Contacts of the strand formed by residues 254 - 259 (chain D) in PDB entry 4JHN
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 HIS 254 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D HIS* 3.5 5.1 - - - -
221D LYS* 4.2 1.7 - - - +
251D GLY* 2.9 32.7 + - - -
252D GLY 3.7 0.2 - - - -
253D GLU* 1.3 80.6 + - - +
255D THR* 1.3 67.0 + - - +
256D VAL* 3.9 14.4 - - + -
266D PHE 3.3 11.7 - - - +
268D LEU 3.5 18.8 - - - +
273D GLN* 3.5 38.1 + - + +
274D LEU* 4.0 5.2 - - + -
302D CYS* 3.6 9.0 - - - -
303D GLY 3.5 24.9 - - - -
304D GLU 3.8 13.2 + - - -
306D HIS 3.7 7.8 + - - -
307D THR* 3.1 19.8 + - - -
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Residues in contact with THR 255 (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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201D HIS* 2.8 18.5 + - + -
203D ALA* 5.4 2.0 - - + -
213D VAL* 5.4 2.5 - - + -
221D LYS 2.7 21.8 + - - +
248D VAL* 3.8 25.6 - - + -
249D ALA 3.6 7.9 - - - +
250D CYS* 4.2 8.1 - - - -
254D HIS* 1.3 71.4 - - - +
256D VAL* 1.3 69.1 + - - +
257D VAL* 4.3 0.7 - - + -
265D THR* 3.3 6.6 - - - -
266D PHE* 2.9 63.5 + - + +
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Residues in contact with VAL 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D VAL* 3.4 3.6 - - - +
249D ALA* 2.9 34.0 + - + +
254D HIS* 3.9 8.7 - - + -
255D THR* 1.3 77.9 - - - +
257D VAL* 1.3 68.0 + - - +
263D VAL* 3.6 26.7 - - + -
264D TYR 3.4 3.8 - - - +
265D THR* 3.9 13.0 - - + -
300D ILE* 3.4 22.9 - - + +
302D CYS* 3.2 29.4 - - - -
307D THR* 3.6 23.1 - - + +
309D LEU* 4.6 0.2 - - + -
319D PHE* 5.6 0.2 - - + -
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Residues in contact with VAL 257 (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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211D LEU* 3.5 24.0 - - + -
241D ILE* 4.0 7.2 - - + -
245D VAL* 3.6 38.4 - - + -
247D GLN 3.5 3.1 - - - -
248D VAL* 4.1 9.4 - - + -
256D VAL* 1.3 80.9 - - - +
258D LEU* 1.3 64.5 + - - +
259D THR* 4.1 5.1 + - + -
263D VAL* 3.3 8.4 - - - +
264D TYR* 2.8 45.2 + - + +
266D PHE* 3.7 22.9 - - + -
300D ILE* 4.0 2.9 - - - -
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Residues in contact with LEU 258 (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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245D VAL* 3.7 4.2 - - - +
246D ILE* 2.8 39.6 + - + -
247D GLN* 2.9 54.3 + - + +
257D VAL* 1.3 73.6 - - - +
259D THR* 1.3 71.2 + - - +
262D ALA 3.8 9.9 - - - +
263D VAL* 3.8 18.4 - - + -
297D ILE* 3.7 30.3 - - + +
298D SER 3.7 16.8 - - - +
299D TYR* 4.3 1.6 - - - +
300D ILE* 3.7 9.5 - - + +
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Residues in contact with THR 259 (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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241D ILE* 4.1 13.9 - - + -
243D GLU* 4.4 12.9 - - + +
244D LYS 3.5 20.2 - - - +
245D VAL* 4.4 5.4 - - + -
246D ILE* 3.7 8.2 - - - +
257D VAL* 4.6 1.1 - - + -
258D LEU* 1.3 92.2 - - - +
260D GLU* 1.3 66.7 + - - +
261D ASN* 3.2 5.1 + - - -
262D ALA* 2.9 38.5 + - - +
264D TYR* 3.9 29.6 - - + -
297D ILE 5.3 0.9 - - - +
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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