Contacts of the strand formed by residues 293 - 299 (chain B) in PDB entry 4LEY
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 ALA 293 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263B LEU* 5.0 5.9 - - - +
267B ARG* 3.8 12.0 + - - -
287B GLU* 5.7 1.6 - - - +
291B SER* 3.2 22.1 + - - +
292B PRO* 1.3 83.2 - - + +
294B VAL* 1.3 65.2 + - - +
295B THR* 4.0 3.6 + - - +
307B ASP* 3.8 31.9 - - + +
308B ILE 3.3 15.0 - - - +
309B ILE* 3.8 7.9 - - + -
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Residues in contact with VAL 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 4.8 6.3 - - + -
266B PHE* 3.9 26.0 - - + -
267B ARG* 4.0 38.1 - - + +
270B ILE* 4.0 30.1 - - + -
284B VAL* 3.8 25.8 - - + -
293B ALA* 1.3 75.7 - - - +
295B THR* 1.3 61.3 + - - +
296B LEU* 3.8 3.3 + - + +
306B VAL 3.4 2.8 - - - +
308B ILE* 2.9 34.5 + - - +
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Residues in contact with THR 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ARG* 4.9 1.6 - - - +
284B VAL* 3.7 3.8 - - - +
285B GLU* 2.7 75.3 + - + +
288B LYS* 5.7 1.2 - - - +
291B SER* 4.8 5.2 + - - -
293B ALA* 4.0 6.2 + - - +
294B VAL* 1.3 73.5 - - - +
296B LEU* 1.3 69.0 + - - +
297B LEU* 6.1 0.2 - - + -
305B SER* 4.3 13.9 - - - -
306B VAL 3.4 4.3 - - - +
307B ASP* 3.0 27.7 + - - +
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B VAL* 3.8 16.8 - - + -
175B VAL* 6.1 0.4 - - + -
178B LEU* 3.6 29.4 - - + -
270B ILE* 4.1 24.0 - - + -
274B VAL* 4.3 7.2 - - + -
282B VAL* 4.1 10.5 - - + -
283B SER 3.3 11.0 - - - +
284B VAL* 4.2 11.4 - - + -
294B VAL* 4.3 7.6 - - + +
295B THR* 1.3 82.0 - - - +
297B LEU* 1.3 60.2 + - - +
298B ILE* 4.0 3.1 - - + -
304B ILE 3.4 1.0 - - - +
305B SER* 3.3 7.1 - - - -
306B VAL* 2.9 52.2 + - + +
308B ILE* 4.1 10.5 - - + -
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B ASP 3.8 1.0 - - - +
282B VAL* 3.4 1.9 - - - -
283B SER* 2.9 42.4 + - - +
285B GLU* 4.8 8.5 - - + +
295B THR* 4.1 1.6 + - + -
296B LEU* 1.3 72.9 - - - +
298B ILE* 1.3 65.4 + - - +
299B ARG* 3.4 38.4 + - - +
303B GLU* 3.9 33.4 - - + +
304B ILE 3.7 11.7 - - - +
305B SER* 4.9 4.3 - - - +
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Residues in contact with ILE 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B THR* 3.7 28.5 - - + -
171B VAL* 4.5 11.9 - - + -
174B VAL* 4.0 28.9 - - + -
280B ILE* 3.8 10.3 - - + -
281B ASP 3.3 2.5 - - - +
282B VAL* 3.8 17.9 - - + -
296B LEU* 4.9 5.4 - - + +
297B LEU* 1.3 75.4 - - - +
299B ARG* 1.3 63.1 + - - +
300B ASN* 3.1 21.1 + - + +
302B GLU 3.2 1.6 - - - +
303B GLU* 3.4 2.0 - - - -
304B ILE* 2.9 46.9 + - + +
306B VAL* 4.3 20.2 - - + -
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Residues in contact with ARG 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B ILE* 5.8 0.2 - - - +
281B ASP* 2.8 54.8 + - - +
283B SER* 4.7 8.3 + - - -
297B LEU* 3.4 31.3 + - - +
298B ILE* 1.3 72.3 - - - +
300B ASN* 1.3 56.1 + - - +
301B PRO* 2.9 27.7 - - + +
302B GLU 3.8 2.2 - - - -
303B GLU* 3.3 38.9 + - - +
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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