Contacts of the strand formed by residues 317 - 330 (chain B) in PDB entry 1G4M
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 317 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B PHE* 4.0 8.1 - - + -
124B PRO* 5.7 0.5 - - - +
127B VAL* 4.1 30.1 - - + +
129B LEU* 4.3 8.1 - - + +
140B CYS* 4.0 19.7 - - - +
141B GLY* 3.9 26.7 - - - -
142B VAL* 5.1 0.6 - - + +
239B ALA* 4.4 9.9 - - + -
240B ASP 3.4 9.2 - - - +
241B ILE* 3.9 18.6 - - + -
288B ALA* 4.7 2.0 - - + -
304B THR* 3.6 10.9 + - - +
315B LEU* 2.8 15.3 + - - +
316B GLY* 1.3 79.1 - - - +
318B ILE* 1.3 69.7 + - - +
319B VAL* 3.9 22.3 + - + +
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Residues in contact with ILE 318 (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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238B TYR 3.5 1.7 - - - +
239B ALA* 3.3 3.1 - - - -
240B ASP* 2.9 40.7 + - + +
242B CYS* 3.7 22.2 - - - -
304B THR* 3.4 14.1 - - + -
306B LEU* 4.0 19.7 - - + -
312B ARG* 3.6 39.5 - - + +
315B LEU* 3.6 41.3 - - + -
317B ILE* 1.3 73.9 - - - +
319B VAL* 1.3 66.1 + - - +
320B SER* 5.4 3.7 + - - +
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Residues in contact with VAL 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 4.3 4.9 - - + -
237B GLN* 4.0 15.5 - - + -
238B TYR 3.3 3.1 - - - -
239B ALA* 4.6 2.0 - - + -
288B ALA* 3.6 26.2 - - + -
301B ALA* 3.9 11.2 - - + +
302B SER 3.7 15.9 - - - +
303B SER* 3.6 1.4 - - - -
304B THR* 2.8 35.9 + - - +
317B ILE* 4.0 13.7 - - + +
318B ILE* 1.3 79.9 - - - +
320B SER* 1.3 66.6 + - - +
321B TYR* 3.6 30.3 - - + +
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Residues in contact with SER 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B GLN* 3.4 4.5 - - - +
238B TYR* 2.8 51.6 + - - +
303B SER* 4.7 4.5 - - - -
318B ILE* 5.4 3.6 + - - +
319B VAL* 1.3 76.7 - - - +
321B TYR* 1.3 71.5 + - - +
322B LYS* 5.1 8.0 + - - -
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Residues in contact with TYR 321 (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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235B VAL* 4.4 11.4 - - + -
236B ARG 3.2 8.1 - - - +
237B GLN* 2.9 52.8 + - + -
238B TYR* 4.7 0.7 - - - -
253B VAL* 4.4 10.3 - - + -
276B PRO* 5.7 0.4 - - + -
300B LEU* 3.5 9.6 - - + +
301B ALA 2.5 33.3 + - - -
303B SER* 3.6 18.6 - - - -
319B VAL* 3.6 12.8 - - + -
320B SER* 1.3 78.2 - - - +
322B LYS* 1.3 72.0 + - - +
348B PRO* 3.7 2.1 - - - +
349B PHE* 3.4 50.4 + + + +
351B LEU* 3.5 26.5 - - + -
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Residues in contact with LYS 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B VAL* 3.6 2.4 - - - +
236B ARG* 2.9 31.9 + - + +
238B TYR* 3.7 23.5 - - + -
320B SER* 5.1 7.9 + - - -
321B TYR* 1.3 81.9 + - - +
323B VAL* 1.3 66.8 + - - +
324B LYS 3.9 0.3 + - - -
346B GLU* 3.5 39.5 - - + +
347B LEU 3.2 9.4 - - - +
348B PRO* 4.2 23.6 - - + +
349B PHE* 4.1 3.6 - - - -
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Residues in contact with VAL 323 (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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203B LEU* 3.8 22.9 - - + -
214B ILE* 4.1 13.0 - - + -
216B VAL* 3.9 28.5 - - + -
233B ILE* 4.2 6.5 - - + -
234B SER 3.3 9.4 - - - +
235B VAL* 4.4 10.5 - - + -
274B LEU* 5.2 0.7 - - + -
322B LYS* 1.3 74.5 - - - +
324B LYS* 1.3 70.9 + - - +
325B VAL* 4.5 0.2 - - + -
346B GLU* 3.2 4.5 - - - -
347B LEU* 2.7 43.7 + - + +
349B PHE* 3.9 23.3 - - + -
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Residues in contact with LYS 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B LYS 3.6 1.3 - - - +
233B ILE* 3.4 5.7 - - - +
234B SER* 2.8 49.9 + - - +
236B ARG* 4.0 27.0 - - - +
322B LYS 3.9 0.8 + - - -
323B VAL* 1.3 73.6 - - - +
325B VAL* 1.3 70.0 + - - +
326B LYS* 3.5 32.3 - - + +
344B ALA* 3.8 22.4 - - - -
345B VAL 3.5 9.4 - - - +
346B GLU* 4.1 17.5 - - + -
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Residues in contact with VAL 325 (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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199B LEU* 3.8 21.7 - - + +
201B ALA* 4.2 9.4 - - + -
216B VAL* 3.7 23.1 - - + -
218B VAL* 4.0 17.0 - - + -
231B ILE* 4.3 7.2 - - + -
232B LYS 3.5 3.1 - - - -
233B ILE* 3.6 28.7 - - + -
323B VAL* 4.5 4.0 - - + -
324B LYS* 1.3 75.1 - - - +
326B LYS* 1.3 63.1 + - - +
327B LEU* 4.6 2.0 - - + -
343B VAL 3.8 0.5 - - - +
344B ALA* 3.0 5.9 - - - +
345B VAL* 2.9 40.4 + - + -
347B LEU* 4.5 3.8 - - + -
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Residues in contact with LYS 326 (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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230B LYS 4.0 0.2 - - - +
231B ILE* 3.4 5.0 - - - +
232B LYS* 2.9 68.1 + - + +
324B LYS* 3.5 33.2 - - + +
325B VAL* 1.3 75.3 - - - +
327B LEU* 1.3 68.1 - - - +
328B VAL* 4.0 5.9 + - + +
342B ASP* 3.2 43.5 + - + +
343B VAL 3.5 3.8 - - - +
344B ALA* 4.0 7.9 - - + -
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Residues in contact with LEU 327 (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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197B LEU* 3.7 34.1 - - + -
199B LEU* 4.1 21.3 - - + -
218B VAL* 5.0 0.4 - - + -
220B VAL* 3.9 27.6 - - + -
228B VAL* 4.1 16.2 - - + -
230B LYS 3.7 2.0 - - - -
231B ILE* 3.8 36.3 - - + -
325B VAL* 4.6 2.7 - - + -
326B LYS* 1.3 74.9 - - - +
328B VAL* 1.3 61.3 + - - +
329B VAL* 3.6 3.8 + - + +
342B ASP* 3.4 8.7 - - - +
343B VAL* 2.7 40.7 + - + +
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Residues in contact with VAL 328 (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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228B VAL* 3.6 2.1 - - - +
229B LYS* 2.7 43.4 + - + +
230B LYS* 2.8 46.4 + - + +
232B LYS* 4.0 20.4 - - + +
326B LYS* 4.5 13.2 - - + +
327B LEU* 1.3 74.1 - - - +
329B VAL* 1.3 54.4 + - - +
340B SER* 3.9 25.8 - - - +
341B SER 3.8 2.5 - - - -
342B ASP* 3.8 12.1 - - - +
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Residues in contact with VAL 329 (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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191B LEU* 4.0 20.0 - - + -
197B LEU* 5.1 1.6 - - + -
226B LYS* 3.8 20.9 - - + -
227B THR 3.6 11.9 - - - +
228B VAL* 4.3 16.4 - - + +
229B LYS* 4.3 1.1 - - - -
327B LEU* 4.0 11.7 - - + +
328B VAL* 1.3 74.3 - - - +
330B SER* 1.3 78.2 + - - +
340B SER* 3.1 26.2 - - - -
341B SER* 3.0 23.9 + - - +
343B VAL* 4.2 20.2 - - + -
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Residues in contact with SER 330 (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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226B LYS* 4.2 12.3 - - - +
227B THR* 2.9 40.1 + - - -
229B LYS* 3.6 26.8 - - - +
329B VAL* 1.3 82.2 - - - +
331B ARG* 1.3 67.2 + - - +
339B ALA 4.4 0.2 - - - -
341B SER* 5.3 1.7 + - - -
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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