Contacts of the strand formed by residues 263 - 268 (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 VAL 263 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256D VAL* 3.6 29.4 - - + -
257D VAL 3.3 6.1 - - - +
258D LEU* 3.8 14.6 - - + -
262D ALA* 1.3 77.4 - - - +
264D TYR* 1.3 64.4 + - - +
288D VAL* 3.4 5.2 - - - +
289D ILE* 2.9 52.0 + - + +
292D ILE* 3.9 12.3 - - + +
297D ILE* 3.7 34.1 - - + -
300D ILE* 4.6 1.3 - - + -
309D LEU* 4.3 9.0 - - + -
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Residues in contact with TYR 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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240D GLU 4.6 4.9 - - - -
241D ILE* 3.7 26.9 - - + -
242D PRO* 4.1 5.9 - - - +
243D GLU* 2.6 37.9 + - - -
256D VAL* 3.4 1.2 - - - +
257D VAL* 2.8 45.5 + - + -
259D THR* 3.9 25.6 - - + -
262D ALA* 4.5 4.0 - - + -
263D VAL* 1.3 78.0 - - - +
265D THR* 1.3 67.1 + - - +
266D PHE* 4.8 1.1 - - + -
286D PRO* 3.7 28.5 - - + -
287D LYS 3.2 15.0 - - - -
288D VAL* 3.5 26.7 - - + +
293D ARG* 5.7 0.5 + - - -
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Residues in contact with THR 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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255D THR 3.3 6.7 - - - -
256D VAL* 3.9 24.9 - - + -
263D VAL 4.3 0.2 + - - -
264D TYR* 1.3 79.0 - - - +
266D PHE* 1.3 64.1 + - - +
273D GLN 4.6 1.6 - - - +
274D LEU* 2.8 43.6 + - - +
276D LEU* 3.5 18.7 - - - +
283D THR* 3.9 5.2 - - - +
287D LYS* 2.9 31.2 + - - +
289D ILE* 3.8 15.7 - - + +
319D PHE* 4.7 1.6 - - + -
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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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211D LEU* 4.5 9.4 - - + -
213D VAL* 4.9 3.6 - - + -
220D GLY 3.7 2.2 - - - +
221D LYS* 3.2 28.0 - - - -
222D LEU 3.7 5.2 - - - -
223D GLY* 3.4 27.1 - - - -
238D VAL* 5.0 2.2 - - + -
241D ILE* 4.2 3.6 - - + -
254D HIS* 3.3 3.3 - - - -
255D THR* 2.9 53.6 + - + -
257D VAL* 3.7 25.8 - - + -
264D TYR* 4.8 0.9 - - + -
265D THR* 1.3 83.7 - - - +
267D GLY* 1.3 60.7 + - - +
274D LEU* 3.5 6.9 - - - +
283D THR* 3.7 17.0 - - - +
285D GLU 3.9 11.4 - - - +
286D PRO* 3.6 29.2 - - + -
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Residues in contact with GLY 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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219D ASN 3.1 20.9 - - - +
220D GLY 3.6 0.8 + - - -
221D LYS* 3.6 11.0 - - - -
253D GLU 3.5 8.1 - - - -
266D PHE* 1.3 75.0 - - - +
268D LEU* 1.3 62.5 + - - -
274D LEU* 3.5 3.1 - - - +
282D GLU* 3.3 4.9 - - - -
283D THR 2.8 35.6 + - - -
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Residues in contact with LEU 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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219D ASN* 3.5 30.4 + - + +
253D GLU* 2.8 37.8 + - + +
254D HIS* 3.5 10.2 - - - +
267D GLY* 1.3 73.0 - - - -
269D GLY* 1.3 60.8 + - - +
270D GLN* 3.5 37.9 - - + +
273D GLN* 3.4 20.1 + - - +
274D LEU* 3.5 4.1 - - - +
281D PHE 4.0 7.9 - - - +
282D GLU* 4.2 12.1 - - + -
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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