Contacts of the helix formed by residues 259 - 271 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A ARG* 3.0 31.6 + - - -
175A HIS 4.4 0.2 - - - +
176A LEU* 3.7 26.1 - - + +
177A LYS* 4.8 8.5 + - - +
77D LYS* 2.8 34.0 + - - -
124D ASP* 3.4 7.6 - - - -
257D ASP* 2.9 10.1 + - - +
258D PRO* 1.3 84.3 - - - +
260D TYR* 1.3 66.7 + - - +
261D GLY 3.1 3.6 - - - -
262D ILE* 2.8 20.8 + - + -
263D ARG* 3.1 10.7 + - - +
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Residues in contact with TYR 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ASP* 3.9 1.1 + - + +
125D THR* 3.8 24.7 - - + -
207D ASP* 2.4 34.9 + - - -
208D GLY* 3.9 17.0 - - - -
245D LEU* 4.4 7.7 - - + +
253D LEU* 3.5 38.7 - - + +
257D ASP* 3.0 35.3 + - + +
258D PRO 3.5 1.4 + - - -
259D ASP* 1.3 74.9 - - - +
261D GLY* 1.3 61.5 + - - +
263D ARG* 3.5 1.8 + - - +
264D ASP* 2.9 43.9 + - + +
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Residues in contact with GLY 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ASP* 3.0 17.3 + - - +
208D GLY* 4.6 7.2 - - - -
209D HIS* 3.9 23.5 + - - -
259D ASP 2.9 1.2 + - - -
260D TYR* 1.3 87.1 - - - +
262D ILE* 1.3 55.4 + - - +
264D ASP* 3.3 4.1 + - - +
265D LEU* 2.9 31.4 + - - +
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Residues in contact with ILE 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A THR 3.3 25.8 - - - +
175A HIS* 4.1 21.3 - - + +
176A LEU* 3.8 10.5 - - + -
77D LYS* 4.0 23.1 - - - -
78D GLY 3.1 28.3 - - - +
79D ALA* 3.7 19.1 - - + -
124D ASP* 3.2 9.0 + - - +
209D HIS* 4.4 0.2 + - - -
259D ASP* 2.8 19.1 + - + +
261D GLY* 1.3 71.3 - - - +
263D ARG* 1.3 58.6 + - - +
265D LEU* 3.4 2.3 + - - +
266D PHE* 3.0 31.8 + - + +
325D TYR* 4.7 3.6 - - + -
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Residues in contact with ARG 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU* 3.5 45.0 - - + +
177A LYS* 5.4 7.3 + - - +
257D ASP* 2.7 39.8 + - - -
259D ASP* 3.1 9.6 + - - +
260D TYR 3.8 6.3 - - - +
262D ILE* 1.3 77.0 - - - +
264D ASP* 1.3 59.4 + - - +
266D PHE* 3.2 2.8 + - - +
267D ASN* 2.8 57.6 + - - +
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Residues in contact with ASP 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D ASP* 5.1 3.4 - - - +
208D GLY* 4.5 14.0 - - - -
209D HIS 4.7 0.9 + - - -
210D ARG* 2.6 49.4 + - - +
211D HIS* 5.7 0.4 - - - -
260D TYR* 2.9 36.1 + - + +
261D GLY* 3.8 5.2 - - - +
263D ARG* 1.3 78.0 - - - +
265D LEU* 1.3 63.7 + - - +
267D ASN* 4.2 6.6 - - - +
268D ALA* 3.2 22.3 + - - +
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Residues in contact with LEU 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D ALA* 4.1 14.1 - - + -
80D GLY 4.1 11.9 - - - +
81D ALA* 4.0 20.9 - - + -
113D PHE* 3.7 37.0 - - + -
209D HIS* 4.4 6.3 - - + -
210D ARG* 4.0 24.0 - - + +
261D GLY 2.9 17.2 + - - +
262D ILE* 3.9 4.0 - - - +
264D ASP* 1.3 82.1 + - - +
266D PHE* 1.3 62.9 + - - +
268D ALA* 3.5 2.6 - - - +
269D ILE* 3.2 35.8 + - + +
275D PRO* 4.3 8.7 - - + -
318D LEU* 4.9 0.7 - - + -
321D ASN* 4.6 0.4 - - - +
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Residues in contact with PHE 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLN* 3.9 28.9 - - + -
174A THR* 3.5 44.4 - - + -
176A LEU* 5.8 1.8 - - + -
262D ILE* 3.0 22.7 + - + +
263D ARG* 3.8 4.7 - - - +
265D LEU* 1.3 76.5 - - - +
267D ASN* 1.3 72.9 + - - +
270D ALA* 2.9 22.4 + - + +
321D ASN* 2.9 57.3 - - + +
322D PRO* 4.3 8.5 - - + -
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Residues in contact with ASN 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D ARG* 2.8 50.1 + - - +
264D ASP* 4.2 5.2 - - - +
266D PHE* 1.3 77.9 - - - +
268D ALA* 1.3 69.3 + - - +
270D ALA* 3.1 6.0 + - - -
271D THR* 2.8 31.4 + - + +
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Residues in contact with ALA 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D ARG* 3.3 42.2 - - - +
264D ASP 3.2 9.2 + - - +
265D LEU 3.5 4.7 - - - +
267D ASN* 1.3 83.7 - - - +
269D ILE* 1.3 65.5 + - + +
271D THR* 2.8 18.3 + - - -
273D LYS* 3.2 32.4 + - + +
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Residues in contact with ILE 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ALA* 3.3 28.3 - - + -
265D LEU* 3.2 16.8 + - + +
268D ALA* 1.3 78.7 - - - +
270D ALA* 1.3 63.9 + - - +
272D GLY 3.0 10.7 + - - -
273D LYS 4.7 0.7 - - - -
274D TYR* 3.3 16.8 + - + -
275D PRO* 3.9 9.2 - - + -
318D LEU* 3.7 24.5 - - + +
319D ASN* 3.3 30.7 - - - +
320D ARG 3.6 4.9 - - - +
321D ASN* 3.2 36.3 - - - +
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Residues in contact with ALA 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D PHE* 2.9 33.4 + - + +
267D ASN* 3.6 5.6 - - - +
269D ILE* 1.3 78.2 - - - +
271D THR* 1.3 62.7 + - + +
272D GLY 3.6 0.7 + - - -
321D ASN* 3.6 8.9 + - - +
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Residues in contact with THR 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D ASN* 2.8 29.9 + - + +
268D ALA* 2.8 11.5 + - - -
270D ALA* 1.3 81.5 - - + +
272D GLY* 1.3 57.9 + - - +
273D LYS* 3.4 31.7 + - - +
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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