALA* 1.3 77.2 - - - +
266A SER* 1.3 64.1 + - - +
268A ALA* 3.3 4.8 + - + +
269A GLU* 3.0 37.3 + - - +
368A PHE* 4.5 18.8 - - + -
370A SER* 5.1 5.6 - - - +
372A LYS* 4.8 11.7 - - + +
377A SER* 4.6 15.0 - - - +
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Residues in contact with SER 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASP* 4.6 7.8 + - - -
262A PRO 4.4 4.2 + - - -
263A LYS* 3.1 35.0 + - - +
265A LEU* 1.3 78.6 - - - +
267A ARG* 1.3 63.3 + - - +
269A GLU* 3.4 15.1 + - - +
270A GLU* 3.3 24.9 + - - +
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Residues in contact with ARG 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A VAL* 5.7 0.2 - - - -
224A GLU* 2.6 33.7 + - - +
261A ASP* 2.9 25.9 + - - -
263A LYS* 2.9 26.7 + - - +
264A ALA* 3.1 27.1 - - - +
265A LEU 3.2 0.2 - - - -
266A SER* 1.3 79.3 - - - +
268A ALA* 1.3 62.4 + - - +
270A GLU* 3.3 21.2 + - - +
271A ARG* 3.9 8.5 + - - +
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ALA* 4.5 1.6 - - - +
222A VAL* 3.8 31.0 - - + +
224A GLU* 4.8 0.4 + - - +
225A LEU* 4.1 13.0 - - + -
229A MET* 4.0 19.7 - - + +
264A ALA 3.0 15.4 + - - +
265A LEU* 3.7 6.1 - - - +
267A ARG* 1.3 77.9 - - - +
269A GLU* 1.3 58.4 + - - +
271A ARG* 3.0 26.4 + - - +
272A LEU* 3.8 7.6 + - - +
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Residues in contact with GLU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ARG* 5.3 2.9 + - - -
229A MET* 4.0 15.9 - - + -
231A GLU* 4.4 3.2 - - - +
242A ILE* 4.1 14.2 - - + +
265A LEU* 3.0 31.0 + - - +
266A SER* 3.6 15.9 + - - +
267A ARG 3.3 0.2 - - - -
268A ALA* 1.3 71.3 - - - +
270A GLU* 1.3 61.8 + - - +
271A ARG 3.0 6.3 + - - -
272A LEU* 3.1 35.2 + - + +
372A LYS* 3.2 30.1 + - - +
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Residues in contact with GLU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A SER 3.3 11.7 + - - +
267A ARG* 3.3 14.7 + - - +
268A ALA 3.2 0.8 - - - -
269A GLU* 1.3 78.0 - - - +
271A ARG* 1.3 59.6 + - + +
272A LEU 3.8 3.0 + - - +
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Residues in contact with ARG 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ALA* 3.6 15.5 - - + +
221A ASP* 2.6 36.8 + - - +
222A VAL* 4.2 19.3 - - - +
223A PRO* 3.8 21.3 - - - +
267A ARG 4.3 8.5 - - - +
268A ALA 3.0 11.8 + - - +
269A GLU 3.0 0.8 - - - -
270A GLU* 1.3 81.7 - - + +
272A LEU* 1.3 63.6 + - - +
273A TYR* 3.6 11.6 + - - +
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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