Contacts of the helix formed by residues 259 - 269 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232L ARG* 3.4 34.3 - - + +
233L ILE* 6.1 0.4 - - + -
235L THR* 3.5 35.9 - - + -
236L GLY* 4.7 2.0 - - - +
239L LEU* 4.6 7.2 - - + -
255L GLN 5.0 5.4 - - - +
256L PRO 2.9 9.2 + - - +
258L THR* 1.3 88.3 - - + +
260L ASP* 1.3 65.4 + - - +
261L ALA 3.4 2.2 - - - -
262L VAL* 3.2 29.4 + - + -
263L LEU* 2.9 32.2 + - + +
280L ILE* 3.8 15.7 - - + -
303L PRO* 6.1 1.3 - - + -
306L MET* 5.7 1.3 - - + -
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Residues in contact with ASP 260 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155I HIS* 4.6 12.9 - - + -
157I VAL* 4.9 16.6 - - + +
183I GLU* 3.6 24.3 - - + +
212I ARG* 4.8 2.8 + - - -
256L PRO 4.1 8.8 - - - +
257L ASP* 3.6 22.2 + - - +
258L THR 3.7 2.2 + - - -
259L LEU* 1.3 76.4 - - - +
261L ALA* 1.3 63.8 + - - +
263L LEU* 3.3 6.4 + - - +
264L ALA* 3.0 22.5 + - - +
267L ARG* 5.2 1.0 + - - -
299L HIS* 6.0 1.0 - - - -
300L PRO* 5.5 8.4 - - + +
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Residues in contact with ALA 261 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157I VAL* 4.7 13.8 - - + +
259L LEU 3.4 0.4 - - - -
260L ASP* 1.3 76.6 - - - +
262L VAL* 1.3 64.8 + - + +
264L ALA* 3.3 8.5 + - - +
265L LYS* 3.0 26.8 + - + +
300L PRO 3.7 23.0 + - - +
301L ALA* 3.8 2.9 - - - +
302L PHE* 3.7 30.5 - - + +
303L PRO* 5.0 1.6 - - + -
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Residues in contact with VAL 262 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236L GLY* 4.6 14.4 - - - +
239L LEU* 5.2 0.9 - - + -
259L LEU* 3.2 31.5 + - + +
261L ALA* 1.3 75.8 - - - +
263L LEU* 1.3 67.1 + - + +
265L LYS* 3.3 3.8 + - - +
266L LEU* 3.0 34.5 + - + +
302L PHE* 4.3 14.4 - - + -
303L PRO* 4.1 24.7 - - + -
306L MET* 4.1 17.7 - - + -
310L PHE* 4.0 16.3 - - + -
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Residues in contact with LEU 263 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239L LEU* 3.7 29.8 - - + -
256L PRO* 4.3 12.1 - - + +
259L LEU* 2.9 32.8 + - + +
260L ASP* 3.9 5.6 - - - +
262L VAL* 1.3 71.7 - - + +
264L ALA* 1.3 64.6 + - - +
266L LEU* 3.2 5.9 + - + +
267L ARG* 3.1 31.3 + - - +
273L ILE* 3.8 21.6 - - + +
275L VAL* 4.2 24.9 - - + -
280L ILE* 4.1 19.1 - - + -
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Residues in contact with ALA 264 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157I VAL* 4.7 17.0 - - + -
260L ASP 3.0 13.4 + - - +
261L ALA* 3.3 12.1 + - - +
263L LEU* 1.3 76.5 - - - +
265L LYS* 1.3 66.2 + - + +
267L ARG* 3.1 32.3 + - - +
268L ASP* 3.1 28.8 + - - +
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Residues in contact with LYS 265 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159I ASP* 3.7 22.9 + - - -
261L ALA* 3.0 19.1 + - + +
262L VAL 3.8 4.0 - - - +
264L ALA* 1.3 80.3 - - + +
266L LEU* 1.3 62.6 + - - +
268L ASP* 3.2 21.4 + - - +
269L ALA* 3.1 20.3 + - - +
292L VAL* 3.9 12.7 - - + +
293L ASN 2.9 30.4 + - - +
294L VAL* 3.9 24.5 - - + +
295L ARG 5.7 0.7 - - - +
302L PHE* 4.5 13.5 - - + -
310L PHE* 3.6 20.9 - - + -
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Residues in contact with LEU 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239L LEU* 3.8 23.8 - - + -
240L VAL* 4.3 8.7 - - + +
243L ALA* 4.2 15.9 - - + -
262L VAL* 3.0 28.6 + - + +
263L LEU* 3.2 4.0 + - + +
265L LYS* 1.3 72.2 - - - +
267L ARG* 1.3 66.0 + - - +
269L ALA* 3.0 15.8 + - + +
270L GLY 3.2 0.7 + - - -
271L ALA* 3.1 22.0 + - + +
273L ILE* 3.6 20.2 - - + -
282L LEU* 3.7 17.9 - - + -
310L PHE* 3.6 23.1 - - + -
313L LEU* 4.1 18.4 - - + -
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Residues in contact with ARG 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155I HIS* 5.4 13.9 + - - +
157I VAL* 5.3 6.1 - - - +
260L ASP 5.2 1.0 + - - -
263L LEU* 3.1 16.9 + - - +
264L ALA* 3.1 36.6 + - - +
266L LEU* 1.3 73.4 - - - +
268L ASP* 1.3 57.9 + - - +
270L GLY* 2.5 30.3 + - - -
271L ALA 3.4 19.6 + - - +
273L ILE* 4.3 19.1 - - + +
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Residues in contact with ASP 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264L ALA* 3.1 18.7 + - - +
265L LYS* 3.2 26.4 + - - +
267L ARG* 1.3 76.9 - - - +
269L ALA* 1.3 58.6 + - - +
270L GLY 3.0 1.1 + - - -
290L LYS* 4.2 9.0 - - - +
291L ALA 4.7 1.0 - - - +
292L VAL* 3.7 18.6 - - + +
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Residues in contact with ALA 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243L ALA* 6.1 0.7 - - + -
265L LYS 3.1 10.3 + - - +
266L LEU* 3.0 13.6 + - + +
268L ASP* 1.3 75.8 - - - +
270L GLY* 1.3 60.2 + - - +
271L ALA* 5.7 0.7 - - + -
284L MET* 4.4 2.8 - - + +
288L ARG 4.7 0.3 - - - +
289L PRO* 3.5 10.1 - - + +
290L LYS* 2.7 51.0 + - - +
292L VAL* 3.8 4.9 - - + -
313L LEU* 4.2 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