Contacts of the strand formed by residues 278 - 283 (chain B) in PDB entry 1DY7
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 PRO 278 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B MET* 3.5 35.3 - - + +
142B MET* 4.1 24.5 - - + -
143B ARG* 3.8 14.0 + - + -
146B TRP* 4.2 10.5 - - + -
236B ILE* 3.5 20.4 - - + -
269B VAL* 4.2 7.2 - - + -
270B ILE 4.0 4.3 - - - +
271B MET* 4.2 4.7 - - + -
276B LEU 3.1 7.6 - - - +
277B GLU* 1.3 93.7 - - + +
279B LYS* 1.3 64.3 + - - +
280B LYS 3.9 0.4 - - - -
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Residues in contact with LYS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLN* 3.0 20.5 + - - -
139B MET* 4.2 1.2 - - - +
257B TYR* 4.7 6.3 - - + -
270B ILE* 2.8 15.6 + - + +
271B MET 4.4 1.6 - - - -
272B ASP* 4.0 19.5 - - + +
277B GLU* 3.5 44.2 + - + +
278B PRO* 1.3 78.2 - - - +
280B LYS* 1.3 61.8 + - - +
330B LEU* 3.8 26.6 - - + +
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Residues in contact with LYS 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A TYR* 5.5 1.8 + - - +
292A GLN* 3.4 17.9 - - - +
321A LYS* 5.0 9.8 - - - +
337A GLU* 5.1 2.7 + - - -
339A SER* 3.3 24.4 + - - -
139B MET* 4.7 0.4 - - - +
268B TYR* 4.0 1.9 - - - +
269B VAL* 3.3 2.9 - - - +
270B ILE* 2.8 42.3 + - + +
279B LYS* 1.3 83.4 - - - +
281B ILE* 1.3 61.7 + - - +
282B GLN* 3.3 33.1 + - + +
330B LEU* 2.7 49.2 + - + +
331B ASP* 4.3 5.1 + - - +
333B LEU* 4.2 16.5 - - + +
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Residues in contact with ILE 281 (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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287A MET* 3.2 39.5 - - + +
292A GLN* 2.9 22.3 + - + +
321A LYS* 5.1 0.3 + - - -
138B GLY* 3.8 3.4 - - - -
139B MET* 3.4 48.7 - - + +
142B MET* 3.8 16.8 - - + -
267B GLN* 4.0 24.0 - - + +
268B TYR 3.5 9.4 - - - +
269B VAL* 3.8 16.4 - - + -
280B LYS* 1.3 76.3 - - - +
282B GLN* 1.3 72.9 + - - +
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Residues in contact with GLN 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A MET* 4.3 1.6 - - - -
321A LYS* 4.3 8.8 - - - +
337A GLU* 3.2 24.9 + - - +
267B GLN* 3.2 5.2 - - - -
268B TYR* 2.9 73.8 + - + +
280B LYS* 3.3 36.7 - - + +
281B ILE* 1.3 83.4 + - - +
283B SER* 1.3 66.4 + - - +
333B LEU* 3.6 18.6 - - + +
335B THR* 5.3 1.7 - - - +
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Residues in contact with SER 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ARG 4.7 2.9 + - - -
286A GLY* 4.0 25.5 - - - -
287A MET* 4.0 12.3 - - - +
294A TYR* 3.9 12.2 - - - -
266B PRO 3.4 8.3 + - - -
267B GLN* 4.2 3.1 - - - -
268B TYR* 5.3 0.3 - - - -
282B GLN* 1.3 78.9 - - - +
284B THR* 1.3 64.3 + - - +
285B ARG* 3.1 37.1 + - - +
323B LEU* 5.9 1.0 - - - +
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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