Contacts of the strand formed by residues 253 - 260 (chain A) in PDB entry 3DB4
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 ARG 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A TRP* 3.5 56.1 - - + +
247A ARG 3.7 3.4 - - - -
248A GLU* 3.8 18.4 - - + +
251A THR 4.4 0.2 + - - -
252A ALA* 1.3 75.4 - - - +
254A GLU* 1.3 62.0 + - - +
255A LEU 4.1 1.2 + - - -
270A ARG* 3.7 12.3 + - - +
271A ILE 5.5 0.2 - - - +
274A VAL* 3.9 19.1 - - + +
275A ASP* 2.7 43.6 + - - -
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Residues in contact with GLU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A TRP* 3.3 7.1 - - - -
245A ARG* 4.5 0.5 + - - -
246A LYS* 3.5 2.4 - - - -
247A ARG* 2.6 85.4 + - + +
249A THR* 4.6 4.5 + - - -
252A ALA* 4.0 19.3 - - + +
253A ARG* 1.3 75.2 - - - +
255A LEU* 1.3 60.7 + - - +
256A TYR* 4.0 23.1 + - + -
270A ARG* 3.5 30.1 - - - +
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Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A TRP* 3.8 12.1 - - + -
217A LEU* 3.9 26.7 - - + -
225A LEU* 5.0 2.5 - - + -
243A ILE* 3.7 37.9 - - + -
245A ARG 3.6 7.9 - - - +
246A LYS* 4.3 9.9 - - + -
253A ARG 4.1 1.4 + - - -
254A GLU* 1.3 74.9 - - - +
256A TYR* 1.3 64.8 + - - +
257A ALA* 5.5 0.4 - - + -
269A CYS 3.5 0.3 - - - +
270A ARG* 3.7 9.8 - - - +
271A ILE* 2.8 45.1 + - + -
274A VAL* 3.6 26.9 - - + +
277A VAL* 4.3 14.4 - - + -
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Residues in contact with TYR 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A ILE* 3.7 4.5 - - - +
244A SER* 2.7 30.1 + - - -
245A ARG* 2.8 70.8 + - + +
247A ARG* 5.5 2.5 - - + -
254A GLU* 4.0 29.9 + - + -
255A LEU* 1.3 77.2 - - - +
257A ALA* 1.3 58.2 + - - +
268A ASP* 3.6 21.3 - - - +
269A CYS 3.1 16.4 - - - +
270A ARG* 3.3 44.6 + - + -
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Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A LEU* 4.4 4.7 - - + -
241A ALA* 3.8 20.6 - - + -
242A GLU 3.1 15.0 - - - +
243A ILE* 4.2 4.5 - - + -
244A SER* 3.9 2.2 - - - -
255A LEU* 5.5 0.7 - - + -
256A TYR* 1.3 76.8 - - - +
258A ASN* 1.3 64.1 + - - +
259A VAL 3.5 0.7 + - - -
268A ASP 3.5 2.1 + - - -
269A CYS* 2.8 36.9 + - - +
271A ILE* 3.8 21.5 - - + -
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Residues in contact with ASN 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A ALA* 3.1 2.3 - - - -
242A GLU* 2.7 69.3 + - + +
244A SER* 3.9 16.7 + - - +
257A ALA* 1.3 69.9 - - - +
259A VAL* 1.3 63.1 + - - +
260A VAL* 3.8 3.8 + - - +
265A SER* 5.2 5.8 - - - -
266A LEU 3.4 5.6 - - - -
267A ASN* 3.1 30.7 + - - +
268A ASP 3.3 15.1 + - - -
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Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A LEU* 4.4 2.2 - - + -
227A TYR* 4.1 15.3 - - + -
239A TYR* 3.5 33.7 - - + -
240A ASP 3.6 3.8 - - - +
241A ALA* 3.9 12.3 - - + -
257A ALA 4.0 2.0 - - - +
258A ASN* 1.3 74.3 - - - +
260A VAL* 1.3 61.5 + - - +
261A LEU* 3.6 15.3 + - + -
265A SER* 3.3 1.6 - - - -
266A LEU* 2.5 48.8 + - + +
269A CYS* 3.9 28.5 - - + -
271A ILE* 4.1 13.5 - - + -
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Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ARG* 5.2 5.4 - - - +
149A GLY 4.0 6.9 - - - +
239A TYR* 3.7 19.9 - - - +
240A ASP* 2.8 36.0 + - + +
241A ALA* 4.8 1.6 - - - +
242A GLU* 5.5 1.6 - - + +
258A ASN 4.4 6.3 - - - +
259A VAL* 1.3 70.9 - - - +
261A LEU* 1.3 64.1 + - - +
263A ASP* 3.4 32.5 - - + +
264A ASP 4.7 0.4 - - - +
265A SER* 4.2 12.8 - - - +
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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