Contacts of the strand formed by residues 269 - 279 (chain A) in PDB entry 2ZB5
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 VAL 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A MET* 4.0 15.9 - - + +
202A SER* 3.9 19.3 - - - +
203A LEU* 4.0 20.6 - - + -
259A VAL 3.5 0.2 - - - +
260A ILE* 4.4 0.9 - - - -
261A ARG* 2.8 40.9 + - + +
263A PRO* 3.8 26.7 - - + -
265A LEU* 4.4 14.8 - - + -
267A ALA 3.6 11.0 - - - +
268A PRO* 1.3 79.8 - - - +
270A PHE* 1.3 75.2 + - - +
271A HIS* 3.5 0.9 + - + -
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Residues in contact with PHE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A MET 4.8 0.6 + - - -
202A SER* 4.5 3.5 - - - +
203A LEU* 2.8 35.2 + - - +
204A SER* 4.0 13.5 - - - -
207A ASP* 4.5 11.2 - - - +
223A THR* 4.2 9.4 - - + -
228A TYR* 3.5 48.0 - + + -
259A VAL 3.7 4.3 - - - -
260A ILE* 4.2 13.5 - - + +
268A PRO* 5.2 0.7 - - + -
269A VAL* 1.3 76.2 - - - +
271A HIS* 1.3 59.2 + - - +
569A GLU* 3.8 26.2 - - + -
571A PHE* 3.9 29.6 - + - -
580A ARG* 5.0 3.8 - - + -
599A MET* 3.4 32.8 - - + -
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Residues in contact with HIS 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LEU* 3.4 28.0 - - + -
228A TYR* 3.7 3.7 - - - -
258A GLY* 3.2 0.5 - - - -
259A VAL 2.8 35.4 + - - +
261A ARG* 3.1 49.8 + - + -
269A VAL* 4.4 0.7 - - + +
270A PHE* 1.3 74.7 - - - +
272A MET* 1.3 77.3 + - - +
273A THR* 3.3 18.8 + - + +
327A TRP* 5.5 2.2 - + - -
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Residues in contact with MET 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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203A LEU 2.9 16.1 + - - +
205A LEU* 3.6 33.4 - - + +
228A TYR* 3.2 17.8 + - - +
256A GLU* 3.6 24.0 - - + +
257A VAL 3.9 3.6 - - - +
271A HIS* 1.3 86.4 + - - +
273A THR* 1.3 62.3 + - - +
274A ASN 4.0 11.2 - - - +
275A TYR* 3.4 43.5 - - + -
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Residues in contact with THR 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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257A VAL 3.1 4.3 + - - -
258A GLY* 3.5 14.7 - - - -
259A VAL* 4.5 2.0 - - + -
261A ARG* 4.1 5.6 - - - +
271A HIS* 3.3 34.1 + - + +
272A MET* 1.3 77.9 - - - +
274A ASN* 1.3 65.4 + - - +
326A VAL* 2.5 30.4 + - - +
327A TRP* 3.7 26.1 - - + -
328A LYS* 4.5 8.8 + - - +
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Residues in contact with ASN 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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257A VAL* 3.2 33.6 + - + +
272A MET* 3.8 3.5 - - - +
273A THR* 1.3 83.1 - - - +
275A TYR* 1.3 76.0 + - - +
324A LEU* 3.5 14.6 - - - +
325A GLY 2.9 36.7 + - - +
326A VAL 4.2 1.3 - - - +
328A LYS* 3.8 33.6 + - - +
332A ASP* 3.2 24.1 + - - +
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Residues in contact with TYR 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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205A LEU* 3.5 30.8 - - + +
254A VAL* 4.0 12.6 - - + -
255A PHE 3.2 12.6 - - - +
256A GLU* 4.2 3.6 - - - -
272A MET* 3.4 32.3 - - + -
274A ASN* 1.3 86.7 + - - +
276A LEU* 1.3 64.1 + - - +
277A GLU* 4.2 21.1 + - + -
324A LEU* 3.9 5.4 - - - -
328A LYS* 5.3 4.2 + - - -
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Residues in contact with LEU 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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254A VAL* 3.5 4.5 - - - +
255A PHE* 2.8 45.1 + - + -
275A TYR* 1.3 76.9 - - - +
277A GLU* 1.3 80.5 + - - +
278A GLN* 4.7 1.3 - - - +
322A VAL* 3.8 25.8 - - + -
324A LEU* 3.8 20.1 - - + +
333A MET 5.7 0.7 - - - +
334A GLN* 3.6 37.7 - - + +
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Residues in contact with GLU 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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209A TYR* 3.3 14.0 + - - -
236A LYS* 2.6 36.6 + - - -
252A TYR* 3.7 20.2 - - + -
253A ARG 3.5 5.2 - - - +
254A VAL* 3.8 25.6 - - + +
275A TYR* 4.2 20.6 - - + -
276A LEU* 1.3 87.9 - - - +
278A GLN* 1.3 68.9 + - - +
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Residues in contact with GLN 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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252A TYR* 3.3 8.1 - - - -
253A ARG* 2.8 39.1 + - + +
255A PHE* 3.9 17.3 - - + -
276A LEU* 5.2 1.3 - - + -
277A GLU* 1.3 78.5 - - - +
279A PRO* 1.3 78.4 - - + +
284A LEU* 3.2 25.5 - - - +
320A GLN* 3.1 28.9 + - - +
322A VAL* 5.8 0.2 - - - -
334A GLN* 3.1 34.1 + - - +
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Residues in contact with PRO 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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250A SER* 5.9 0.7 - - - +
251A MET 3.4 11.4 - - - +
252A TYR* 3.6 21.7 - - + +
278A GLN* 1.3 95.2 - - + +
280A VAL* 1.3 65.1 + - - +
281A SER* 3.3 6.2 + - - -
284A LEU* 5.1 2.1 - - - +
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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