Contacts of the helix formed by residues 259 - 274 (chain A) in PDB entry 5FSJ
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 GLY 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A SER* 2.8 25.4 + - - -
246A GLN* 4.8 1.8 - - - -
257A GLY 3.7 0.4 - - - -
258A ILE* 1.3 82.1 - - - +
260A ARG* 1.3 65.7 + - - -
261A ASP 3.4 2.6 + - - -
262A LYS 3.5 1.7 + - - -
263A LEU* 3.1 19.6 + - - +
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Residues in contact with ARG 260 (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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175A LEU* 3.8 21.6 - - + +
178A PHE* 3.3 64.6 - - - +
186A TRP* 3.7 9.6 - - + -
245A SER* 3.1 16.1 + - - +
246A GLN* 4.0 17.6 + - - +
259A GLY* 1.3 70.0 - - - -
261A ASP* 1.3 72.8 + - - +
263A LEU* 3.3 5.6 + - - +
264A GLY* 2.9 21.1 + - - -
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Residues in contact with ASP 261 (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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87A VAL* 6.1 4.5 - - + +
259A GLY 3.4 0.6 - - - -
260A ARG* 1.3 81.6 + - - +
262A LYS* 1.3 60.3 + - + +
264A GLY* 3.3 2.8 + - - -
265A LYS* 3.0 33.8 + - + +
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Residues in contact with LYS 262 (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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258A ILE* 3.6 38.7 + - + +
259A GLY 3.5 1.6 + - - -
260A ARG 3.3 0.4 - - - -
261A ASP* 1.3 76.5 - - + +
263A LEU* 1.3 66.0 + - - +
265A LYS* 3.2 1.1 + - + +
266A ILE* 2.9 31.6 + - - +
296A TYR* 3.4 30.3 - - + +
302A GLU* 2.6 37.4 + - + +
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Residues in contact with LEU 263 (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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171A ILE* 4.3 15.3 - - + -
175A LEU* 4.5 9.4 - - + -
186A TRP* 4.0 16.6 - - + -
241A ALA* 3.6 40.4 - - + +
244A ILE* 3.9 18.8 - - + -
245A SER* 4.0 13.7 - - - -
258A ILE* 4.6 1.6 - - - +
259A GLY 3.1 14.6 + - - +
260A ARG 3.4 7.4 - - - +
262A LYS* 1.3 75.9 - - - +
264A GLY* 1.3 58.9 + - - +
266A ILE* 3.8 2.3 - - - +
267A PHE* 2.9 63.7 + - + +
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Residues in contact with GLY 264 (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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83A TYR* 4.6 1.1 - - - -
88A HIS* 3.5 11.4 - - - -
172A PHE* 3.9 8.3 - - - -
175A LEU* 3.6 24.5 - - - -
260A ARG 2.9 12.0 + - - -
261A ASP* 3.7 3.4 - - - -
263A LEU* 1.3 77.6 - - - +
265A LYS* 1.3 56.9 + - - +
267A PHE* 5.0 0.2 - - - -
268A TYR* 2.9 33.3 + - - +
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Residues in contact with LYS 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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87A VAL* 4.0 20.2 + - + +
88A HIS* 4.4 20.3 + - + +
89A ASN* 5.5 6.1 - - - +
261A ASP* 3.0 21.6 + - + +
262A LYS 3.2 0.4 + - - +
264A GLY* 1.3 75.4 - - - +
266A ILE* 1.3 64.1 + - - +
268A TYR* 4.0 1.9 - - + +
269A ARG* 3.1 25.6 + - - +
295A LEU* 3.7 23.9 - - + +
296A TYR* 3.7 21.8 - - - +
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Residues in contact with ILE 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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244A ILE* 4.9 2.2 - - + -
258A ILE* 3.7 26.2 - - + -
262A LYS 2.9 20.8 + - - +
263A LEU* 3.8 5.2 - - - +
265A LYS* 1.3 77.3 - - - +
267A PHE* 1.3 69.8 + - + +
269A ARG 3.4 0.2 + - - -
270A ALA* 2.9 26.9 + - - +
288A ALA* 3.7 34.5 - - + +
291A SER* 3.5 7.2 - - - -
292A ALA* 3.9 22.9 - - + -
295A LEU* 4.0 5.4 - - + -
296A TYR* 3.9 22.4 - - + -
302A GLU* 4.6 0.9 - - + -
306A VAL* 4.1 13.2 - - + -
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Residues in contact with PHE 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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168A ILE* 3.9 17.1 - - + +
171A ILE* 3.8 30.1 - - + -
172A PHE* 4.0 19.3 - - + -
237A ILE* 4.4 11.4 - - + -
241A ALA* 4.4 10.8 - - + -
244A ILE* 3.9 16.6 - - + -
263A LEU* 2.9 43.2 + - + +
266A ILE* 1.3 86.2 - - + +
268A TYR* 1.3 60.0 + - - +
270A ALA* 3.7 6.5 - - + +
271A LEU* 2.9 30.0 + - - +
284A LEU* 4.3 20.9 - - + -
288A ALA* 4.8 6.5 - - + -
310A PHE* 4.3 20.6 - + - -
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Residues in contact with TYR 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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84A TYR* 4.3 14.6 - + - -
88A HIS* 3.6 54.2 + + + +
90A ARG* 3.0 48.5 + - - +
148A VAL* 4.9 3.1 - - + -
172A PHE* 3.6 10.6 - + + -
264A GLY 2.9 21.1 + - - +
265A LYS* 4.0 2.9 - - + +
267A PHE* 1.3 76.5 - - - +
269A ARG* 1.3 64.1 + - - +
271A LEU* 3.3 7.5 + - + +
272A THR* 2.8 56.0 + - + +
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Residues in contact with ARG 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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265A LYS 3.1 19.0 + - - +
266A ILE 3.8 2.9 - - - +
268A TYR* 1.3 77.2 - - + +
270A ALA* 1.3 66.1 + - - +
272A THR* 3.8 5.2 - - - -
273A GLN* 2.9 55.7 + - + +
274A TYR* 4.3 5.0 + - + -
291A SER* 3.6 26.8 + - - +
294A ASP* 2.8 38.7 + - - +
295A LEU* 4.0 20.3 - - + +
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Residues in contact with ALA 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 ILE 2.9 18.0 + - - +
267A PHE* 3.7 9.0 - - + +
268A TYR 3.3 0.2 - - - -
269A ARG* 1.3 74.2 - - - +
271A LEU* 1.3 59.9 + - - +
274A TYR* 3.0 10.7 + - - -
275A LEU* 2.9 37.4 + - + +
284A LEU* 4.8 6.7 - - + -
287A ALA* 4.0 22.0 - - + +
288A ALA* 4.3 5.8 - - + +
291A SER* 3.1 14.8 + - - +
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Residues in contact with LEU 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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84A TYR* 5.8 0.4 - - - +
145A THR* 5.4 0.7 - - + -
148A VAL* 4.0 21.1 - - + -
149A THR* 3.8 20.9 - - + +
152A THR* 3.6 15.6 - - - +
153A ALA* 3.4 42.3 + - + +
155A LEU* 4.5 1.3 - - + -
168A ILE* 3.9 37.2 - - + -
172A PHE* 4.6 10.1 - - + -
267A PHE 2.9 18.0 + - - +
268A TYR* 3.6 9.2 - - + +
270A ALA* 1.3 76.9 - - - +
272A THR* 1.3 63.8 + - + +
275A LEU* 4.0 14.0 - - + +
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Residues in contact with THR 272 (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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90A ARG* 4.1 3.1 - - - +
148A VAL* 5.4 0.2 - - + -
152A THR* 4.0 29.0 - - + +
268A TYR* 2.8 58.3 + - + +
269A ARG* 3.6 7.1 + - - -
271A LEU* 1.3 84.0 - - + +
273A GLN* 1.3 78.3 + - - +
275A LEU 5.9 0.2 - - - -
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Residues in contact with GLN 273 (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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269A ARG* 2.9 45.0 + - + +
272A THR* 1.3 95.7 + - - +
274A TYR* 1.3 83.4 + - + +
275A LEU 5.1 1.3 - - - -
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Residues in contact with TYR 274 (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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269A ARG* 4.1 7.2 + - - -
270A ALA 3.0 4.1 + - - +
272A THR 3.9 0.4 - - - -
273A GLN* 1.3 101.9 - - + +
275A LEU* 1.3 69.5 + - - +
276A THR* 3.7 11.4 - - - +
279A SER* 4.7 0.5 + - - -
287A ALA* 3.6 28.2 - - + +
290A GLN* 3.4 27.3 + - + +
291A SER* 3.3 26.0 - - - -
294A ASP* 2.6 32.7 + - - -
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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