Contacts of the strand formed by residues 316 - 324 (chain A) in PDB entry 1SDW
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 ASN 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A LEU* 4.1 3.4 - - + -
207A MET 3.4 3.4 - - - -
208A MET* 3.5 11.9 - - - +
240A ARG 4.6 0.2 - - - -
241A VAL* 3.4 6.5 - - - +
242A HIS* 2.9 46.5 + - + +
250A VAL* 4.0 6.3 - - - +
293A CYS* 4.2 1.0 - - - -
314A MET* 4.6 0.2 - - - -
315A CYS* 1.3 85.9 + - - +
317A LEU* 1.3 61.1 + - - +
318A TYR* 3.6 17.9 - - + -
701A IYT 3.0 64.5 + - - +
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Residues in contact with LEU 317 (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 TYR 3.6 3.3 - - - +
206A LEU* 3.7 1.0 - - - -
207A MET* 2.9 41.6 + - + +
225A ILE* 5.7 0.9 - - + +
239A TYR* 4.2 16.2 - - + -
240A ARG 3.6 12.8 - - - +
241A VAL* 3.9 17.3 - - + -
250A VAL* 4.4 9.9 - - + +
251A SER 4.3 1.1 - - - -
252A GLY* 3.4 37.0 - - - +
263A ILE* 5.7 3.1 - - + -
264A GLY* 5.3 3.8 - - - +
291A ALA* 4.0 13.7 - - + -
316A ASN* 1.3 75.1 - - - +
318A TYR* 1.3 65.7 + - - +
319A ILE* 4.0 24.2 - - + +
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Residues in contact with TYR 318 (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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137A ILE* 3.6 23.6 - - + -
204A MET* 3.8 14.6 - - + -
205A TYR 3.8 3.4 - - - -
206A LEU* 3.8 18.2 - - + -
239A TYR* 3.1 9.7 - - - +
240A ARG* 2.8 58.2 + - + +
242A HIS* 4.4 1.3 - - + -
274A PHE* 3.8 14.2 - + + -
316A ASN* 3.6 19.1 - - + -
317A LEU* 1.3 73.9 - - - +
319A ILE* 1.3 60.8 + - - +
320A MET 3.9 0.6 + - - -
368A GOL 3.7 19.1 - - - -
701A IYT 2.6 66.5 + + + +
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Residues in contact with ILE 319 (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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204A MET* 3.5 3.2 - - - -
205A TYR* 2.8 51.5 + - + +
207A MET* 4.0 27.4 - - + -
234A MET* 4.3 10.5 - - + -
236A VAL* 3.3 40.6 - - + -
238A ALA 3.9 2.7 - - - -
239A TYR* 4.7 0.9 - - + +
263A ILE* 4.0 28.0 - - + -
289A LEU* 4.4 8.1 - - + -
317A LEU* 4.0 21.1 - - + +
318A TYR* 1.3 75.0 - - - +
320A MET* 1.3 59.6 + - - +
321A TYR* 3.7 2.6 - - - -
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Residues in contact with MET 320 (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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138A LEU 3.7 10.8 - - - +
156A PHE* 4.0 12.1 - - + -
202A ALA* 5.0 0.2 - - + -
203A GLY 3.5 13.2 - - - +
204A MET* 3.6 23.6 - - + -
236A VAL* 3.5 3.3 - - - -
237A PHE* 2.9 53.0 + - + -
238A ALA* 2.8 26.1 + - + +
274A PHE* 3.8 21.1 - - + -
318A TYR 3.9 2.0 + - - -
319A ILE* 1.3 71.5 - - - +
321A TYR* 1.3 61.6 + - - +
364A GOL 3.5 47.6 - - - +
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Residues in contact with TYR 321 (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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201A ILE 4.9 0.7 - - - -
202A ALA* 3.1 7.0 - - - +
203A GLY* 2.8 42.9 + - - +
204A MET 3.3 22.6 + - - -
205A TYR* 3.6 2.2 - - + -
234A MET* 3.4 27.1 - - + -
235A HIS 3.1 19.7 - - - +
236A VAL* 4.1 3.6 - - + -
237A PHE* 3.5 8.4 - - - -
319A ILE 3.7 12.1 - - - -
320A MET* 1.3 76.0 - - - +
322A TYR* 1.3 62.9 + - - +
323A MET* 3.6 27.1 - - + -
329A LEU 2.8 26.2 + - - -
330A SER 3.4 14.0 - - - -
331A PHE* 3.4 3.6 + - - -
332A MET* 3.2 27.9 - - + +
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Residues in contact with TYR 322 (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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151A PRO* 5.1 3.8 - - + -
154A VAL* 4.1 28.9 - - + -
200A LEU* 3.9 33.4 - - + -
201A ILE 3.2 9.4 - - - +
233A PRO 4.6 0.2 - - - +
234A MET* 3.7 0.3 - - - -
235A HIS* 3.0 71.1 + + + +
237A PHE* 3.7 27.6 - + + -
280A PRO* 5.9 1.9 - - - +
321A TYR* 1.3 75.3 - - - +
323A MET* 1.3 68.6 + - - +
324A GLU* 5.3 3.4 - - - -
367A GOL 5.0 8.3 - - - -
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Residues in contact with MET 323 (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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200A LEU* 3.4 7.5 - - - -
201A ILE* 2.9 28.0 + - - +
229A TYR* 3.8 6.1 - - - +
232A TYR* 3.2 37.9 - - + +
233A PRO 3.5 15.7 - - - +
234A MET* 3.8 2.0 - - - -
321A TYR* 3.6 25.8 - - + -
322A TYR* 1.3 81.8 - - - +
324A GLU* 1.3 65.9 + - - +
325A ALA 3.4 0.2 + - - -
327A TYR* 3.5 22.9 - - + +
328A ALA* 3.8 14.6 - - + -
329A LEU* 3.6 37.5 - - + -
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Residues in contact with GLU 324 (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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199A PRO* 3.8 7.3 - - - +
200A LEU* 3.7 19.8 - - - +
233A PRO 5.2 1.2 + - - -
322A TYR* 5.2 3.8 - - - -
323A MET* 1.3 73.4 - - - +
325A ALA* 1.3 66.0 + - - +
326A LYS* 4.6 5.6 - - + +
327A TYR* 3.0 43.9 + - + +
328A ALA* 3.0 10.6 + - - +
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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