Contacts of the helix formed by residues 372 - 389 (chain A) in PDB entry 5F85
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 ARG 372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A PRO 4.9 0.8 + - - -
69A GLN* 3.2 47.8 + - - +
70A ASP* 4.4 4.9 + - - +
203A TRP* 4.9 0.4 - - - -
207A ARG* 3.6 11.0 - - - +
368A TRP 3.4 21.1 - - - +
369A GLU* 3.1 16.9 + - - +
371A LEU* 1.3 82.6 - - - +
373A MET* 1.3 66.9 + - - +
374A LYS* 3.3 29.8 - - - +
375A ASP* 2.9 45.8 + - - +
376A ILE* 3.3 13.0 + - - +
505A SO4 3.5 26.9 - - - +
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Residues in contact with MET 373 (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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131A HIS* 4.7 10.3 - - + -
132A PHE* 3.4 39.0 - - + -
186A PHE 3.9 13.7 - - - +
187A TRP* 4.8 5.4 - - + -
203A TRP* 4.3 11.4 - - + -
204A ASP* 3.5 45.1 - - + +
207A ARG* 4.6 2.0 - - - +
372A ARG* 1.3 70.2 - - - +
374A LYS* 1.3 56.6 + - - +
376A ILE* 3.0 9.8 + - + +
377A LYS* 2.8 47.3 + - + +
505A SO4 2.9 23.5 + - - +
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Residues in contact with LYS 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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69A GLN 4.8 3.4 + - - -
70A ASP 4.2 12.6 + - - -
71A SER* 4.3 15.8 + - - +
73A CYS* 5.6 0.9 - - - -
372A ARG* 3.1 40.9 - - + +
373A MET* 1.3 76.0 - - - +
375A ASP* 1.3 57.3 + - - +
377A LYS* 4.0 11.5 - - + +
378A CYS* 2.8 46.1 + - + +
505A SO4 3.0 17.2 + - - +
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Residues in contact with ASP 375 (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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70A ASP* 4.4 12.5 - - - +
73A CYS* 4.5 0.2 - - - -
75A CYS* 5.5 0.7 - - - +
76A HIS* 4.8 10.3 - - + +
319A PHE* 4.8 3.1 - - + -
369A GLU 4.5 0.2 - - - +
370A HIS* 3.1 33.2 - - - +
371A LEU* 4.3 1.8 - - - -
372A ARG* 2.9 63.6 + - - +
374A LYS* 1.3 75.5 - - - +
376A ILE* 1.3 63.0 + - + +
378A CYS* 3.6 10.7 - - - -
379A TYR* 3.0 30.3 + - - +
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Residues in contact with ILE 376 (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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132A PHE* 3.6 32.3 - - + -
182A PRO* 3.7 22.8 - - + +
186A PHE* 3.9 30.1 - - + -
203A TRP* 4.8 0.9 - - + -
319A PHE* 3.7 14.4 - - + -
371A LEU* 3.6 31.4 - - + -
372A ARG 3.4 14.8 - - - +
373A MET* 3.0 13.7 + - - +
375A ASP* 1.3 74.1 - - - +
377A LYS* 1.3 65.0 + - - +
379A TYR* 3.3 5.6 + - - +
380A TRP* 3.1 24.8 + - + -
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Residues in contact with LYS 377 (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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131A HIS* 5.4 8.3 - - + -
132A PHE* 4.0 26.5 - - + -
135A PRO* 6.2 4.3 - - + -
136A LEU* 4.5 7.9 - - + +
373A MET* 2.8 35.3 + - + +
374A LYS* 4.0 9.0 - - - +
376A ILE* 1.3 77.9 - - - +
378A CYS* 1.3 62.9 + - - +
380A TRP* 3.4 7.8 - - - +
381A ARG* 3.1 21.3 + - - +
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Residues in contact with CYS 378 (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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70A ASP* 5.5 0.2 - - - -
73A CYS* 2.0 51.4 - - + +
374A LYS* 2.8 42.4 + - + +
375A ASP* 3.6 15.5 - - - -
377A LYS* 1.3 71.3 - - - +
379A TYR* 1.3 68.3 + - - +
381A ARG* 3.4 10.5 + - - +
382A LYS* 2.9 26.5 + - - +
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Residues in contact with TYR 379 (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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73A CYS* 4.1 7.9 - - - -
76A HIS* 3.1 35.0 - + + -
79A VAL* 3.4 14.3 - - + +
80A LEU* 3.1 44.6 + - + +
83A ASP* 4.7 0.7 + - - -
180A MET 4.0 20.1 + - - -
182A PRO* 3.8 20.0 - - + -
319A PHE* 3.5 37.7 - + + +
375A ASP 3.0 21.5 + - - +
376A ILE 3.7 3.8 - - - +
378A CYS* 1.3 78.8 - - - +
380A TRP* 1.3 61.3 + - - +
382A LYS* 3.3 3.1 + - - +
383A LEU* 2.9 31.9 + - + +
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Residues in contact with TRP 380 (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 ILE* 4.2 29.2 - - + -
132A PHE* 3.5 44.2 - + + +
133A LEU* 3.8 15.3 - - + -
136A LEU* 4.2 11.4 - - + -
147A ILE* 4.5 10.1 - - + -
168A PHE* 5.5 3.4 - + - -
181A TYR* 3.4 46.7 - + + -
182A PRO* 3.7 29.1 + - + +
376A ILE 3.1 16.9 + - - +
377A LYS* 3.4 9.9 - - - +
379A TYR* 1.3 81.2 - - - +
381A ARG* 1.3 63.0 + - - +
383A LEU* 3.3 9.2 + - + +
384A LEU* 3.0 58.3 + - + +
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Residues in contact with ARG 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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136A LEU* 3.8 32.2 - - + +
139A THR* 5.4 10.7 + - - -
140A LEU* 4.8 7.4 - - + +
377A LYS 3.1 11.1 + - - +
378A CYS* 3.7 13.0 - - - +
380A TRP* 1.3 79.7 - - - +
382A LYS* 1.3 65.1 + - - +
384A LEU* 3.3 3.5 + - - +
385A LYS* 3.0 70.8 + - + +
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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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72A ASP* 3.4 15.8 + - - -
73A CYS* 3.1 33.2 + - + +
74A SER* 4.3 7.9 - - - +
77A ALA* 4.3 10.2 - - + +
80A LEU* 3.7 29.8 - - + -
81A LYS* 6.2 0.8 - - - +
378A CYS 2.9 18.3 + - - +
379A TYR* 3.8 3.6 - - - +
381A ARG* 1.3 77.5 - - - +
383A LEU* 1.3 61.6 + - - +
385A LYS* 3.9 9.4 - - - +
386A ARG* 3.2 38.2 + - - +
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Residues in contact with LEU 383 (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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80A LEU* 4.1 24.7 - - + +
84A LEU* 4.0 12.7 - - + +
168A PHE* 3.8 24.2 - - + -
179A ILE* 3.6 24.2 - - + -
180A MET 3.5 21.5 - - - +
181A TYR* 4.2 11.2 - - + -
379A TYR* 2.9 30.2 + - + +
380A TRP* 3.7 14.4 - - + +
381A ARG 3.3 0.2 - - - -
382A LYS* 1.3 74.6 - - - +
384A LEU* 1.3 67.5 + - + +
386A ARG* 3.4 4.1 + - - +
387A TYR* 3.0 25.6 + - - +
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Residues in contact with LEU 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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109A ILE* 5.0 1.8 - - + -
133A LEU* 3.8 26.7 - - + -
136A LEU* 4.5 8.5 - - + -
140A LEU* 3.9 26.5 - - + -
143A MET* 3.9 14.1 - - - +
145A LEU* 3.8 35.9 - - + -
168A PHE* 4.7 11.4 - - + -
380A TRP* 3.0 34.1 + - + +
381A ARG 3.9 2.7 - - - +
383A LEU* 1.3 79.2 - - + +
385A LYS* 1.3 62.2 + - - +
387A TYR* 3.6 2.8 - - + +
388A VAL* 3.0 27.4 + - - +
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Residues in contact with LYS 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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139A THR 5.0 9.1 + - - -
140A LEU* 3.8 18.1 - - + +
141A PRO* 5.8 1.3 - - + -
381A ARG* 3.0 72.5 + - + +
382A LYS* 3.9 7.0 - - - +
384A LEU* 1.3 75.5 - - - +
386A ARG* 1.3 61.4 + - - +
388A VAL* 3.2 23.2 - - - +
389A LYS* 3.6 17.6 - - - +
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Residues in contact with ARG 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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77A ALA* 6.2 0.4 - - - +
80A LEU* 3.9 23.4 - - + +
81A LYS* 3.8 37.6 - - - +
84A LEU* 3.6 24.5 - - + -
382A LYS* 3.2 34.3 + - - +
383A LEU 4.0 0.2 - - - +
385A LYS* 1.3 76.5 - - - +
387A TYR* 1.3 62.1 + - - +
389A LYS* 3.6 25.3 - - + +
390A LEU* 3.6 12.3 - - + +
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Residues in contact with TYR 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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84A LEU* 3.7 19.5 - - + +
92A VAL* 4.9 2.7 - - + -
97A ILE* 3.5 19.6 - - - +
143A MET* 4.1 14.4 - - + -
144A ASP 2.6 22.7 + - - -
145A LEU* 3.3 28.6 - - + -
146A ILE 5.0 0.5 + - - -
166A PRO* 3.7 25.7 + - + +
168A PHE* 3.7 28.3 - + + -
179A ILE* 4.5 1.1 - - + -
383A LEU 3.0 19.2 + - - +
384A LEU* 3.3 4.0 + - + +
386A ARG* 1.3 74.8 - - - +
388A VAL* 1.3 60.8 + - - +
389A LYS 3.1 2.5 - - - -
390A LEU* 2.8 39.6 + - + +
391A LEU* 3.5 23.8 - - + +
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Residues in contact with VAL 388 (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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141A PRO* 4.1 26.5 - - + -
142A ASP 3.1 28.9 - - - +
143A MET* 3.8 16.8 - - + -
384A LEU 3.0 15.1 + - - +
385A LYS* 3.2 23.6 - - - +
387A TYR* 1.3 78.8 - - - +
389A LYS* 1.3 60.3 - - + +
390A LEU 3.0 5.5 + - - -
391A LEU* 3.2 27.7 + - + +
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Residues in contact with LYS 389 (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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385A LYS* 3.6 19.1 - - - +
386A ARG* 3.6 19.2 - - + +
387A TYR 3.1 0.4 - - - -
388A VAL* 1.3 80.0 - - + +
390A LEU* 1.3 61.8 + - + +
391A LEU 3.4 3.1 - - - +
392A GLN* 4.5 6.6 + - - -
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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