Contacts of the helix formed by residues 297 - 320 (chain B) in PDB entry 3GEB
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 ASP 297 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B LYS* 1.3 71.1 - - - +
298B THR* 1.3 67.9 + - - +
299B THR* 3.6 12.8 + - - -
300B THR* 2.9 47.5 + - - +
301B SER* 3.1 16.0 + - - -
420B LEU* 4.5 3.4 - - + +
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Residues in contact with THR 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLY* 5.0 8.2 - - - +
291B ALA* 3.6 26.6 - - + +
292B SER* 4.9 6.5 - - - +
296B LYS 3.3 5.8 + - - +
297B ASP* 1.3 73.0 + - - +
299B THR* 1.3 67.8 + - - +
301B SER* 3.5 2.4 + - - -
302B VAL* 3.2 31.3 + - - +
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Residues in contact with THR 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ASP* 3.3 12.6 + - - +
298B THR* 1.3 80.6 + - - +
300B THR* 1.3 65.4 + - - +
302B VAL* 3.6 5.2 + - - +
303B ARG* 3.0 26.7 + - + +
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Residues in contact with THR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ASP* 2.9 35.7 + - - +
299B THR* 1.3 75.9 - - - +
301B SER* 1.3 59.0 + - - +
303B ARG* 3.5 21.2 + - - +
304B ILE* 3.0 53.6 + - + +
416B GLU* 5.0 2.9 - - - +
420B LEU* 3.9 12.6 - - + -
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Residues in contact with SER 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU* 3.5 33.0 - - - +
288B GLY* 6.0 0.4 - - - -
290B PHE* 4.6 0.3 - - - -
291B ALA* 3.4 24.0 - - - +
296B LYS* 4.2 0.3 - - - +
297B ASP 3.1 12.4 + - - -
298B THR 3.6 7.4 - - - -
300B THR* 1.3 75.3 - - - +
302B VAL* 1.3 55.4 + - - +
304B ILE* 3.3 2.1 + - - +
305B GLY 2.8 30.1 + - - -
420B LEU* 3.5 27.4 - - - +
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Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU 3.2 18.4 - - - +
286B LEU* 4.1 20.0 - - + +
287B THR 5.8 0.2 - - - -
288B GLY* 5.2 7.0 - - - +
298B THR* 3.2 19.2 + - - +
299B THR* 4.0 5.2 - - - +
301B SER* 1.3 74.7 - - - +
303B ARG* 1.3 54.6 + - - +
305B GLY* 3.3 0.9 + - - -
306B LEU* 2.7 52.4 + - + +
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Residues in contact with ARG 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B THR* 3.0 22.7 + - + +
300B THR* 3.5 19.6 + - - +
302B VAL* 1.3 79.4 - - - +
304B ILE* 1.3 70.7 + - - +
306B LEU* 3.4 8.3 + - - +
307B MET* 3.0 55.2 + - + +
413B LEU* 5.0 0.2 - - - +
416B GLU* 2.4 45.7 + - - -
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Residues in contact with ILE 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU* 4.5 3.1 - - + -
300B THR* 3.0 37.1 + - + +
301B SER* 3.7 4.7 - - - +
303B ARG* 1.3 89.9 - - - +
305B GLY* 1.3 61.9 + - - +
307B MET* 3.2 3.5 + - - +
308B MET* 2.9 32.2 + - + +
413B LEU* 3.9 23.4 - - + +
416B GLU* 3.8 25.8 - - + +
417B LEU* 4.0 34.3 - - + +
420B LEU* 4.0 17.9 - - + -
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Residues in contact with GLY 305 (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 PHE* 3.5 9.5 - - - -
285B LEU* 4.0 22.6 - - - +
286B LEU* 3.7 12.0 - - - +
301B SER 2.8 20.9 + - - -
302B VAL 3.6 1.3 - - - -
304B ILE* 1.3 74.4 - - - +
306B LEU* 1.3 55.0 + - - +
308B MET* 4.5 3.8 - - - -
309B GLU* 2.8 29.8 + - - +
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Residues in contact with LEU 306 (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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286B LEU* 4.2 11.0 - - + -
302B VAL* 2.7 37.2 + - + +
303B ARG* 3.7 7.6 - - - +
305B GLY* 1.3 71.8 - - - +
307B MET* 1.3 64.0 + - + +
309B GLU* 3.4 25.1 + - - +
310B GLU* 3.1 23.4 + - - +
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Residues in contact with MET 307 (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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303B ARG* 3.0 48.0 + - + +
304B ILE 3.6 4.3 - - - +
306B LEU* 1.3 78.3 - - + +
308B MET* 1.3 60.0 + - - +
310B GLU* 3.5 9.9 + - - +
311B MET* 3.1 27.5 + - - +
409B THR* 5.4 7.2 - - - +
413B LEU* 3.7 32.3 - - + -
416B GLU* 5.2 4.9 - - - +
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Residues in contact with MET 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PHE* 3.9 12.3 - - + -
285B LEU* 6.0 0.9 - - + -
304B ILE* 2.9 19.3 + - + +
305B GLY* 3.8 5.4 - - - +
307B MET* 1.3 74.8 - - - +
309B GLU* 1.3 64.9 + - - +
310B GLU 3.1 0.2 - - - -
311B MET* 3.2 25.9 + - + -
312B ILE* 3.0 26.5 + - + +
410B TRP* 4.8 2.0 - - + -
413B LEU* 3.6 12.7 - - + +
414B ARG* 5.4 5.8 - - - -
417B LEU* 5.5 4.7 - - + -
460B LEU* 3.2 44.4 - - + +
461B TYR* 3.8 38.4 - - + +
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Residues in contact with GLU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PHE* 3.6 20.6 - - + -
286B LEU* 3.9 19.7 - - + +
305B GLY 2.8 20.7 + - - +
306B LEU* 3.4 28.5 + - - +
308B MET* 1.3 75.9 - - - +
310B GLU* 1.3 63.2 + - - +
312B ILE* 3.4 2.6 + - - +
313B PHE* 3.1 51.5 + - + -
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Residues in contact with GLU 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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306B LEU 3.1 13.7 + - - +
307B MET* 3.6 12.7 - - - +
308B MET 3.1 0.2 - - - -
309B GLU* 1.3 76.9 - - - +
311B MET* 1.3 54.6 + - - +
313B PHE* 3.4 3.4 + - - +
314B ASN* 2.7 61.9 + - - +
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Residues in contact with MET 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B MET 3.1 12.6 - - - +
308B MET* 3.2 22.3 + - + +
310B GLU* 1.3 77.7 - - + +
312B ILE* 1.3 57.2 + - - +
314B ASN* 3.6 7.0 - - - +
315B LEU* 2.9 33.1 + - - +
406B LYS* 5.2 1.3 - - - +
409B THR* 4.6 7.9 - - - +
410B TRP* 3.4 49.1 - - + -
413B LEU* 3.1 33.4 - - + -
414B ARG* 5.8 0.4 - - + +
460B LEU* 3.7 7.7 - - + +
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Residues in contact with ILE 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PHE* 3.9 23.8 - - + -
308B MET* 3.0 28.5 + - + +
309B GLU 3.6 6.7 - - - +
311B MET* 1.3 77.5 - - - +
313B PHE* 1.3 69.8 + - + +
316B ALA* 3.1 20.4 + - - +
453B PRO* 3.8 17.7 - - + +
456B ALA* 3.3 13.5 - - + +
457B LYS* 3.3 47.6 - - + -
460B LEU* 3.4 22.0 - - + -
461B TYR* 4.5 2.5 - - + -
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Residues in contact with PHE 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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282B PHE* 5.4 6.3 - + - -
309B GLU* 3.1 47.9 + - + +
310B GLU* 4.3 2.2 - - - +
312B ILE* 1.3 81.5 - - + +
314B ASN* 1.3 60.0 + - - +
315B LEU 3.2 2.0 - - - -
316B ALA* 3.7 4.7 - - + -
317B ASP* 3.0 43.1 + - - +
322B PHE* 3.4 33.2 - + - -
449B THR* 6.2 0.7 - - + -
453B PRO* 3.8 28.3 - - + -
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Residues in contact with ASN 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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310B GLU* 2.7 50.9 + - - +
311B MET* 3.6 8.5 - - - +
313B PHE* 1.3 74.2 - - - +
315B LEU* 1.3 58.0 + - - +
317B ASP* 4.4 1.7 - - - +
318B THR* 3.0 40.2 + - - -
406B LYS* 2.9 32.3 + - + +
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Residues in contact with LEU 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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311B MET 2.9 16.3 + - - +
312B ILE 3.9 1.6 - - - +
314B ASN* 1.3 76.7 - - - +
316B ALA* 1.3 58.9 + - - +
317B ASP 3.4 0.2 - - - -
319B HIS* 3.0 37.6 + - + +
320B LEU* 3.4 27.1 + - + -
398B VAL* 4.9 1.8 - - + -
401B LEU* 4.8 8.7 - - + -
402B ILE* 3.6 37.7 - - + -
456B ALA* 3.6 14.6 - - + +
459B LEU* 4.8 10.5 - - + -
460B LEU* 3.6 31.2 - - + -
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Residues in contact with ALA 316 (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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312B ILE 3.1 19.5 + - - +
313B PHE* 4.0 8.3 - - + -
315B LEU* 1.3 78.3 - - - +
317B ASP* 1.3 55.6 + - - +
320B LEU* 2.9 44.0 + - + +
322B PHE* 3.0 25.1 + - + -
452B ILE* 4.1 13.0 - - + +
453B PRO* 4.7 5.4 - - + -
456B ALA* 4.3 8.5 - - + -
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Residues in contact with ASP 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B PHE* 3.0 30.0 + - - +
314B ASN* 4.4 3.1 - - - +
316B ALA* 1.3 79.2 - - - +
318B THR* 1.3 61.9 + - - +
321B PHE* 4.4 5.5 + - - -
322B PHE* 3.1 37.7 + - - +
323B ASN* 3.6 34.1 + - - +
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Residues in contact with THR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ASN* 3.0 28.0 + - - -
317B ASP* 1.3 81.1 - - - +
319B HIS* 1.3 84.8 + - + +
406B LYS* 5.4 2.4 + - - +
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Residues in contact with HIS 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ASN 5.4 0.2 - - - -
315B LEU* 3.0 25.5 + - + +
318B THR* 1.3 102.9 - - + +
320B LEU* 1.3 68.3 + - + +
321B PHE* 3.5 10.9 + - - -
390B MET* 3.3 30.5 - - - +
401B LEU* 2.8 55.9 + - + -
402B ILE* 4.5 13.5 - - + -
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 3.4 30.7 + - + +
316B ALA* 2.9 16.7 + - - +
319B HIS* 1.3 84.9 - - + +
321B PHE* 1.3 60.4 + - - +
322B PHE* 2.4 23.6 + - - -
325B LEU* 4.0 5.3 - - - +
387B VAL* 3.8 34.3 - - + +
390B MET* 4.3 10.3 - - + -
391B TYR* 6.2 0.9 - - + +
452B ILE* 3.3 35.5 - - + +
455B LEU* 4.6 7.9 - - + -
456B ALA* 4.0 11.0 - - + +
459B LEU* 5.0 6.7 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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