Contacts of the strand formed by residues 293 - 299 (chain D) in PDB entry 1SMK
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 293 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284D ARG* 5.6 0.6 - - - +
291D GLY* 3.1 19.8 + - - +
292D VAL* 1.3 78.7 - - - +
294D GLU* 1.3 73.4 + - - +
311D LYS* 4.0 29.4 + - + +
312D VAL 3.1 12.6 - - - +
313D ARG* 3.8 17.7 - - + -
323D TYR* 3.7 34.1 - - + +
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Residues in contact with GLU 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D MET* 3.6 26.9 - - + +
277D LYS* 4.6 8.5 - - - +
278D PHE* 3.7 25.8 - - + -
281D ALA* 3.7 32.3 - - + +
284D ARG* 3.9 14.9 + - - -
292D VAL* 4.2 0.6 + - + -
293D ILE* 1.3 84.9 - - - +
295D CYS* 1.3 59.2 + - - +
311D LYS* 4.2 5.8 - - - +
312D VAL* 2.7 43.7 + - + +
314D LEU* 4.3 6.5 - - + +
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Residues in contact with CYS 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D THR* 3.6 10.0 + - - +
191D MET* 4.3 13.3 + - - +
194D VAL* 3.6 24.5 - - + -
215D PRO* 4.1 6.1 - - - -
216D VAL 3.6 39.3 - - - +
217D VAL* 5.6 0.7 - - - -
278D PHE* 3.8 9.5 - - - -
294D GLU* 1.3 75.3 + - - +
296D ALA* 1.3 65.3 + - - +
310D SER* 3.2 6.3 - - - +
311D LYS* 3.8 33.9 - - - -
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Residues in contact with ALA 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D LEU* 4.1 4.7 - - + -
188D GLY 3.8 7.2 - - - +
190D THR* 3.4 9.1 + - - +
278D PHE* 3.5 28.0 - - + -
294D GLU 3.9 0.2 + - - -
295D CYS* 1.3 77.1 - - - +
297D PHE* 1.3 60.3 + - - +
298D VAL* 3.4 23.7 + - + +
308D PHE 3.5 0.7 - - - +
309D ALA* 3.0 22.3 - - - +
310D SER 3.3 11.7 + - - +
312D VAL* 4.4 5.6 - - + -
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Residues in contact with PHE 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D VAL* 3.5 29.8 - - + -
165D ASN* 3.8 13.9 - - - -
168D VAL* 3.7 22.7 - - + +
169D PRO* 4.2 0.7 - - + -
187D LEU* 3.6 1.6 - - - -
188D GLY* 2.7 46.7 + - - +
190D THR* 3.7 13.5 - - + +
218D GLY 3.4 27.4 - - - -
219D GLY* 4.3 5.6 - - - -
296D ALA* 1.3 69.4 - - - +
298D VAL* 1.3 61.5 + - - +
307D PHE* 3.4 42.6 - - + -
308D PHE* 3.5 3.8 - - - -
309D ALA* 3.5 7.6 - - + +
343D LEU* 3.7 24.7 - - + -
347D ILE* 4.5 1.1 - - + -
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Residues in contact with VAL 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D VAL* 5.3 0.7 - - - -
186D LEU 4.1 4.7 - - - +
187D LEU* 3.8 19.5 - - + -
296D ALA* 4.0 12.1 - - + +
297D PHE* 1.3 78.6 - - - +
299D SER* 1.3 72.2 + - - +
300D SER* 3.4 3.5 + - - -
307D PHE* 3.3 10.0 - - - -
308D PHE 2.9 38.0 + - - +
310D SER* 5.5 0.2 - - - +
312D VAL* 4.0 22.4 - - + -
319D ILE* 3.3 31.2 - - + -
322D VAL* 4.1 13.0 - - + -
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Residues in contact with SER 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D TYR* 3.7 15.1 + - - -
183D PRO* 3.6 40.1 + - - +
186D LEU 4.9 1.4 + - - -
298D VAL* 1.3 78.7 - - - +
300D SER* 1.3 62.4 + - - +
301D GLN* 4.2 10.8 + - - -
306D PRO 3.4 10.8 + - - -
307D PHE* 3.7 13.8 - - - -
319D ILE* 5.6 0.2 - - - +
322D VAL* 4.1 7.4 - - - +
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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