Contacts of the strand formed by residues 307 - 315 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168G VAL* 3.8 20.6 - - + -
169G PRO* 3.8 30.1 - - + -
172G ALA* 3.4 30.3 - - + -
173G GLU* 5.7 2.2 - - - -
176G LYS* 5.9 3.8 - - - -
181G TYR* 3.8 9.9 - + - -
186G LEU* 5.0 3.4 - - + -
297G PHE* 3.5 23.6 - - + -
298G VAL 3.0 23.8 - - - +
299G SER* 3.6 22.4 - - - -
300G SER* 4.2 1.1 - - - +
305G LEU* 3.7 8.9 - - - +
306G PRO* 1.3 99.1 - - + +
308G PHE* 1.3 62.6 + - - +
343G LEU* 3.9 3.3 - - - +
347G ILE* 3.5 18.8 - - + +
351G VAL* 5.2 4.5 - - + -
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Residues in contact with PHE 308 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217G VAL* 4.3 1.1 - - + -
218G GLY* 3.3 31.4 - - - -
296G ALA 3.9 0.3 - - - +
297G PHE* 3.5 10.2 - - - -
298G VAL* 3.0 22.4 + - - +
300G SER* 3.5 21.7 + - - +
302G VAL* 5.0 2.5 - - + -
303G THR* 3.8 26.2 - - - +
305G LEU* 4.3 6.1 - - + +
307G PHE* 1.3 73.8 - - - +
309G ALA* 1.3 74.6 + - - +
310G SER* 3.5 5.2 + - - -
325G LEU* 3.7 33.4 - - + -
336G LEU* 3.6 24.7 - - + -
339G ALA* 5.3 1.3 - - + -
340G LYS* 4.4 18.6 - - + -
343G LEU* 3.3 24.5 - - + -
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Residues in contact with ALA 309 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G THR* 4.4 13.0 - - + +
216G VAL 4.6 3.6 - - - +
217G VAL* 3.0 15.3 - - - +
218G GLY 2.7 50.3 + - - +
219G GLY 4.6 3.6 - - - +
296G ALA* 3.1 18.6 - - - +
297G PHE* 3.2 15.8 - - + +
308G PHE* 1.3 74.5 - - - +
310G SER* 1.3 59.4 + - - +
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Residues in contact with SER 310 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216G VAL 4.8 0.9 + - - -
217G VAL* 3.9 9.4 - - - +
295G CYS* 4.4 6.1 - - - -
296G ALA 3.2 15.1 + - - +
298G VAL* 5.2 0.7 - - - +
300G SER* 4.8 0.3 + - - -
302G VAL* 4.1 5.5 - - - +
308G PHE* 3.5 8.1 + - - -
309G ALA* 1.3 75.7 - - - +
311G LYS* 1.3 66.0 + - - +
312G VAL* 3.3 13.0 + - - +
322G VAL* 3.5 19.2 - - - +
323G TYR 3.3 21.9 + - - -
324G SER 5.2 0.7 - - - -
325G LEU* 3.9 19.7 - - - -
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Residues in contact with LYS 311 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213G ASP* 4.7 12.7 + - - -
215G PRO* 4.1 30.2 - - + +
217G VAL* 4.8 3.7 - - + +
231G GLN* 4.7 7.9 - - - +
233G LYS* 5.3 11.3 - - - +
293G ILE* 4.3 21.2 - - + +
294G GLU 3.6 7.4 - - - +
295G CYS* 4.3 18.0 - - - +
310G SER* 1.3 77.9 + - - +
312G VAL* 1.3 62.1 + - - +
323G TYR* 2.9 50.5 + - + +
324G SER 5.2 6.0 + - - +
325G LEU 6.1 0.4 - - - +
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Residues in contact with VAL 312 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187G LEU* 4.6 4.7 - - + -
278G PHE* 5.5 0.2 - - + -
292G VAL 3.8 0.2 - - - +
293G ILE* 3.3 3.5 - - - -
294G GLU* 2.9 44.1 + - + +
296G ALA* 4.5 14.8 - - + +
298G VAL* 4.2 28.7 - - + -
310G SER 3.3 12.1 - - - +
311G LYS* 1.3 79.6 - - - +
313G ARG* 1.3 59.7 + - - +
314G LEU* 3.9 22.3 + - + +
319G ILE* 4.1 12.1 - - + -
321G GLU 3.3 12.3 - - - +
322G VAL* 4.3 6.5 - - + -
323G TYR* 4.0 6.5 - - - -
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Residues in contact with ARG 313 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291G GLY* 4.6 12.6 - - - +
292G VAL 3.3 17.3 - - - +
293G ILE* 4.3 7.9 - - + +
312G VAL* 1.3 72.9 - - - +
314G LEU* 1.3 64.3 + - - +
319G ILE* 3.5 6.4 - - - -
320G GLU* 3.0 67.3 + - - +
321G GLU* 2.9 38.3 + - + +
323G TYR* 3.2 25.8 + - + +
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Residues in contact with LEU 314 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G ILE* 6.3 0.2 - - + -
187G LEU* 3.9 27.8 - - + -
278G PHE* 4.4 5.8 - - + -
281G ALA* 3.6 21.1 - - + +
282G CYS* 3.6 41.3 - - - +
285G GLY* 3.6 13.5 - - - -
289G ASP 4.1 7.1 - - - +
292G VAL* 2.6 36.2 + - + +
294G GLU* 4.3 9.9 - - + -
312G VAL* 4.2 15.7 - - + +
313G ARG* 1.3 75.6 - - - +
315G GLY* 1.3 58.3 + - - +
318G GLY* 3.4 15.3 - - - +
319G ILE* 4.6 0.9 - - + -
320G GLU* 4.2 4.8 - - - +
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Residues in contact with GLY 315 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282G CYS 4.9 0.5 - - - +
285G GLY* 3.2 18.6 - - - -
286G LEU* 3.8 4.9 + - - +
288G GLY* 5.8 0.2 - - - -
289G ASP 5.3 2.0 - - - -
314G LEU* 1.3 74.7 - - - +
316G ARG* 1.3 61.3 + - - -
317G ASN 3.1 3.1 - - - -
318G GLY* 2.6 32.0 + - - +
320G GLU* 3.4 22.7 - - - +
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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