Contacts of the helix formed by residues 373 - 387 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A PHE* 3.9 4.2 - - - -
329A TRP* 3.6 28.6 - - - -
361A TYR* 3.4 12.7 + - - -
369A ALA 3.2 6.5 + - - -
371A ILE 3.2 0.8 - - - -
372A PHE* 1.3 78.1 - - - +
374A LEU* 1.3 58.8 + - - +
375A VAL 3.6 0.4 - - - -
376A PRO* 3.7 6.5 - - - +
377A SER* 2.9 30.0 + - - -
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Residues in contact with LEU 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ASP* 4.0 29.2 - - + +
125A ILE* 4.8 7.2 - - + -
126A ILE* 4.0 21.3 - - + -
181A GLU* 5.8 1.1 - - - +
329A TRP* 4.8 3.1 - - + -
370A GLU 3.7 15.5 + - - +
371A ILE* 2.9 19.9 + - + +
373A GLY* 1.3 77.7 - - - +
375A VAL* 1.3 67.5 + - - +
377A SER* 3.2 7.8 - - - -
378A LEU* 3.1 43.3 + - + +
413A LEU* 4.4 7.0 - - + -
421A LEU* 4.0 34.5 - - + -
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Residues in contact with VAL 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ILE 4.3 1.4 + - - +
374A LEU* 1.3 77.6 - - + +
376A PRO* 1.3 71.4 - - + +
378A LEU* 3.4 2.6 + - - +
379A TRP* 3.0 26.9 + - - +
402A ALA* 3.7 21.3 - - + -
406A THR* 4.0 2.2 - - - +
407A PRO 4.0 4.9 - - - +
409A ALA* 4.1 16.6 - - + -
412A VAL* 3.6 33.8 - - + +
413A LEU* 3.9 17.3 - - + -
421A LEU* 3.8 26.5 - - + -
438A ILE* 4.3 9.2 - - + -
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Residues in contact with PRO 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A PHE* 3.7 25.9 - - + -
361A TYR* 4.2 1.1 - - - +
372A PHE 3.4 23.6 - - - +
373A GLY 3.7 3.4 - - - +
375A VAL* 1.3 96.8 - - + +
377A SER* 1.3 51.9 + - - +
379A TRP* 3.8 1.2 - - - +
380A PHE* 2.9 35.2 + - - +
400A ALA* 3.6 29.2 - - + +
402A ALA* 4.3 10.5 - - + +
406A THR* 3.8 22.6 - - + +
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Residues in contact with SER 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A GLU* 3.0 28.4 + - - +
210A SER* 3.2 19.3 + - - -
327A PHE* 3.8 5.6 - - - -
329A TRP* 3.6 16.0 - - - -
373A GLY 2.9 23.6 + - - -
374A LEU* 3.2 8.1 - - - -
376A PRO* 1.3 73.5 - - - +
378A LEU* 1.3 59.6 + - - +
380A PHE* 3.4 4.2 + - - +
381A ILE* 3.0 29.6 + - - +
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Residues in contact with LEU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 4.3 11.4 - - + -
125A ILE 5.0 0.9 - - - +
126A ILE* 4.2 30.7 - - + -
129A TRP* 3.1 60.4 - - + -
181A GLU* 4.5 7.2 - - + +
374A LEU* 3.1 38.3 + - + +
375A VAL 4.2 2.0 - - - +
377A SER* 1.3 80.7 - - - +
379A TRP* 1.3 65.4 - - - +
381A ILE* 3.2 2.5 + - + +
382A LYS 2.9 19.6 + - - -
412A VAL* 4.5 5.6 - - + -
413A LEU* 3.9 15.3 - - + -
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Residues in contact with TRP 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A VAL 3.0 18.4 + - - +
376A PRO 3.8 3.1 - - - +
378A LEU* 1.3 74.7 - - - +
380A PHE* 1.3 64.8 + - - +
382A LYS* 3.2 35.5 + - + +
383A GLN* 3.0 66.6 + - + +
405A THR 5.2 1.9 + - - -
406A THR* 3.8 19.8 - - + +
407A PRO* 3.3 38.4 - - + +
411A GLN 5.8 1.6 - - - -
412A VAL* 3.8 30.6 - - + +
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Residues in contact with PHE 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ALA 3.6 14.8 - - - -
210A SER* 4.0 7.4 - - - -
325A PRO* 3.4 19.7 - - + -
326A ARG 3.4 33.9 - - - -
327A PHE* 3.5 37.5 - + + -
357A ASN* 4.9 11.0 - - + -
376A PRO 2.9 20.8 + - - +
377A SER 3.4 4.9 - - - +
378A LEU 3.3 0.2 - - - -
379A TRP* 1.3 77.4 - - - +
381A ILE* 1.3 63.4 + - + +
383A GLN* 3.4 13.7 + - - +
384A ALA* 2.9 30.4 + - + +
389A THR* 3.8 21.8 - - + -
390A PRO* 5.6 2.7 - - + -
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Residues in contact with ILE 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PHE* 3.9 26.5 - - + -
129A TRP* 4.4 6.3 - - + -
179A ALA* 3.8 19.3 - - + -
180A LEU 3.6 17.0 - - - +
181A GLU* 4.5 4.3 - - + -
208A GLY* 4.5 0.7 - - - -
209A ALA* 4.3 8.1 - - - +
210A SER* 3.6 27.8 - - - +
377A SER 3.0 20.0 + - - +
378A LEU* 3.2 9.3 + - - +
380A PHE* 1.3 79.2 - - + +
382A LYS* 1.3 63.3 + - - +
384A ALA* 3.2 5.1 + - - +
385A PHE* 3.0 47.4 + - + -
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Residues in contact with LYS 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TRP* 4.0 14.5 - - + -
133A GLN* 4.4 18.6 + - - +
135A TYR* 3.7 19.0 + - - +
378A LEU 2.9 12.5 + - - +
379A TRP* 3.5 37.7 - - + +
381A ILE* 1.3 76.7 - - - +
383A GLN* 1.3 56.7 + - + +
385A PHE* 3.4 3.6 + - - +
386A ASP* 3.0 54.1 + - - +
412A VAL* 5.8 3.4 - - + +
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Residues in contact with GLN 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A TRP* 3.0 59.6 + - + +
380A PHE* 3.5 16.1 - - - +
382A LYS* 1.3 75.7 - - + +
384A ALA* 1.3 56.0 + - - +
386A ASP* 3.1 2.4 + - - -
387A GLY 2.8 10.0 + - - -
388A THR* 2.8 60.3 + - - +
389A THR* 3.7 10.3 - - + -
390A PRO* 3.6 22.0 - - - +
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Residues in contact with ALA 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LYS* 5.3 0.9 + - - +
179A ALA* 5.4 1.3 - - + -
207A VAL* 3.4 41.1 - - + +
208A GLY* 3.9 14.1 - - - -
325A PRO* 5.7 0.4 - - - -
380A PHE* 2.9 18.1 + - + +
381A ILE* 3.2 11.9 + - - +
383A GLN* 1.3 74.6 - - - +
385A PHE* 1.3 62.0 + - - +
387A GLY* 3.4 11.2 + - - +
389A THR* 3.4 16.8 - - + +
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Residues in contact with PHE 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LYS* 3.7 38.5 + - + -
87A ILE 3.3 28.7 - - - -
88A PHE* 4.7 2.7 - + - -
135A TYR* 3.3 39.0 - + - +
177A LYS* 3.1 64.9 + - + +
178A VAL 4.0 1.6 - - - -
179A ALA* 3.6 13.7 - - + -
207A VAL* 3.8 6.1 - - + -
381A ILE* 3.0 36.6 + - + -
382A LYS 3.5 7.4 - - - +
384A ALA* 1.3 75.3 - - - +
386A ASP* 1.3 61.6 + - - +
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Residues in contact with ASP 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LYS* 4.7 6.8 - - - -
135A TYR* 5.3 1.0 + - - -
177A LYS* 5.1 2.7 - - - -
382A LYS* 3.0 45.1 + - - +
383A GLN* 3.1 5.0 + - - +
385A PHE* 1.3 84.0 - - - +
387A GLY* 1.3 59.3 + - - +
388A THR* 3.4 24.0 + - + +
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Residues in contact with GLY 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LYS* 5.2 2.7 - - - +
383A GLN 2.8 3.6 + - - -
384A ALA* 3.4 8.5 + - - -
385A PHE 3.4 4.0 + - - -
386A ASP* 1.3 77.9 - - - +
388A THR* 1.3 61.3 + - - +
389A THR* 3.6 4.1 + - - +
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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