Contacts of the strand formed by residues 307 - 315 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B VAL* 4.1 14.6 - - + -
169B PRO* 3.3 40.4 - - + -
172B ALA* 3.5 26.9 - - + -
173B GLU* 6.2 0.2 - - - -
176B LYS* 6.2 1.8 - - - -
181B TYR* 3.5 19.3 - + - -
186B LEU* 5.2 1.8 - - + -
297B PHE* 3.7 21.8 - - + -
298B VAL 3.3 8.1 - - - +
299B SER* 3.3 26.7 - - - -
300B SER* 4.3 0.7 - - - +
305B LEU* 3.2 9.7 - - - +
306B PRO* 1.3 99.8 - - + +
308B PHE* 1.3 69.1 + - - +
343B LEU* 4.1 3.1 - - - +
347B ILE* 3.6 18.6 - - + +
351B VAL* 5.3 3.1 - - + -
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Residues in contact with PHE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B VAL* 4.1 1.6 - - + -
218B GLY* 3.4 33.4 - - - -
296B ALA 3.5 1.6 - - - +
297B PHE* 3.9 8.4 - - - -
298B VAL* 2.9 31.4 + - - +
300B SER* 3.5 18.2 + - - +
302B VAL* 4.6 4.7 - - + -
303B THR* 3.7 37.9 - - + +
305B LEU* 4.8 2.9 - - + +
307B PHE* 1.3 79.6 - - - +
309B ALA* 1.3 78.9 + - - +
310B SER* 3.8 2.7 + - - -
325B LEU* 3.9 22.9 - - + -
336B LEU* 3.7 24.0 - - + -
339B ALA* 5.3 1.8 - - + -
340B LYS* 4.4 16.6 - - + -
343B LEU* 3.7 17.9 - - + -
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B THR* 4.3 14.8 - - + +
216B VAL 4.5 3.4 - - - +
217B VAL* 3.0 16.1 - - - +
218B GLY 2.9 46.5 + - - +
219B GLY 4.6 1.3 - - - +
296B ALA 3.1 20.9 - - - +
297B PHE* 3.9 8.1 - - + +
308B PHE* 1.3 78.2 - - - +
310B SER* 1.3 61.3 + - - +
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Residues in contact with SER 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B VAL 4.8 0.9 + - - -
217B VAL* 3.9 10.3 - - - +
295B CYS* 3.4 6.0 - - - -
296B ALA 3.2 22.9 + - - +
298B VAL* 5.3 0.2 - - - +
302B VAL* 4.0 7.8 - - - +
308B PHE* 3.8 5.1 + - - -
309B ALA* 1.3 76.0 - - - +
311B LYS* 1.3 69.2 + - - +
312B VAL* 3.6 5.5 - - - +
322B VAL* 3.5 17.0 - - - +
323B TYR 3.0 23.7 + - - -
324B SER 5.1 0.7 - - - -
325B LEU* 4.1 17.0 - - - -
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Residues in contact with LYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B ASP* 3.0 33.3 + - - -
215B PRO* 3.5 29.9 - - + +
217B VAL* 5.0 2.3 - - + +
231B GLN* 5.7 1.8 - - - +
233B LYS* 4.8 7.4 - - - +
293B ILE* 3.7 26.1 + - + +
294B GLU* 3.6 8.7 - - - +
295B CYS* 4.1 16.0 - - - +
310B SER* 1.3 79.3 + - - +
312B VAL* 1.3 61.3 + - - +
323B TYR* 2.9 41.3 + - + +
324B SER 5.5 3.0 + - - +
259H GLU* 3.7 17.9 + - + +
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Residues in contact with VAL 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B LEU* 4.8 2.7 - - + -
278B PHE* 5.6 0.2 - - + -
292B VAL 3.6 0.3 - - - +
293B ILE* 3.0 26.5 - - - +
294B GLU* 2.9 23.4 + - + +
296B ALA* 4.6 12.1 - - + +
298B VAL* 4.2 30.3 - - + -
310B SER 3.6 9.6 - - - +
311B LYS* 1.3 81.4 - - - +
313B ARG* 1.3 60.3 + - - +
314B LEU* 4.0 25.4 - - + -
319B ILE* 4.0 10.5 - - + -
321B GLU 3.2 12.8 - - - +
322B VAL* 4.3 7.4 - - + -
323B TYR* 4.2 3.1 - - - -
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Residues in contact with ARG 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B ALA* 6.3 1.0 - - - +
291B GLY* 4.7 7.8 - - - +
292B VAL 3.1 14.8 - - - +
293B ILE* 4.4 2.5 - - + +
312B VAL* 1.3 73.3 - - - +
314B LEU* 1.3 64.6 + - - +
315B GLY* 5.2 1.2 - - - -
319B ILE* 3.4 4.9 - - - -
320B GLU* 2.6 81.8 + - - +
321B GLU* 2.9 22.4 + - + +
323B TYR* 3.4 30.3 + - + +
126H PRO 4.8 11.2 + - - -
127H GLY* 5.3 5.6 - - - +
262H ALA 4.0 20.2 - - - -
263H GLY* 4.1 12.4 + - - -
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ILE* 6.5 0.2 - - + -
187B LEU* 3.8 27.8 - - + -
278B PHE* 4.5 7.2 - - + -
281B ALA* 3.7 34.5 - - + +
282B CYS* 3.7 25.1 - - - +
285B GLY* 3.5 14.6 - - - -
289B ASP 4.3 5.2 - - - +
292B VAL* 2.6 35.6 + - + +
294B GLU* 4.3 10.3 - - + -
312B VAL* 4.0 15.3 - - + +
313B ARG* 1.3 80.8 + - - +
315B GLY* 1.3 58.8 + - - +
318B GLY* 3.2 15.9 - - - +
319B ILE* 4.3 1.3 - - + -
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Residues in contact with GLY 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B CYS 4.9 0.7 - - - +
285B GLY* 3.1 19.0 - - - +
286B LEU* 3.7 2.9 + - - +
288B GLY* 6.1 0.2 - - - -
289B ASP 5.3 2.9 - - - -
313B ARG* 5.2 2.2 - - - -
314B LEU* 1.3 73.8 - - - +
316B ARG* 1.3 65.8 + - - -
317B ASN 3.0 3.6 - - - -
318B GLY* 2.5 23.8 + - - +
320B GLU* 3.4 21.5 - - - +
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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