Contacts of the strand formed by residues 276 - 284 (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 SER 276 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239D ASP* 2.7 49.1 + - - +
240D GLN* 2.6 20.3 + - - +
274D TYR 3.8 2.7 + - - -
275D PRO* 1.3 76.0 - - - +
277D TRP* 1.3 65.6 + - - +
315D LYS* 4.5 5.9 + - - +
316D LEU 2.8 20.0 - - - -
317D VAL* 4.0 15.7 - - - -
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Residues in contact with TRP 277 (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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113D PHE* 3.7 18.4 - + - -
132D PHE* 3.3 29.0 - + - -
209D HIS 3.6 21.5 - - - -
210D ARG* 4.2 10.3 - - + -
212D MET 3.0 19.7 + - - -
236D TYR* 3.3 34.3 - - + -
237D LYS 3.1 5.8 - - - +
238D THR* 3.3 22.7 - - - +
239D ASP* 3.5 7.6 - - - +
240D GLN* 4.3 2.5 - - - -
275D PRO* 3.7 30.5 - - + -
276D SER* 1.3 93.1 - - - +
278D THR* 1.3 60.8 + - - +
315D LYS* 3.4 4.0 - - - +
316D LEU* 2.8 48.1 + - + +
318D LEU* 3.6 25.6 - - + -
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Residues in contact with THR 278 (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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236D TYR* 3.0 3.8 - - - -
237D LYS* 2.9 32.0 + - - -
239D ASP* 2.6 22.9 + - - -
277D TRP* 1.3 71.7 - - - +
279D PHE* 1.3 63.9 + - - +
280D TYR* 3.3 43.2 + - + +
312D PRO* 5.2 5.8 - - + -
314D GLY 3.8 10.1 - - - +
315D LYS* 3.0 17.6 + - + +
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Residues in contact with PHE 279 (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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85D PHE* 4.0 13.0 - + + -
100D PHE* 4.6 8.3 - + - -
134D VAL* 6.5 0.2 - - + -
136D PHE* 4.4 11.0 - + - -
143D TRP* 4.0 19.7 - + - -
145D LEU* 4.0 11.7 - - + -
234D PHE* 3.6 36.1 - + + -
235D HIS 3.5 2.0 - - - -
236D TYR* 3.9 33.4 - + + +
277D TRP 3.7 1.2 + - - -
278D THR* 1.3 73.6 - - - +
280D TYR* 1.3 61.6 + - - +
281D ILE* 4.2 5.2 - - + -
312D PRO* 3.6 2.3 - - - +
313D VAL* 2.7 48.8 + - + -
314D GLY 2.8 27.0 + - - +
315D LYS* 4.3 3.1 - - - +
316D LEU* 4.3 13.9 - - + -
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Residues in contact with TYR 280 (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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234D PHE* 3.8 1.7 - - - -
235D HIS* 2.8 37.3 + - + +
237D LYS* 3.6 27.4 - - + +
278D THR* 3.3 41.7 + - + +
279D PHE* 1.3 77.5 - - - +
281D ILE* 1.3 73.7 + - - +
310D LEU* 3.7 37.0 - - + -
311D ILE 3.1 9.0 - - - +
312D PRO* 3.5 34.3 - - + -
313D VAL* 4.1 0.2 - - - -
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Residues in contact with ILE 281 (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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91D ILE* 4.2 23.1 - - + -
94D TYR* 4.3 9.9 - - + -
100D PHE* 5.7 0.2 - - + -
222D LEU* 4.1 19.5 - - + -
232D CYS* 4.8 2.9 - - + -
233D LYS 3.1 11.0 - - - +
234D PHE* 3.7 27.1 - - + -
235D HIS* 4.7 0.9 - - - -
279D PHE* 4.2 3.6 - - + -
280D TYR* 1.3 81.7 - - - +
282D GLN* 1.3 64.4 + - - +
283D VAL* 3.8 21.8 - - + -
310D LEU* 3.6 1.9 - - - -
311D ILE* 2.8 47.2 + - + +
313D VAL* 3.5 14.8 - - + -
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Residues in contact with GLN 282 (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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232D CYS* 2.9 30.1 - - - +
233D LYS* 3.0 20.2 + - + +
235D HIS* 2.5 38.6 + - - +
281D ILE* 1.3 75.7 - - - +
283D VAL* 1.3 61.7 + - - +
303D TRP* 2.8 48.8 + - + +
305D HIS* 3.8 10.7 - - - -
308D TYR* 2.7 30.0 + - + +
309D PRO 3.9 5.8 - - - +
310D LEU* 3.9 11.9 - - + -
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Residues in contact with VAL 283 (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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94D TYR* 4.0 33.2 - - + +
222D LEU* 5.3 0.4 - - + -
230D VAL* 3.6 37.9 - - + -
231D TYR 3.4 2.5 - - - +
232D CYS* 5.0 1.3 - - + -
281D ILE* 3.8 25.8 - - + -
282D GLN* 1.3 79.4 - - - +
284D MET* 1.3 65.3 + - - +
285D THR* 4.6 4.7 - - + +
288D GLN* 4.0 4.3 - - - +
303D TRP* 4.3 2.0 - - - -
308D TYR* 3.5 19.7 - - - +
309D PRO* 4.7 4.1 + - - +
311D ILE* 4.5 8.4 - - + +
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Residues in contact with MET 284 (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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231D TYR* 2.9 32.0 + - + +
283D VAL* 1.3 76.3 - - - +
285D THR* 1.3 75.4 + - - +
288D GLN* 3.4 18.2 - - + +
289D ALA* 3.8 14.6 - - + +
292D PHE* 3.7 18.4 - - + -
296D PRO* 3.8 19.7 - - - -
303D TRP* 3.4 55.2 - - + +
308D TYR* 3.5 28.7 - - + +
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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