Contacts of the helix formed by residues 373 - 387 (chain B) in PDB entry 3GUU
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 GLY 373 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B PHE* 4.0 3.5 - - - -
329B TRP* 3.6 27.6 - - - -
361B TYR* 3.3 13.2 + - - -
369B ALA 3.1 10.1 + - - -
372B PHE* 1.3 78.2 - - - +
374B LEU* 1.3 54.7 + - - +
376B PRO* 3.4 5.5 - - - +
377B SER* 2.8 37.2 + - - -
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Residues in contact with LEU 374 (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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122B ASP* 3.6 35.2 - - + +
125B ILE* 4.5 7.2 - - + -
126B ILE* 3.8 22.2 - - + -
181B GLU* 5.6 1.1 - - - +
329B TRP* 4.9 3.1 - - - -
370B GLU 3.7 13.7 + - - +
371B ILE* 3.1 17.6 + - + +
373B GLY* 1.3 76.7 - - - +
375B VAL* 1.3 71.0 + - + +
377B SER* 3.2 8.0 + - - -
378B LEU* 3.0 48.1 + - + +
413B LEU* 4.5 5.8 - - + -
421B LEU* 4.0 32.3 - - + -
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Residues in contact with VAL 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ILE 4.4 1.9 + - - +
374B LEU* 1.3 77.9 - - + +
376B PRO* 1.3 67.1 - - + +
378B LEU* 3.4 3.7 + - - +
379B TRP* 2.9 27.5 + - - +
402B ALA* 3.9 19.5 - - + -
406B THR* 4.2 1.1 - - - +
407B PRO 4.0 5.4 - - - +
408B SER 4.2 3.6 - - - +
409B ALA* 3.8 18.8 - - + -
412B VAL* 3.6 32.3 - - + +
413B LEU* 4.0 10.5 - - + -
421B LEU* 3.6 29.8 - - + -
438B ILE* 4.5 6.5 - - + -
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Residues in contact with PRO 376 (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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327B PHE* 4.0 9.3 - - + -
372B PHE 3.4 20.0 - - - +
373B GLY* 3.4 11.0 - - - +
375B VAL* 1.3 93.6 - - + +
377B SER* 1.3 54.6 + - - +
379B TRP* 3.7 2.7 - - + +
380B PHE* 2.8 35.3 + - - +
400B ALA* 3.5 39.7 - - + +
402B ALA* 4.2 10.1 - - + +
406B THR* 3.7 25.0 - - + +
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Residues in contact with SER 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLU* 3.0 27.0 + - - +
210B SER* 2.6 27.3 + - - -
327B PHE* 3.8 5.6 - - - -
329B TRP* 3.5 15.3 - - - -
373B GLY 2.8 23.2 + - - -
374B LEU 3.2 7.4 + - - -
376B PRO* 1.3 72.0 - - - +
378B LEU* 1.3 58.9 + - - +
380B PHE* 3.4 4.3 + - - +
381B ILE* 3.1 28.9 + - - +
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Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B PHE* 4.4 7.9 - - + -
125B ILE 4.8 0.2 - - - +
126B ILE* 3.9 35.4 - - + -
129B TRP* 3.2 67.6 - - + -
181B GLU* 4.3 7.0 - - + +
374B LEU* 3.0 39.0 + - + +
375B VAL* 4.1 2.7 - - - +
377B SER* 1.3 82.2 - - - +
379B TRP* 1.3 67.9 + - - +
381B ILE* 3.1 10.5 + - + -
382B LYS 3.1 10.7 + - - -
412B VAL* 4.5 5.2 - - + -
413B LEU* 3.9 6.5 - - + -
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Residues in contact with TRP 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B VAL 2.9 19.2 + - - +
376B PRO* 3.7 5.6 - - + +
378B LEU* 1.3 77.6 - - - +
380B PHE* 1.3 65.7 + - + +
382B LYS* 3.3 31.4 + - + +
383B GLN* 2.8 61.8 + - + +
390B PRO* 5.8 1.0 - - - +
405B THR 5.5 1.0 + - - -
406B THR* 4.0 22.8 - - + +
407B PRO* 3.5 36.3 - - + +
411B GLN 6.1 0.4 - - - -
412B VAL* 4.0 23.1 - - + +
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Residues in contact with PHE 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ALA 3.8 9.9 - - - -
210B SER* 4.5 4.5 - - - -
325B PRO* 3.6 25.1 - - + -
326B ARG 3.5 30.5 - - - -
327B PHE* 3.5 39.5 - + + -
357B ASN* 4.5 15.5 - - + -
376B PRO 2.8 22.3 + - - +
377B SER 3.5 4.7 - - - +
379B TRP* 1.3 76.5 - - + +
381B ILE* 1.3 61.6 + - + +
383B GLN* 3.3 9.3 + - + +
384B ALA* 2.9 31.0 + - + +
389B THR* 3.8 21.3 - - + -
390B PRO* 5.1 8.1 - - + -
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Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B PHE* 3.8 25.8 - - + -
129B TRP* 4.2 10.8 - - + -
179B ALA* 4.0 15.7 - - + -
180B LEU 3.5 28.0 - - - +
181B GLU* 4.5 4.5 - - + -
208B GLY* 4.8 0.9 - - - -
209B ALA* 4.4 5.2 - - - +
210B SER* 3.9 17.0 - - - +
377B SER 3.1 21.7 + - - +
378B LEU* 3.1 9.8 + - - +
380B PHE* 1.3 72.1 - - + +
382B LYS* 1.3 61.5 + - - +
384B ALA* 3.1 6.5 + - - +
385B PHE* 2.9 54.5 + - + -
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Residues in contact with LYS 382 (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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129B TRP* 4.0 8.5 - - + -
133B GLN* 3.7 24.0 + - - +
135B TYR* 3.6 20.2 - - - +
378B LEU 3.1 10.0 + - - +
379B TRP* 3.5 34.1 - - + +
381B ILE* 1.3 73.5 - - - +
383B GLN* 1.3 68.1 + - - +
385B PHE* 3.2 2.6 + - - +
386B ASP* 2.9 52.6 + - - +
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Residues in contact with GLN 383 (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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379B TRP* 2.8 61.0 + - + +
380B PHE* 3.4 11.9 - - - +
382B LYS* 1.3 77.3 - - - +
384B ALA* 1.3 59.3 + - - +
386B ASP* 3.0 2.7 + - - -
387B GLY 2.8 25.8 + - - -
388B THR* 2.9 38.5 + - - +
389B THR* 3.6 20.2 - - + +
390B PRO* 3.7 20.6 - - + +
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Residues in contact with ALA 384 (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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177B LYS* 5.2 0.9 + - - -
179B ALA* 5.3 1.8 - - + -
207B VAL* 3.3 39.5 - - + +
208B GLY* 3.8 15.5 - - - +
325B PRO* 5.1 0.4 - - + -
380B PHE* 2.9 19.1 + - + +
381B ILE* 3.1 11.2 + - - +
383B GLN* 1.3 76.4 - - - +
385B PHE* 1.3 63.1 + - - +
386B ASP 3.3 0.5 + - - -
387B GLY* 3.4 10.3 + - - +
389B THR* 3.6 15.9 - - + -
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Residues in contact with PHE 385 (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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86B LYS* 3.6 40.2 - - + -
87B ILE 3.3 26.9 - - - -
88B PHE* 4.1 3.4 - - + -
135B TYR* 3.4 39.9 - + - +
177B LYS* 3.1 64.3 + - + +
178B VAL 4.0 0.4 - - - -
179B ALA* 3.5 19.3 - - + -
207B VAL* 3.9 7.2 - - + -
381B ILE* 2.9 39.9 + - + -
382B LYS 3.2 7.2 + - - +
384B ALA* 1.3 75.3 - - - +
386B ASP* 1.3 59.8 + - - +
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Residues in contact with ASP 386 (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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86B LYS* 4.4 10.0 - - - +
135B TYR* 5.0 1.2 + - - -
177B LYS* 4.8 4.4 + - - -
382B LYS* 2.9 50.7 + - - +
383B GLN* 3.0 5.1 + - - +
385B PHE* 1.3 84.3 - - - +
387B GLY* 1.3 62.4 + - - +
388B THR* 3.5 22.4 + - + +
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Residues in contact with GLY 387 (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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177B LYS* 4.9 4.0 - - - +
383B GLN 2.8 4.1 + - - -
384B ALA* 3.4 7.8 + - - -
385B PHE 3.3 3.8 + - - -
386B ASP* 1.3 79.6 - - - +
388B THR* 1.3 59.3 + - - +
389B THR 3.8 2.2 - - - -
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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