Contacts of the strand formed by residues 307 - 315 (chain E) 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 PHE 307 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E VAL* 4.0 15.3 - - + -
169E PRO* 3.6 34.3 - - + -
172E ALA* 3.3 29.6 - - + -
173E GLU* 5.7 0.4 - - - -
176E LYS* 5.1 8.1 - - - -
181E TYR* 3.4 20.0 - + - -
186E LEU* 5.6 1.1 - - + -
297E PHE* 3.3 23.7 - + + -
298E VAL 3.2 7.6 - - - +
299E SER* 3.5 25.4 - - - -
300E SER* 4.2 0.9 - - - -
305E LEU* 3.5 9.5 - - - +
306E PRO* 1.3 92.6 - - + +
308E PHE* 1.3 67.9 + - - +
343E LEU* 4.1 0.9 - - - +
347E ILE* 3.5 28.1 - - + +
351E VAL* 5.3 4.0 - - + -
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Residues in contact with PHE 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E VAL* 4.2 1.3 - - + -
218E GLY* 3.3 27.4 - - - -
226E LEU* 5.9 0.2 - - + -
296E ALA 3.7 1.7 - - - +
297E PHE* 3.4 12.2 - - - -
298E VAL* 2.9 26.6 + - - +
300E SER* 3.1 21.8 + - - +
302E VAL* 5.0 2.5 - - + -
303E THR* 3.7 33.7 - - + +
305E LEU* 4.1 7.9 - - + -
307E PHE* 1.3 74.6 - - - +
309E ALA* 1.3 77.8 + - - +
310E SER* 3.7 4.3 + - - -
325E LEU* 3.8 27.1 - - + -
336E LEU* 3.7 23.8 - - + -
339E ALA* 5.4 1.1 - - + -
340E LYS* 4.4 11.0 - - + -
343E LEU* 3.5 27.8 - - + -
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Residues in contact with ALA 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E THR* 4.3 12.6 - - + +
216E VAL* 4.4 5.8 - - + +
217E VAL* 2.9 15.6 - - - +
218E GLY 2.6 52.8 + - - +
219E GLY* 4.1 2.5 - - - +
296E ALA* 3.5 7.9 - - - +
297E PHE* 3.7 20.6 - - + +
308E PHE* 1.3 74.8 - - - +
310E SER* 1.3 62.3 + - - +
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Residues in contact with SER 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216E VAL 4.6 2.6 + - - -
217E VAL* 3.9 9.2 - - - -
295E CYS* 4.2 6.3 - - - -
296E ALA 3.4 14.7 + - - +
298E VAL* 5.9 0.2 - - - +
300E SER* 5.1 0.6 + - - -
302E VAL* 4.2 3.3 - - - +
308E PHE* 3.7 5.9 + - - -
309E ALA* 1.3 75.7 - - - +
311E LYS* 1.3 65.6 + - - +
312E VAL* 3.2 13.9 + - - +
322E VAL* 3.5 16.6 - - - +
323E TYR 3.1 24.8 + - - -
324E SER 5.1 2.0 - - - -
325E LEU* 4.0 19.5 - - - -
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Residues in contact with LYS 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215E PRO* 4.1 19.5 - - + -
217E VAL* 5.0 2.0 - - + +
231E GLN* 5.1 4.9 - - - +
233E LYS* 5.9 3.8 - - - +
293E ILE* 3.4 36.1 - - + +
294E GLU* 3.3 8.3 - - - +
295E CYS* 3.5 23.1 - - - +
310E SER* 1.3 76.4 + - - +
312E VAL* 1.3 59.6 + - - +
323E TYR* 2.9 42.2 + - + +
324E SER 5.5 4.6 + - - +
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Residues in contact with VAL 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E LEU* 4.4 4.3 - - + -
293E ILE* 3.4 1.2 - - - -
294E GLU* 2.6 47.6 + - + +
296E ALA* 4.0 20.2 - - + +
298E VAL* 3.8 28.0 - - + -
310E SER 3.4 13.0 - - - +
311E LYS* 1.3 75.3 - - - +
313E ARG* 1.3 60.7 + - - +
314E LEU* 3.7 20.7 + - + +
319E ILE* 4.0 13.5 - - + -
321E GLU 3.3 6.3 - - - +
322E VAL* 4.1 14.1 - - + -
323E TYR* 4.3 4.5 - - - -
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Residues in contact with ARG 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291E GLY* 5.0 12.6 - - - +
292E VAL 3.4 17.9 - - - +
293E ILE* 4.4 5.2 - - + +
312E VAL* 1.3 72.9 - - - +
314E LEU* 1.3 68.3 + - - +
319E ILE* 3.6 3.3 - - - -
320E GLU* 2.8 68.6 + - - +
321E GLU* 2.8 35.3 + - + +
323E TYR* 3.5 26.8 + - + +
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Residues in contact with LEU 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E LEU* 3.7 29.8 - - + -
278E PHE* 4.4 3.6 - - + -
281E ALA* 3.5 44.6 - - + +
282E CYS* 3.7 15.5 - - - +
285E GLY* 3.6 13.6 - - - -
289E ASP 4.4 5.5 - - - +
292E VAL* 2.8 36.3 + - + +
294E GLU* 3.8 13.5 - - + -
312E VAL* 4.0 16.2 - - + +
313E ARG* 1.3 81.3 - - - +
315E GLY* 1.3 59.8 + - - +
318E GLY* 3.4 8.7 - - - +
319E ILE* 4.9 0.7 - - + -
320E GLU* 4.8 0.2 - - - -
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Residues in contact with GLY 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282E CYS 4.8 1.0 - - - +
285E GLY* 3.4 19.6 - - - -
286E LEU* 3.5 4.9 + - - +
289E ASP 5.5 1.3 - - - -
313E ARG 3.6 2.0 + - - -
314E LEU* 1.3 74.6 - - - +
316E ARG* 1.3 63.0 + - - -
317E ASN 3.1 7.4 + - - -
318E GLY* 2.6 23.0 + - - +
320E GLU* 4.2 17.0 - - - +
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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