Contacts of the strand formed by residues 268 - 279 (chain A) in PDB entry 3D0O
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 GLU 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A LEU 3.4 5.6 - - - -
262A GLU* 3.8 8.7 - - + +
263A GLY* 3.3 23.2 - - - +
266A GLU 5.7 0.4 - - - -
267A GLU* 1.3 81.5 + - - +
269A ASP* 1.3 70.3 + - + +
270A VAL* 3.3 4.1 + - - +
307A LYS* 2.8 31.5 + - - +
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Residues in contact with ASP 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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131A TYR* 2.6 40.6 + - - -
134A TRP* 4.5 7.7 - - - -
135A LYS* 4.5 3.7 + - - -
260A LEU* 4.4 6.0 - - - +
261A LEU 3.1 9.6 + - - -
262A GLU* 5.0 1.6 - - - +
268A GLU* 1.3 79.4 - - + +
270A VAL* 1.3 59.3 + - - +
307A LYS* 3.8 16.5 - - - +
310A MET* 4.3 4.3 - - - +
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Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TYR* 4.2 4.9 - - - -
259A ALA 3.6 0.5 - - - +
260A LEU* 3.9 8.1 - - - +
261A LEU* 2.9 36.1 + - + +
267A GLU* 4.3 21.5 - - + -
268A GLU 3.3 10.7 - - - +
269A ASP* 1.3 79.4 - - - +
271A TYR* 1.3 74.3 - - - +
272A ILE* 4.5 3.8 - - + -
303A ALA* 4.3 12.1 - - + +
306A LEU* 4.0 22.0 - - + -
307A LYS* 3.7 24.2 - - + -
310A MET* 4.0 6.5 - - + -
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Residues in contact with TYR 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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127A ASP* 3.4 33.5 - - - +
130A ALA* 3.6 20.9 - - + -
131A TYR* 3.5 24.2 - + + +
134A TRP* 3.7 28.8 - + + +
141A LYS* 3.5 10.6 + - - -
144A VAL* 2.8 42.0 + - + +
258A SER* 3.5 28.5 - - - +
259A ALA* 3.2 10.1 - - - -
260A LEU* 3.4 37.0 - - + -
270A VAL* 1.3 80.6 - - - +
272A ILE* 1.3 65.2 + - - +
283A ILE* 5.0 0.2 - - + -
306A LEU* 3.6 1.7 - - - +
310A MET* 4.8 1.3 - - - +
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Residues in contact with ILE 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASP* 3.5 10.3 - - - -
177A GLY* 3.3 30.1 - - - +
178A GLU 3.6 2.2 - - - +
258A SER* 3.5 3.6 + - - -
259A ALA 3.0 22.0 + - - +
261A LEU* 3.5 34.5 - - + -
270A VAL* 4.5 6.1 - - + -
271A TYR* 1.3 77.9 - - - +
273A GLY* 1.3 72.3 + - - +
274A VAL* 3.3 6.7 + - + +
299A PHE* 3.8 16.8 - - + +
302A SER* 3.8 6.5 - - - +
303A ALA* 3.7 37.9 - - + +
306A LEU* 3.7 9.6 - - + -
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Residues in contact with GLY 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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127A ASP* 3.7 4.7 + - - -
149A THR* 4.1 15.3 - - - -
176A ILE* 3.3 8.5 - - - +
177A GLY 2.8 45.2 + - - -
257A VAL 3.3 13.7 - - - -
258A SER* 4.1 1.3 - - - -
272A ILE* 1.3 70.4 - - - +
274A VAL* 1.3 65.6 + - - +
299A PHE* 3.7 2.1 - - - -
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Residues in contact with VAL 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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149A THR* 4.7 0.4 + - - -
176A ILE* 4.3 3.1 - - + -
256A THR* 4.0 5.2 - - - -
257A VAL 3.0 26.7 + - - +
259A ALA* 3.9 20.4 - - + -
261A LEU* 4.2 9.4 - - + -
265A TYR* 3.7 20.6 - - + -
272A ILE* 3.6 13.7 - - + +
273A GLY* 1.3 78.8 - - - +
275A PRO* 1.4 77.5 - - + +
276A ALA* 3.5 2.2 + - + +
286A VAL* 3.8 23.3 - - + -
299A PHE* 3.6 25.8 - - + -
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Residues in contact with PRO 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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174A GLN* 3.4 24.7 - - - +
176A ILE* 3.9 18.4 - - + -
254A VAL* 3.7 17.9 - - + -
255A LEU 3.6 7.2 - - - +
256A THR* 4.0 5.3 - - + -
265A TYR* 3.8 11.2 - - - +
274A VAL* 1.4 87.5 - - + +
276A ALA* 1.3 60.0 + - - +
286A VAL* 3.7 4.5 - - - +
287A VAL* 2.9 40.5 + - + +
289A ILE* 4.0 16.4 - - + -
193B ALA* 4.2 2.2 - - + -
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Residues in contact with ALA 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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253A ALA 3.4 0.7 - - - +
254A VAL* 3.4 4.3 - - - +
255A LEU 3.0 28.5 + - - +
257A VAL* 4.0 24.7 - - + -
259A ALA* 4.6 6.7 - - + -
274A VAL 4.2 1.8 - - - +
275A PRO* 1.3 77.4 - - - +
277A VAL* 1.3 63.6 + - - +
278A ILE* 3.6 5.2 + - + +
283A ILE* 4.0 16.4 - - + -
285A ASN 3.4 13.5 - - - +
286A VAL* 4.3 3.8 - - + -
287A VAL* 4.1 3.4 - - - +
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Residues in contact with VAL 277 (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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252A ASP* 3.6 39.3 - - + +
253A ALA 3.5 4.5 - - - -
254A VAL* 4.0 13.0 - - + -
276A ALA* 1.3 71.2 - - - +
278A ILE* 1.3 57.2 + - - +
283A ILE* 3.6 4.2 - - - -
284A ARG* 2.8 58.7 + - + +
285A ASN* 2.9 29.9 + - - +
287A VAL* 3.9 20.2 - - + -
166B VAL* 4.1 9.6 - - + -
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Residues in contact with ILE 278 (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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145A ILE* 4.7 6.5 - - + -
243A ILE* 4.4 6.3 - - + +
246A ALA* 3.7 28.4 - - + +
247A ILE* 3.7 24.7 - - + -
252A ASP* 2.9 23.3 + - - -
253A ALA 2.8 18.0 + - - +
255A LEU* 4.0 20.4 - - + -
257A VAL* 4.1 18.6 - - + -
276A ALA* 3.8 10.5 - - + +
277A VAL* 1.3 81.1 - - - +
279A ASN* 1.3 62.7 + - - +
282A GLY 3.4 5.8 - - - +
283A ILE* 3.9 25.4 - - + +
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Residues in contact with ASN 279 (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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246A ALA 3.7 8.3 - - - -
247A ILE* 3.4 18.1 - - - +
250A ASN* 3.2 14.8 + - - +
251A GLU 4.1 1.1 - - - +
252A ASP* 2.9 35.1 + - - +
278A ILE* 1.3 71.4 - - - +
280A ARG* 1.3 59.5 + - - +
281A ASN* 2.8 28.0 + - - +
282A GLY* 2.9 29.9 + - - +
284A ARG* 3.8 27.0 - - - +
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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