Contacts of the strand formed by residues 268 - 276 (chain A) in PDB entry 5BUG
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 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A PHE* 4.3 20.1 - - + +
258A PHE* 3.1 6.0 - - - -
259A HIS* 2.6 64.1 + - + +
261A GLN* 4.4 7.3 + - - +
266A LYS* 3.7 14.6 - - - +
267A LYS* 1.3 74.6 - - - +
269A LYS* 1.3 60.5 + - - +
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Residues in contact with LYS 269 (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 10.4 - - - -
256A GLU* 3.4 27.3 + - + +
257A PHE 4.0 0.7 - - - +
258A PHE* 3.8 21.3 - - + -
266A LYS* 3.4 24.4 - - - +
268A ASP* 1.3 72.8 - - - +
270A MET* 1.3 65.0 + - - +
271A PHE* 5.3 0.7 - - - +
272A HIS* 5.6 4.6 + - - -
327A LYS* 3.6 36.7 + - + +
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Residues in contact with MET 270 (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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200A PHE* 4.3 11.0 - - + -
204A PRO* 3.4 41.7 - - + -
206A PHE* 3.5 27.9 - - + -
211A CYS* 3.7 13.2 - - + -
213A PRO* 4.4 11.0 - - - -
257A PHE* 2.9 18.8 + - - +
258A PHE 3.7 24.7 - - - +
259A HIS* 3.7 18.6 - - + +
268A ASP 3.7 0.2 + - - -
269A LYS* 1.3 75.4 - - - +
271A PHE* 1.3 77.3 + - + +
327A LYS* 3.7 17.0 - - - +
328A ALA 4.1 0.2 + - - -
337A PHE* 3.8 13.3 - - + -
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Residues in contact with PHE 271 (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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200A PHE* 3.8 17.9 - + - -
256A GLU* 3.7 2.1 - - - +
257A PHE* 2.8 64.2 + + + +
269A LYS* 3.9 1.5 - - - +
270A MET* 1.3 93.9 - - + +
272A HIS* 1.3 70.8 + - - +
273A PHE* 4.1 9.4 - + - -
325A LEU* 3.8 27.1 - - + -
327A LYS* 4.2 9.4 - - - +
328A ALA* 3.9 21.5 - - + +
337A PHE* 3.9 15.0 - + - -
341A PHE* 4.0 11.9 - + - -
343A VAL* 3.7 31.2 - - + -
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Residues in contact with HIS 272 (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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93A HIS* 4.8 11.7 - - + -
94A ASN* 4.9 2.2 - - - -
168A ILE* 5.6 0.2 - - + -
254A LYS* 3.6 28.1 + - - -
255A VAL 3.2 14.8 - - - +
256A GLU* 3.7 24.5 - - + +
269A LYS* 5.6 5.0 + - - -
271A PHE* 1.3 81.8 - - - +
273A PHE* 1.3 69.8 + - - +
274A TRP* 4.6 3.0 - + - -
325A LEU* 3.8 2.4 - - - -
326A ASP* 2.8 66.4 + - + +
327A LYS* 4.5 9.7 + - + +
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Residues in contact with PHE 273 (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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170A SER* 3.8 7.6 - - - +
173A ARG* 4.3 11.4 - - - +
198A MET* 4.4 0.7 - - - -
253A ILE* 5.2 1.6 - - + -
254A LYS* 3.3 4.8 - - - +
255A VAL* 2.9 74.5 + - + +
257A PHE* 4.8 1.1 - + - -
271A PHE* 4.1 16.2 - + - -
272A HIS* 1.3 79.7 - - - +
274A TRP* 1.3 65.6 + - - +
275A VAL* 3.9 13.9 - - + -
320A LEU* 3.7 16.2 - - + -
324A ASP 4.6 4.0 - - - +
325A LEU* 3.8 22.0 - - + -
326A ASP* 4.3 1.6 - - - -
343A VAL* 4.8 5.6 - - + -
345A LEU* 3.6 43.3 - - + -
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Residues in contact with TRP 274 (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* 2.8 33.4 + - + -
95A PRO* 3.4 36.3 - - + -
170A SER* 3.1 18.0 + - - +
173A ARG* 2.8 29.1 + - - -
174A TYR* 4.1 16.1 - - + -
220A LEU* 4.1 31.4 - - + -
252A ASP* 4.0 25.1 - - + -
253A ILE 3.2 22.7 - - - -
254A LYS* 3.3 39.0 - - + +
272A HIS* 4.6 1.3 - + - -
273A PHE* 1.3 77.5 - - - +
275A VAL* 1.3 60.5 + - - +
326A ASP* 4.4 5.4 - - - -
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Residues in contact with VAL 275 (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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173A ARG* 4.3 8.1 - - - +
174A TYR* 3.8 5.4 + - - -
177A TYR* 3.7 11.2 - - - +
252A ASP* 3.7 1.6 - - - -
253A ILE* 2.8 42.9 + - + +
273A PHE* 3.9 23.3 - - + -
274A TRP* 1.3 79.6 - - - +
276A ASN* 1.3 64.3 + - - +
277A THR* 4.7 1.8 - - + +
280A ILE* 3.4 32.1 - - + -
318A LEU* 3.7 22.0 - - + -
320A LEU* 4.4 5.6 - - + -
345A LEU* 4.6 5.8 - - + -
347A PHE* 5.0 3.8 - - + -
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Residues in contact with ASN 276 (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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98A LEU* 3.7 10.9 - - - +
177A TYR* 3.1 29.1 + - + -
188A TYR* 3.3 26.8 + - - -
251A GLY 3.3 7.8 - - - +
252A ASP* 2.7 32.3 + - - +
275A VAL* 1.3 76.7 - - - +
277A THR* 1.3 59.5 + - - +
278A PHE* 2.9 26.9 + - - +
279A PHE* 2.9 34.6 + - + +
280A ILE* 3.9 4.7 - - - +
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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