Contacts of the helix formed by residues 259 - 269 (chain H) in PDB entry 3SWD
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 259 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232H ARG* 3.4 34.1 - - + +
233H ILE* 6.1 0.4 - - + -
235H THR* 3.6 35.7 - - + +
236H GLY* 4.7 3.6 - - - +
239H LEU* 4.7 5.6 - - + -
255H GLN 4.9 5.4 - - - +
256H PRO 2.9 8.3 + - - +
258H THR* 1.3 88.1 - - + +
260H ASP* 1.3 65.1 + - - +
261H ALA 3.3 2.2 - - - -
262H VAL* 3.2 30.0 + - + -
263H LEU* 2.9 34.0 + - + +
280H ILE* 3.8 15.9 - - + -
303H PRO* 6.1 1.6 - - + -
306H MET* 5.6 1.8 - - + -
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Residues in contact with ASP 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A HIS* 3.8 15.5 - - + -
157A VAL* 4.1 22.2 - - + +
183A GLU* 3.0 28.5 - - + +
212A ARG* 4.6 2.1 + - - -
256H PRO 4.0 8.0 + - - +
257H ASP* 3.6 22.0 + - - +
258H THR 3.8 1.8 + - - -
259H LEU* 1.3 74.5 - - - +
261H ALA* 1.3 64.0 + - - +
263H LEU* 3.4 7.0 + - - +
264H ALA* 3.0 23.4 + - - +
267H ARG* 5.4 0.3 + - - -
299H HIS* 6.1 0.8 - - - -
300H PRO* 5.5 8.4 - - + +
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Residues in contact with ALA 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A VAL* 4.1 16.4 - - + +
259H LEU 3.3 1.0 - - - -
260H ASP* 1.3 76.7 - - - +
262H VAL* 1.3 63.1 + - - +
264H ALA* 3.3 5.1 + - - +
265H LYS* 3.1 27.4 + - + +
300H PRO 3.6 23.0 + - - +
301H ALA* 3.7 3.4 - - - +
302H PHE* 3.7 30.3 - - + +
303H PRO* 4.9 2.2 - - + -
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Residues in contact with VAL 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236H GLY* 4.6 13.9 - - - +
239H LEU* 5.1 0.9 - - + -
259H LEU* 3.2 31.1 + - + +
261H ALA* 1.3 75.4 - - - +
263H LEU* 1.3 68.1 + - + +
265H LYS* 3.2 5.0 + - - +
266H LEU* 3.0 38.2 + - + +
302H PHE* 4.3 15.5 - - + -
303H PRO* 4.0 24.9 - - + -
306H MET* 4.1 17.7 - - + -
310H PHE* 4.0 13.2 - - + -
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Residues in contact with LEU 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239H LEU* 3.7 30.5 - - + -
256H PRO* 4.4 11.9 - - + +
259H LEU* 2.9 33.3 + - + +
260H ASP* 4.0 5.6 - - - +
262H VAL* 1.3 76.1 - - + +
264H ALA* 1.3 64.0 + - - +
266H LEU* 3.2 5.9 + - + +
267H ARG* 3.1 42.0 + - - +
273H ILE* 3.8 18.7 - - + +
275H VAL* 4.1 24.5 - - + -
280H ILE* 4.1 19.1 - - + -
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Residues in contact with ALA 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A VAL* 4.5 21.8 - - + +
260H ASP 3.0 14.7 + - - +
261H ALA* 3.5 9.2 - - - +
263H LEU* 1.3 77.4 - - - +
265H LYS* 1.3 65.5 + - + +
267H ARG* 3.2 17.2 + - - +
268H ASP* 3.1 29.4 + - - +
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Residues in contact with LYS 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ASP* 3.1 29.6 + - - -
261H ALA* 3.1 18.2 + - + +
262H VAL 3.2 4.7 + - - +
264H ALA* 1.3 79.2 - - + +
266H LEU* 1.3 63.1 + - - +
268H ASP* 3.2 22.8 + - - +
269H ALA* 3.0 20.8 + - - +
292H VAL* 3.8 12.1 - - + +
293H ASN* 2.7 31.0 + - - +
294H VAL* 3.9 24.2 - - + +
295H ARG 5.6 0.9 - - - +
302H PHE* 4.5 12.1 - - + -
310H PHE* 3.6 22.1 - - + -
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Residues in contact with LEU 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239H LEU* 3.7 23.8 - - + -
240H VAL* 4.4 8.7 - - + +
243H ALA* 4.2 16.2 - - + -
262H VAL* 3.0 29.0 + - + +
263H LEU* 3.7 3.4 - - + +
264H ALA 3.2 0.4 - - - -
265H LYS* 1.3 71.4 - - - +
267H ARG* 1.3 66.6 + - - +
269H ALA* 3.0 16.3 + - + +
270H GLY 3.2 0.5 + - - -
271H ALA* 3.1 21.4 + - + +
273H ILE* 3.5 20.9 - - + -
282H LEU* 3.7 19.5 - - + -
310H PHE* 3.7 22.4 - - + -
313H LEU* 4.1 18.8 - - + -
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Residues in contact with ARG 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260H ASP 5.4 0.2 + - - -
263H LEU* 3.1 37.1 + - - +
264H ALA* 3.2 14.6 + - - +
266H LEU* 1.3 76.3 - - - +
268H ASP* 1.3 56.0 + - - +
270H GLY* 2.5 29.1 + - - -
271H ALA 3.5 18.5 + - - +
273H ILE* 4.1 40.7 + - + +
275H VAL* 5.1 6.1 - - - +
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Residues in contact with ASP 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264H ALA* 3.1 19.3 + - - +
265H LYS* 3.2 27.1 + - - +
267H ARG* 1.3 77.8 - - - +
269H ALA* 1.3 59.8 + - - +
270H GLY* 3.0 1.3 + - - -
290H LYS* 4.2 8.1 - - - +
291H ALA 4.7 1.0 - - - +
292H VAL* 3.7 17.3 - - + +
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Residues in contact with ALA 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243H ALA* 6.1 0.9 - - + -
265H LYS 3.0 11.6 + - - +
266H LEU* 3.0 13.2 + - + +
268H ASP* 1.3 74.8 - - - +
270H GLY* 1.3 58.7 + - - +
271H ALA* 3.7 0.9 - - + +
284H MET* 4.3 3.0 - - + +
288H ARG 4.7 0.3 - - - +
289H PRO* 3.5 10.4 - - + +
290H LYS* 2.8 50.9 + - - +
292H VAL* 3.7 5.1 - - + +
310H PHE* 5.8 0.2 - - + -
313H LEU* 4.2 25.8 - - + -
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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