Contacts of the strand formed by residues 254 - 263 (chain L) in PDB entry 1DZH
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 GLN 254 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227L SER* 2.6 35.6 + - - +
228L LYS 3.1 23.0 + - - +
229L PHE* 3.2 41.4 - - + -
230L SER 5.4 0.9 - - - +
233L ASN* 5.8 0.7 - - - +
253L TYR* 1.3 88.6 - - - +
255L GLU* 1.3 65.0 + - - +
256L GLY* 5.5 0.4 - - - -
258L PHE* 3.3 26.1 - - + -
317L VAL* 3.3 6.1 - - - +
318L VAL* 2.8 35.0 + - + -
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Residues in contact with GLU 255 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228I LYS* 2.7 43.6 + - - +
386I THR* 5.2 1.9 - - - +
253L TYR* 3.7 18.8 + - + +
254L GLN* 1.3 81.6 + - - +
256L GLY* 1.3 57.8 + - - +
258L PHE* 5.0 0.2 - - - -
315L MET* 3.6 26.3 - - + +
316L LEU 3.3 10.5 - - - +
317L VAL* 3.4 15.5 - - + +
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Residues in contact with GLY 256 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254L GLN* 5.5 0.9 - - - -
255L GLU* 1.3 77.0 - - - +
257L LYS* 1.3 62.8 + - - -
258L PHE* 3.8 16.1 + - - -
314L MET 3.1 1.9 - - - +
315L MET* 3.5 14.1 - - - -
316L LEU 2.9 32.0 + - - +
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Residues in contact with LYS 257 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256L GLY* 1.3 70.8 - - - -
258L PHE* 1.3 69.7 + - - +
313L GLU* 3.9 26.8 - - + +
314L MET* 3.1 8.8 - - - +
315L MET* 3.7 33.9 - - + +
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Residues in contact with PHE 258 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227L SER* 3.6 13.5 - - - -
229L PHE* 6.0 0.2 - + - -
254L GLN* 3.3 34.5 - - + -
256L GLY* 3.8 17.0 - - - -
257L LYS* 1.3 82.9 - - - +
259L ARG* 1.3 64.8 + - - +
260L TYR* 3.1 6.9 + - - +
270L LEU* 3.6 18.4 - - + -
271L GLU 3.5 17.7 - - - -
272L LEU* 3.5 22.4 - - + -
273L PRO* 4.3 15.3 - - + -
313L GLU* 4.3 2.5 - - - -
314L MET 3.0 25.4 + - - +
316L LEU* 3.4 26.5 - - + -
318L VAL* 3.9 13.0 - - + -
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Residues in contact with ARG 259 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258L PHE* 1.3 70.0 - - - +
260L TYR* 1.3 58.7 + - - +
269L VAL 4.2 0.2 - - - +
270L LEU* 3.8 2.3 - - - +
271L GLU* 2.7 71.6 + - + +
273L PRO* 5.9 0.6 - - - +
308L LEU* 2.8 37.2 + - - +
309L ASP* 5.0 1.4 - - - +
311L LEU* 3.7 31.7 + - + +
312L GLU 3.4 13.0 - - - -
313L GLU* 4.7 6.5 - - + +
413L ARG* 5.0 4.0 - - - +
415L VAL* 5.6 4.9 - - - +
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Residues in contact with TYR 260 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232I GLU* 2.9 36.1 + - - -
387I ALA* 3.7 11.6 - - + +
389I VAL* 3.5 22.2 - - + -
258L PHE 3.7 5.2 - - - +
259L ARG* 1.3 75.7 - - - +
261L ARG* 1.3 74.9 + - - +
262L ARG* 3.9 13.5 - - - +
268L GLN* 2.8 47.3 + - + +
269L VAL 3.5 13.5 - - - -
270L LEU* 4.2 6.5 - - + -
311L LEU* 3.7 4.4 - - - +
312L GLU* 2.7 34.0 + - - +
314L MET* 3.5 23.7 - - + +
316L LEU* 3.4 28.5 - - + -
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Residues in contact with ARG 261 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260L TYR* 1.3 90.7 - - - +
262L ARG* 1.3 76.0 + - - +
263L VAL* 3.4 15.5 + - + +
268L GLN* 3.5 0.5 - - - -
269L VAL 3.0 32.9 + - - -
310L GLU* 3.6 44.9 + - + +
311L LEU* 3.7 20.4 - - + +
312L GLU* 3.8 24.5 - - - +
314L MET* 5.7 5.8 - - - +
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Residues in contact with ARG 262 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232I GLU* 3.0 68.1 + - - +
233I ASN* 4.2 13.2 + - - +
260L TYR* 3.9 12.5 - - - +
261L ARG* 1.3 80.5 + - - +
263L VAL* 1.3 64.1 + - - +
266L GLY* 3.8 26.4 + - - -
267L THR 3.4 5.6 - - - +
268L GLN* 4.2 11.4 - - + +
287L LYS* 5.9 2.2 - - - +
314L MET* 5.8 0.4 - - - +
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Residues in contact with VAL 263 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261L ARG* 3.5 22.9 - - + +
262L ARG* 1.3 77.6 - - - +
264L ALA* 1.3 79.5 + - + +
266L GLY* 3.1 14.9 + - - -
267L THR* 2.7 17.3 + - - +
269L VAL* 3.6 24.9 - - + -
307L TRP* 3.5 33.9 - - + +
310L GLU* 3.2 28.3 - - + +
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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