Contacts of the strand formed by residues 279 - 285 (chain A) in PDB entry 1SR5
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 ILE 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU* 4.6 1.1 - - - +
133A LYS* 3.9 12.3 - - + +
134A ALA* 3.2 47.1 - - + +
138A SER* 5.7 0.9 - - - +
221A PHE* 4.7 5.6 - - + -
273A PRO* 4.5 0.3 - - - +
274A PHE* 3.0 53.1 + - + +
276A GLY 4.9 0.2 - - - -
277A ASP* 3.0 1.2 - - - +
278A ASP* 1.3 88.6 - - + +
280A THR* 1.3 70.3 + - - +
412A ILE* 3.9 12.1 - - + -
413A ARG 3.3 13.0 - - - +
414A GLU* 4.5 4.9 - - + -
421A ILE* 4.2 14.4 - - + -
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Residues in contact with THR 280 (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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271A GLU* 3.0 40.2 + - - +
272A LEU 3.5 7.4 - - - -
273A PRO* 3.7 17.3 - - + -
274A PHE* 3.5 12.1 - - - -
277A ASP* 4.2 4.9 - - - +
279A ILE* 1.3 78.8 - - - +
281A MET* 1.3 63.2 + - - +
282A VAL* 4.2 1.0 - - - +
412A ILE* 3.6 2.9 - - - +
413A ARG* 3.0 39.5 + - - +
415A VAL* 3.4 26.2 - - + -
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Residues in contact with MET 281 (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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225A TRP* 3.5 28.5 - - + -
270A LEU 3.9 0.2 - - - +
271A GLU* 3.6 0.3 - - - -
272A LEU* 2.7 37.5 + - + +
274A PHE* 3.7 19.1 - - + -
280A THR* 1.3 76.9 - - - +
282A VAL* 1.3 62.3 + - - +
283A LEU* 3.4 20.9 + - + +
320A MET* 4.7 4.5 - - + -
323A PHE* 5.0 2.2 - - + -
373A LEU* 4.1 18.6 - - + -
375A VAL* 4.5 11.4 - - + -
408A PHE* 6.2 0.2 - - + -
410A VAL* 3.1 37.7 - - + -
411A PHE 3.2 9.4 - - - +
412A ILE* 4.3 9.2 - - + +
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Residues in contact with VAL 282 (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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269A VAL* 4.2 20.6 - - + -
270A LEU 3.4 8.7 - - - +
271A GLU* 3.9 19.5 - - + +
280A THR* 4.2 1.3 - - - +
281A MET* 1.3 71.8 - - - +
283A LEU* 1.3 71.3 + - - +
284A ILE* 4.6 9.4 - - + -
304A LEU* 5.0 5.8 - - + -
308A LEU* 3.3 31.2 - - + -
409A LEU 3.9 0.3 - - - +
410A VAL* 3.5 2.8 - - - -
411A PHE* 2.6 54.2 + - + +
413A ARG* 4.2 12.6 - - + +
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Residues in contact with LEU 283 (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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268A GLN 3.6 1.6 - - - +
269A VAL* 3.6 2.9 - - - -
270A LEU* 2.7 43.5 + - + +
272A LEU* 4.4 18.6 - - + -
281A MET* 3.4 37.7 - - + +
282A VAL* 1.3 83.8 - - - +
284A ILE* 1.3 62.8 + - - +
285A LEU 3.7 0.5 + - - -
318A VAL* 6.0 0.2 - - + -
320A MET* 4.2 25.8 - - + -
402A PHE* 3.9 31.0 - - + -
404A ALA* 5.5 0.2 - - + -
408A PHE* 4.0 21.5 - - + -
409A LEU 3.6 5.6 - - - +
410A VAL* 4.5 3.1 - - + -
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Residues in contact with ILE 284 (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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267A THR* 4.6 11.4 - - - +
268A GLN 3.6 7.0 - - - +
269A VAL* 4.6 6.3 - - + -
282A VAL* 4.6 7.6 - - + -
283A LEU* 1.3 72.6 - - - +
285A LEU* 1.3 60.3 + - - +
286A PRO* 3.2 10.3 - - + +
292A LEU* 4.3 0.8 - - + +
295A VAL* 4.3 18.4 - - + -
304A LEU* 5.0 0.9 - - + -
307A TRP* 2.7 48.9 - - + -
408A PHE* 2.9 22.8 - - - +
409A LEU* 3.0 31.9 + - + -
411A PHE* 3.6 33.0 - - + -
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Residues in contact with LEU 285 (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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267A THR* 4.4 0.9 - - - -
268A GLN* 2.7 62.2 + - + +
283A LEU 3.7 0.6 + - - -
284A ILE* 1.3 70.3 - - - +
286A PRO* 1.3 65.8 - - + +
402A PHE* 3.4 35.2 - - + -
403A LYS 3.5 28.3 - - - +
404A ALA* 3.8 11.0 - - - -
406A ARG* 3.4 51.1 - - + +
408A PHE* 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