Contacts of the helix formed by residues 259 - 269 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232F ARG* 3.5 32.5 - - + +
233F ILE* 6.1 0.4 - - + -
235F THR* 3.6 35.4 - - + -
236F GLY* 4.6 3.4 - - - +
239F LEU* 4.6 6.5 - - + -
255F GLN 5.0 4.3 - - - +
256F PRO 2.9 9.5 + - - +
258F THR* 1.3 87.5 - - + +
260F ASP* 1.3 65.2 + - - +
261F ALA 3.3 2.2 - - - -
262F VAL* 3.2 29.6 + - + +
263F LEU* 2.9 32.3 + - + +
280F ILE* 3.8 15.9 - - + -
303F PRO* 6.1 1.8 - - + -
306F MET* 5.6 1.6 - - + -
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Residues in contact with ASP 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D HIS* 4.3 9.7 + - - -
157D VAL* 4.3 22.4 - - + +
183D GLU* 3.1 33.3 - - + +
212D ARG* 4.9 2.3 + - - -
256F PRO 4.1 8.5 - - - +
257F ASP* 3.7 20.8 + - - +
258F THR 3.7 2.0 + - - -
259F LEU* 1.3 77.0 - - - +
261F ALA* 1.3 63.3 + - - +
263F LEU* 3.3 6.6 + - - +
264F ALA* 3.0 21.8 + - - +
267F ARG* 5.4 0.3 + - - -
299F HIS* 6.1 0.8 - - - -
300F PRO* 5.5 7.9 - - + +
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Residues in contact with ALA 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D VAL* 4.1 15.4 - - + +
259F LEU 3.3 0.6 - - - -
260F ASP* 1.3 76.9 - - - +
262F VAL* 1.3 61.7 + - - +
264F ALA* 3.3 4.0 + - - +
265F LYS* 3.1 28.2 + - + +
300F PRO 3.6 22.8 + - - +
301F ALA* 3.8 3.1 - - - +
302F PHE* 3.7 31.0 - - + +
303F PRO* 5.0 1.6 - - + -
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Residues in contact with VAL 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236F GLY* 4.6 14.4 - - - +
239F LEU* 5.2 0.9 - - + -
259F LEU* 3.2 29.2 + - + +
261F ALA* 1.3 73.2 - - - +
263F LEU* 1.3 71.3 + - + +
265F LYS* 3.2 4.0 + - - +
266F LEU* 3.1 34.4 + - + +
302F PHE* 4.3 15.3 - - + -
303F PRO* 4.1 18.8 - - + -
306F MET* 4.0 23.8 - - + -
310F PHE* 4.0 16.3 - - + -
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Residues in contact with LEU 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239F LEU* 3.7 30.3 - - + -
256F PRO* 4.4 11.9 - - + +
259F LEU* 2.9 34.4 + - + +
260F ASP* 3.9 5.6 - - - +
262F VAL* 1.3 76.3 - - + +
264F ALA* 1.3 62.0 + - - +
266F LEU* 3.2 7.7 + - + +
267F ARG* 3.1 43.1 + - - +
273F ILE* 3.8 19.3 - - + +
275F VAL* 4.1 25.4 - - + -
280F ILE* 4.1 18.2 - - + -
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Residues in contact with ALA 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D VAL* 3.9 30.5 - - + +
260F ASP 3.0 13.6 + - - +
261F ALA* 3.5 9.2 - - - +
263F LEU* 1.3 75.6 - - - +
265F LYS* 1.3 66.7 + - + +
267F ARG* 3.2 17.2 + - - +
268F ASP* 3.0 29.9 + - - +
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Residues in contact with LYS 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ASP* 2.6 31.4 + - - +
261F ALA* 3.1 19.0 + - + +
262F VAL 3.2 4.9 + - - +
264F ALA* 1.3 78.6 - - + +
266F LEU* 1.3 55.7 - - - +
268F ASP* 3.2 23.5 + - - +
269F ALA* 3.0 26.3 + - - +
292F VAL* 3.8 12.9 - - + +
293F ASN 2.8 31.1 + - - +
294F VAL* 3.9 23.8 - - + +
295F ARG 5.7 0.7 - - - +
302F PHE* 4.5 13.5 - - + -
310F PHE* 3.6 21.7 - - + -
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Residues in contact with LEU 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239F LEU* 3.8 23.1 - - + -
240F VAL* 4.4 8.7 - - + +
243F ALA* 4.2 15.7 - - + -
262F VAL* 3.1 30.2 + - + +
263F LEU* 3.2 2.9 + - + +
265F LYS* 1.3 71.2 - - - +
267F ARG* 1.3 67.4 + - - +
269F ALA* 3.0 15.5 + - + +
270F GLY 3.2 0.7 + - - -
271F ALA* 3.1 18.8 + - + +
273F ILE* 3.6 20.0 - - + -
282F LEU* 3.7 22.4 - - + -
310F PHE* 3.6 22.9 - - + -
313F LEU* 4.1 18.4 - - + -
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Residues in contact with ARG 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D HIS* 5.9 7.8 - - - -
157D VAL* 6.0 2.8 - - - +
260F ASP 5.4 0.2 + - - -
263F LEU* 3.1 40.4 + - - +
264F ALA* 3.2 13.6 + - - +
266F LEU* 1.3 76.3 - - - +
268F ASP* 1.3 56.7 + - - +
270F GLY* 2.7 26.5 + - - -
271F ALA 3.6 18.2 + - - +
273F ILE* 4.2 40.5 + - + +
275F VAL* 5.1 6.1 - - - +
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Residues in contact with ASP 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D ASP* 5.1 3.1 - - - +
264F ALA* 3.0 19.9 + - - +
265F LYS* 3.2 28.3 + - - +
267F ARG* 1.3 76.7 - - - +
269F ALA* 1.3 60.6 + - - +
270F GLY* 3.1 1.3 + - - -
290F LYS* 4.2 9.0 - - - +
291F ALA 4.8 1.4 - - - +
292F VAL* 3.8 17.0 - - + +
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Residues in contact with ALA 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243F ALA* 6.1 0.9 - - + -
265F LYS 3.0 10.8 + - - +
266F LEU* 3.0 14.7 + - + +
268F ASP* 1.3 75.4 - - - +
270F GLY* 1.3 58.8 + - - +
271F ALA* 5.8 0.2 - - + -
284F MET* 4.4 3.1 - - + +
288F ARG 4.6 0.5 - - - +
289F PRO* 3.5 10.1 - - + +
290F LYS* 2.7 52.0 + - - +
292F VAL* 3.7 5.1 - - + +
310F PHE* 5.8 0.4 - - + -
313F LEU* 4.1 26.2 - - + -
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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