Contacts of the helix formed by residues 259 - 271 (chain A) in PDB entry 1F4J
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 ASP 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A LYS* 2.6 35.3 + - - +
124A ASP* 3.5 6.7 - - - -
257A ASP* 3.0 11.6 + - - +
258A PRO* 1.3 87.6 - - - +
260A TYR* 1.3 65.2 + - - +
261A GLY 3.4 2.0 - - - -
262A ILE* 3.1 15.8 + - + +
263A ARG* 3.1 13.7 + - - +
170D ARG* 2.9 32.6 + - - -
175D HIS 4.4 0.7 - - - +
176D LEU* 3.8 22.2 - - + +
177D LYS* 4.9 9.0 + - - +
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Residues in contact with TYR 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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124A ASP* 4.2 0.9 - - + +
125A THR* 3.8 27.1 - - + -
207A ASP* 2.5 34.7 + - - -
208A GLY* 4.1 15.9 - - - -
245A LEU* 4.6 3.2 - - + +
253A LEU* 3.5 36.7 - - + +
257A ASP* 3.1 31.4 + - + +
258A PRO 3.4 1.8 + - - -
259A ASP* 1.3 76.3 - - - +
261A GLY* 1.3 71.2 + - - +
262A ILE 2.9 1.6 + - - -
263A ARG* 3.1 2.2 + - - +
264A ASP* 3.0 36.8 + - + +
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Residues in contact with GLY 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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124A ASP* 3.1 18.7 + - - +
208A GLY* 4.8 7.4 - - - -
209A HIS* 3.3 34.3 + - - -
260A TYR* 1.3 87.8 - - - +
262A ILE* 1.3 59.9 + - - +
264A ASP* 4.1 5.0 - - - +
265A LEU* 3.4 14.6 + - - +
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Residues in contact with ILE 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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77A LYS* 4.4 10.5 - - + +
78A GLY 3.4 26.2 - - - +
79A ALA* 3.8 17.4 - - + +
124A ASP* 3.2 10.0 + - - +
259A ASP* 3.1 26.7 + - + +
260A TYR 2.9 0.2 + - - -
261A GLY* 1.3 75.0 - - - +
263A ARG* 1.3 66.6 + - - +
265A LEU* 3.4 2.6 + - - +
266A PHE* 3.0 27.0 + - + +
325A TYR* 4.9 2.9 - - + -
174D THR 3.4 25.1 - - - +
175D HIS* 4.0 24.2 - - + +
176D LEU* 3.6 9.6 - - + -
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Residues in contact with ARG 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ASP* 2.8 41.1 + - - +
259A ASP* 3.1 5.6 + - - +
260A TYR 3.1 6.8 + - - +
262A ILE* 1.3 78.9 - - - +
264A ASP* 1.3 52.7 + - - +
266A PHE* 3.4 2.5 + - - +
267A ASN* 2.7 60.2 + - - +
176D LEU* 3.6 43.0 - - + +
177D LYS* 5.6 6.7 + - - +
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Residues in contact with ASP 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASP* 5.0 4.1 - - - +
208A GLY* 4.5 16.2 - - - -
209A HIS 4.6 1.4 + - - -
210A ARG* 2.8 44.6 + - - +
211A HIS* 5.6 0.3 - - - -
260A TYR* 3.0 33.6 + - + +
261A GLY* 4.1 5.1 - - - +
263A ARG* 1.3 78.1 - - - +
265A LEU* 1.3 63.5 + - - +
267A ASN* 3.5 3.7 + - - +
268A ALA* 3.1 23.0 + - - +
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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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79A ALA* 4.3 14.1 - - + -
80A GLY 4.2 10.8 - - - +
81A ALA* 4.1 16.4 - - + -
113A PHE* 3.7 36.8 - - + -
209A HIS* 4.4 4.5 - - + -
210A ARG* 4.0 22.9 - - + +
261A GLY 3.4 16.2 + - - +
262A ILE* 3.9 3.4 - - - +
263A ARG 3.4 0.2 - - - -
264A ASP* 1.3 86.3 + - - +
266A PHE* 1.3 65.8 + - - +
268A ALA* 3.3 2.1 + - - +
269A ILE* 3.2 40.2 + - + +
275A PRO* 4.2 11.0 - - + -
318A LEU* 4.7 2.2 - - + -
321A ASN* 4.9 0.9 - - - +
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Residues in contact with PHE 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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262A ILE* 3.0 22.9 + - + +
263A ARG* 3.8 4.7 - - - +
265A LEU* 1.3 79.4 - - - +
267A ASN* 1.3 68.0 + - - +
270A ALA* 2.8 30.1 + - + -
321A ASN* 2.8 57.5 - - + +
322A PRO* 4.2 8.5 - - + -
173D GLN* 3.8 33.9 - - + -
174D THR* 3.6 45.1 - - + +
176D LEU* 5.6 1.6 - - + -
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Residues in contact with ASN 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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263A ARG* 2.7 44.8 + - - +
264A ASP* 4.2 3.5 - - - +
266A PHE* 1.3 82.8 - - - +
268A ALA* 1.3 65.3 + - - +
270A ALA* 3.1 7.8 + - - +
271A THR* 2.9 31.3 + - + +
273A LYS* 5.8 0.4 - - - -
176D LEU* 5.8 1.7 - - - +
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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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210A ARG* 3.7 28.9 - - - +
264A ASP 3.1 17.9 + - - +
265A LEU 3.3 4.5 + - - +
267A ASN* 1.3 77.9 - - - +
269A ILE* 1.3 63.2 + - + +
271A THR* 3.1 5.9 + - - -
272A GLY 3.1 3.1 + - - -
273A LYS* 2.9 52.9 + - + +
275A PRO* 4.9 0.2 - - + -
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Residues in contact with ILE 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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81A ALA* 3.6 25.4 - - + -
265A LEU* 3.2 20.7 + - + +
268A ALA* 1.3 75.7 - - - +
270A ALA* 1.3 62.8 + - - +
272A GLY* 3.1 12.5 + - - -
273A LYS 4.7 0.4 - - - -
274A TYR* 3.8 11.6 - - + -
275A PRO* 3.9 17.3 - - + -
318A LEU* 3.9 16.6 - - + +
319A ASN* 3.5 10.8 - - - +
320A ARG* 3.4 32.3 - - - +
321A ASN* 3.3 30.7 - - - +
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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 PHE* 2.8 38.3 + - + +
267A ASN* 3.1 9.6 + - - +
269A ILE* 1.3 77.2 - - - +
271A THR* 1.3 61.5 + - + +
272A GLY 3.3 0.6 + - - -
321A ASN* 3.5 3.7 + - - +
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Residues in contact with THR 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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267A ASN* 2.9 18.2 + - + +
268A ALA 3.1 10.6 + - - -
270A ALA* 1.3 80.2 - - + +
272A GLY* 1.3 57.6 + - - +
273A LYS* 2.9 36.7 + - - +
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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