Contacts of the strand formed by residues 256 - 263 (chain D) in PDB entry 3HN3
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 PHE 256 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250D VAL* 3.8 36.1 - - + -
253D SER 3.3 24.7 - - - -
254D ASN* 3.8 15.4 + - + -
255D LEU* 1.3 79.9 - - - +
257D LYS* 1.3 66.3 + - - +
258D LEU* 4.0 5.8 - - + -
276D THR* 4.0 26.0 - - + -
307D LEU* 3.5 25.1 - - + -
308D THR 3.1 14.6 - - - +
309D ALA* 3.7 8.1 - - + +
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Residues in contact with LYS 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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256D PHE* 1.3 76.2 - - - +
258D LEU* 1.3 65.2 + - - +
259D GLU* 3.1 31.3 + - + +
306D GLN 3.8 0.7 - - - +
307D LEU* 3.5 5.2 - - - +
308D THR* 2.7 66.0 + - + +
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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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228D ILE* 4.7 1.3 - - + -
248D ILE* 3.9 23.8 - - + -
250D VAL* 4.2 5.2 - - + -
256D PHE* 4.0 9.8 - - + -
257D LYS* 1.3 77.3 - - - +
259D GLU* 1.3 62.8 + - - +
260D VAL* 5.0 0.2 - - + -
274D THR* 3.2 12.1 - - - +
275D GLY* 3.2 49.0 + - - +
276D THR* 3.7 27.1 - - + -
305D VAL* 3.8 27.1 - - + -
306D GLN 3.5 1.3 - - - +
307D LEU* 3.9 31.2 - - + -
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Residues in contact with GLU 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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257D LYS* 3.1 38.2 + - + -
258D LEU* 1.3 75.2 - - - +
260D VAL* 1.3 65.8 + - - +
261D ARG* 5.6 4.3 + - + -
273D GLY 3.7 6.1 - - - +
274D THR* 4.5 6.7 - - + +
304D GLU 3.8 0.9 - - - +
306D GLN* 2.9 64.1 + - + +
308D THR* 4.4 5.1 + - - -
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Residues in contact with VAL 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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246D TYR* 4.1 22.9 - - + +
248D ILE* 3.5 31.0 - - + -
258D LEU* 5.0 1.6 - - + -
259D GLU* 1.3 80.8 - - - +
261D ARG* 1.3 61.7 + - - +
272D ASN* 3.1 6.1 - - - +
273D GLY 2.8 40.6 + - - +
274D THR* 5.2 0.2 - - - -
275D GLY 4.7 4.0 - - - +
280D LEU* 4.4 7.4 - - + +
303D LEU* 3.0 44.0 - - + -
304D GLU 3.4 5.2 - - - +
305D VAL* 4.4 5.8 - - + -
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Residues in contact with ARG 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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259D GLU* 5.6 5.3 + - + -
260D VAL* 1.3 77.9 - - - +
262D LEU* 1.3 60.9 - - - +
263D LEU* 4.0 15.9 - - + +
269D VAL* 3.5 30.7 - - + +
271D ALA 3.6 7.0 - - - +
272D ASN* 4.3 8.5 - - + -
280D LEU* 4.8 0.2 - - - -
302D SER 3.5 0.5 - - - +
303D LEU* 3.4 7.3 - - - +
304D GLU* 2.8 84.4 + - + +
306D GLN* 4.7 9.5 + - - -
319D PHE* 6.3 0.4 - - - -
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Residues in contact with LEU 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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244D VAL* 3.8 19.1 - - + -
261D ARG* 1.3 72.9 - - - +
263D LEU* 1.3 61.3 + - - +
269D VAL* 3.6 3.0 - - - -
270D VAL* 2.9 37.9 + - + +
271D ALA* 2.9 13.5 + - + +
280D LEU* 3.9 14.3 - - + +
282D VAL* 3.3 35.0 - - + -
301D TYR* 3.9 28.9 - - + -
302D SER 3.4 17.3 - - - +
303D LEU* 4.1 16.6 - - + +
324D VAL* 4.4 13.2 - - + -
326D ILE* 4.6 0.2 - - + -
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Residues in contact with LEU 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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261D ARG* 4.1 14.6 - - + +
262D LEU* 1.3 75.9 - - - +
264D ASP* 1.3 59.7 + - - +
267D ASN* 3.7 37.9 - - + +
268D LYS 3.2 5.2 - - - -
269D VAL* 3.6 30.5 - - + +
301D TYR* 3.2 10.8 - - - +
302D SER* 2.8 52.8 + - - +
304D GLU* 3.9 30.1 - - + +
321D THR* 5.3 2.9 - - + -
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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