Contacts of the strand formed by residues 295 - 300 (chain A) in PDB entry 1SR0
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 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A HIS* 3.1 43.3 - - + +
199A SER 3.7 13.9 - - - +
200A PRO* 4.2 4.5 - - + -
289A ARG* 2.9 8.3 - - - +
290A PHE* 2.9 32.7 + - + +
293A GLN* 3.4 28.0 - - + +
294A GLN* 1.3 82.3 - - - +
296A PRO* 1.3 66.2 - - + +
308A ASP* 3.7 15.0 - - - +
312A SER* 4.2 1.3 - - - -
316A LYS* 4.1 6.5 - - - +
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Residues in contact with PRO 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A HIS* 2.8 29.3 + - - -
287A THR* 6.2 0.2 - - - -
288A HIS 3.4 15.0 - - - +
289A ARG* 3.5 16.4 - - - +
295A VAL* 1.3 85.8 - - + +
297A TYR* 1.3 63.8 + - - +
307A TYR* 3.0 58.0 + - + +
309A ASP* 3.4 26.9 - - - +
312A SER* 4.0 4.9 - - - -
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Residues in contact with TYR 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A THR* 4.1 11.6 - - + +
252A ASP* 4.8 11.0 - - - +
253A VAL* 5.0 3.6 + - - +
287A THR* 3.7 1.2 - - - -
288A HIS* 2.9 71.7 + + + +
289A ARG* 3.7 12.8 - - - -
290A PHE* 3.7 39.2 - + + -
296A PRO* 1.3 82.0 - - - +
298A ALA* 1.3 61.0 + - - +
299A THR* 4.6 0.7 - - - -
304A TRP* 3.0 47.3 - + + -
305A VAL 3.1 14.4 - - - +
306A ALA* 4.2 0.4 - - + -
307A TYR* 3.8 5.7 - - - -
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Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE* 4.1 13.7 - - + -
282A LEU* 3.9 28.3 - - + -
285A ALA* 4.4 2.9 - - + -
286A THR 3.2 13.5 - - - +
287A THR* 4.4 4.3 - - + -
297A TYR* 1.3 74.6 - - - +
299A THR* 1.3 65.1 + - - +
303A GLN 4.4 0.2 - - - -
304A TRP* 3.5 2.3 - - - -
305A VAL* 2.6 36.5 + - + +
307A TYR* 3.7 8.2 - - + -
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Residues in contact with THR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 3.9 16.2 - - + -
251A THR* 3.6 28.5 - - - +
281A PHE* 4.3 2.2 - - - -
285A ALA* 3.4 1.6 - - - -
286A THR* 3.0 36.7 + - - -
288A HIS* 4.8 3.0 - - - -
297A TYR* 4.6 1.6 - - - -
298A ALA* 1.3 71.7 + - - +
300A LYS* 1.3 67.6 + - - +
301A GLY 4.2 7.2 - - - +
303A GLN 3.0 14.6 - - - +
304A TRP* 3.0 26.7 + - - -
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Residues in contact with LYS 300 (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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280A ASP* 4.9 2.4 + - - -
281A PHE* 3.1 47.5 + - + +
283A HIS 2.9 30.4 + - - -
284A GLY* 3.5 22.9 - - - +
285A ALA* 4.0 1.6 - - + +
299A THR* 1.3 76.1 - - - +
301A GLY* 1.3 65.6 + - - +
302A ASN 3.3 0.3 + - - -
303A GLN* 2.8 25.0 + - - +
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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