Contacts of the strand formed by residues 261 - 268 (chain A) in PDB entry 3SMZ
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 LEU 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A GLY* 4.2 16.6 - - - -
232A PHE 3.4 31.0 - - - +
233A ASN* 3.5 33.4 - - + +
253A LEU* 4.3 12.6 - - + -
254A ALA 3.6 13.7 - - - +
255A CYS* 4.0 6.5 - - + -
259A GLY 4.0 1.9 + - - +
260A GLN* 1.3 94.5 + - - +
262A LYS* 1.3 60.3 + - - +
263A GLY* 3.2 9.0 + - - +
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Residues in contact with LYS 262 (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 ALA 3.0 13.4 + - - +
255A CYS* 3.9 4.0 - - - +
256A GLY* 3.5 39.4 - - - +
257A GLN* 4.7 2.6 - - - +
258A ASP* 3.9 17.6 + - - -
260A GLN* 3.9 8.1 - - - -
261A LEU* 1.3 72.6 - - - +
263A GLY* 1.3 58.5 + - - +
264A PHE* 3.5 27.7 + - + -
311A ILE* 4.3 21.7 + - + +
314A GLN* 4.0 29.8 + - + +
315A ALA* 5.9 2.0 - - - +
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Residues in contact with GLY 263 (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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226A ASP* 4.1 8.8 - - - +
227A ARG 4.5 2.4 + - - -
228A LEU* 3.6 26.2 + - - +
254A ALA 4.2 1.4 + - - -
261A LEU* 3.2 10.4 - - - +
262A LYS* 1.3 78.8 - - - +
264A PHE* 1.3 60.4 + - - +
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Residues in contact with PHE 264 (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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224A CYS* 4.1 18.2 - - - -
225A VAL 3.4 10.5 - - - +
226A ASP* 3.9 12.6 - - + -
228A LEU* 4.0 6.9 - - - +
253A LEU* 3.7 2.6 - - - +
254A ALA* 2.8 55.5 + - + +
262A LYS* 3.5 19.9 - - + -
263A GLY* 1.3 79.4 - - - +
265A ALA* 1.4 57.8 + - - +
266A VAL* 4.0 16.8 - - + -
307A LEU* 4.5 2.2 - - + -
310A LEU* 3.7 33.2 - - + -
311A ILE* 3.7 17.9 - - + -
314A GLN* 3.4 30.7 - - - -
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Residues in contact with ALA 265 (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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223A LEU 3.8 0.3 - - - +
224A CYS* 3.3 7.6 - - - -
225A VAL* 2.7 44.2 + - + +
228A LEU* 4.8 2.7 - - + -
238A LEU* 3.8 28.7 - - + -
252A GLN 3.3 15.7 - - - +
253A LEU* 4.1 7.0 - - + +
254A ALA 4.5 0.7 - - - +
264A PHE* 1.4 75.1 - - - +
266A VAL* 1.3 62.0 + - - +
267A LEU* 4.1 8.5 - - + -
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Residues in contact with VAL 266 (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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222A CYS* 4.8 1.6 - - + -
223A LEU 3.4 8.5 - - - +
224A CYS* 5.0 0.2 - - - -
250A PHE* 3.2 20.4 - - - -
252A GLN 3.2 16.6 + - - +
264A PHE* 4.0 6.7 - - + -
265A ALA* 1.3 75.8 - - - +
267A LEU* 1.3 64.0 + - - +
297A CYS* 4.5 3.4 - - - -
303A GLY* 3.4 29.2 - - - +
306A MET* 4.0 18.6 - - + -
307A LEU* 3.8 31.7 - - + +
310A LEU* 3.8 28.0 - - + -
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Residues in contact with LEU 267 (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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221A ARG 4.0 0.3 - - - +
222A CYS* 3.0 7.9 - - - +
223A LEU* 2.7 42.7 + - + +
225A VAL* 3.8 22.4 - - + -
238A LEU* 4.6 2.5 - - + -
242A LEU* 3.9 25.4 - - + -
248A PRO* 4.2 6.7 - - + -
250A PHE* 3.3 9.9 - - - +
251A CYS* 3.6 36.1 - - + -
265A ALA* 4.1 12.8 - - + -
266A VAL* 1.3 79.9 - - - +
268A GLU* 1.3 59.7 + - - +
269A TYR* 3.7 31.4 - - + +
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Residues in contact with GLU 268 (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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221A ARG* 3.5 16.9 - - - +
222A CYS* 3.9 13.2 - - - -
248A PRO* 3.5 4.7 - - - +
249A THR* 2.8 40.9 + - + +
250A PHE* 3.0 29.9 + - + +
267A LEU* 1.3 73.9 - - - +
269A TYR* 1.3 69.0 + - - +
301A PRO 4.9 0.2 - - - +
302A PRO* 3.5 19.6 - - - +
303A GLY* 2.7 30.4 + - - +
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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