Contacts of the strand formed by residues 252 - 259 (chain A) in PDB entry 1D5R
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 ASP 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A PRO 5.0 0.2 - - - -
97A GLN* 3.3 21.7 - - + +
98A LEU* 3.1 21.3 + - - +
99A GLU 5.0 0.3 + - - -
174A TYR* 2.9 32.1 + - - +
219A GLN* 3.9 7.7 - - - +
220A LEU* 3.5 33.2 + - + +
250A CYS 4.0 0.8 + - - -
251A GLY* 1.3 70.9 - - - -
253A ILE* 1.3 60.4 + - - +
274A TRP* 4.3 14.5 - - + -
275A VAL 3.4 3.6 - - - -
276A ASN* 2.8 24.3 + - - -
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Residues in contact with ILE 253 (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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195A PHE* 4.0 21.5 - - + -
217A VAL* 3.7 25.6 - - + -
218A CYS 3.4 13.5 - - - +
219A GLN* 5.0 1.8 - - + -
224A ILE* 5.0 1.6 - - + -
247A LEU* 6.0 0.2 - - + -
249A VAL* 3.3 37.0 - - + -
251A GLY 4.0 6.1 - - - +
252A ASP* 1.3 76.1 - - - +
254A LYS* 1.3 66.8 + - - +
255A VAL* 4.6 5.5 - - + +
273A PHE* 3.8 2.2 - - + +
274A TRP* 3.2 8.3 - - - -
275A VAL* 2.7 55.6 + - + +
277A THR* 4.6 6.3 - - + +
347A PHE* 5.4 6.5 - - + -
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Residues in contact with LYS 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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94A ASN* 4.8 9.7 + - - +
216A VAL 3.9 0.7 - - - +
217A VAL* 3.5 3.6 - - - +
218A CYS* 2.9 53.9 + - + +
253A ILE* 1.3 72.6 - - - +
255A VAL* 1.3 75.6 + - - +
256A GLU* 3.8 34.2 + - - +
272A HIS* 4.5 15.3 + - + -
273A PHE 3.5 7.4 - - - +
274A TRP* 3.6 45.9 - - + +
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Residues in contact with VAL 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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195A PHE* 4.5 19.1 - - + -
198A MET* 3.9 17.7 - - + -
215A PHE* 4.6 4.5 - - + -
216A VAL 3.7 8.3 - - - +
217A VAL* 4.6 5.2 - - + -
253A ILE* 4.6 10.3 - - + -
254A LYS* 1.3 82.5 - - - +
256A GLU* 1.3 62.8 + - - +
257A PHE* 3.9 27.6 - - + -
271A PHE* 5.3 0.5 - - - -
272A HIS* 3.0 5.6 - - - +
273A PHE* 2.9 64.2 + - + -
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Residues in contact with GLU 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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215A PHE* 3.2 4.2 - - - -
216A VAL* 3.0 36.9 + - + +
254A LYS* 3.8 26.6 + - - -
255A VAL* 1.3 74.9 - - - +
257A PHE* 1.3 66.5 + - - +
258A PHE* 3.4 40.1 - - + -
269A LYS* 3.7 25.2 + - + +
271A PHE 3.5 10.3 - - - +
272A HIS* 3.7 13.5 - - + -
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Residues in contact with PHE 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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198A MET* 3.4 37.9 - - + -
200A PHE* 3.4 37.0 - + - -
213A PRO* 4.2 11.7 - - + -
214A GLN 3.2 7.6 - - - -
215A PHE* 3.6 26.9 - + + -
241A PHE* 3.8 18.4 - + - -
255A VAL* 3.9 13.7 - - + -
256A GLU* 1.3 77.3 - - - +
258A PHE* 1.3 65.7 + - - +
269A LYS* 4.0 0.9 - - - -
270A MET* 2.9 37.6 + - + +
271A PHE* 2.9 39.7 + + + +
273A PHE* 5.2 0.4 - + - -
343A VAL* 5.5 0.7 - - + -
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Residues in contact with PHE 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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213A PRO* 3.3 0.7 - - - +
214A GLN* 2.7 63.7 + - + +
216A VAL* 3.8 17.9 - - + -
256A GLU* 3.4 50.5 - - + -
257A PHE* 1.3 75.5 - - - +
259A HIS* 1.3 61.1 + - - +
260A LYS 4.0 0.4 + - - -
267A LYS* 3.4 44.6 - - + -
268A ASP 3.1 10.1 - - - +
269A LYS* 4.3 20.0 - - + -
270A MET* 3.3 13.6 - - - +
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Residues in contact with HIS 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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206A PHE* 3.8 21.5 - - + -
207A SER* 3.4 17.1 - - - -
211A CYS* 3.5 13.4 - - + -
212A ASN* 2.9 47.7 + - - -
258A PHE* 1.3 72.8 - - - +
260A LYS* 1.3 60.6 + - - +
261A GLN* 2.6 38.3 + - - -
267A LYS* 3.4 4.6 - - - +
268A ASP* 2.7 62.7 + - + +
270A MET* 3.6 13.9 - - + +
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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