Contacts of the helix formed by residues 328 - 349 (chain C) in PDB entry 4UC5
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 328 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C HIS 3.3 11.0 - - - -
307C LEU 3.9 1.3 - - - -
309C GLU* 3.5 30.9 + - - +
327C ILE* 1.3 72.9 - - - +
329C TRP* 1.3 60.8 + - - -
330C GLY 3.3 3.3 + - - -
331C ALA* 3.4 6.9 + - - +
332C THR* 2.9 29.0 + - - -
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Residues in contact with TRP 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C TYR* 4.0 32.8 - + - -
77C ARG* 3.4 68.1 - - + +
78C LEU* 3.5 18.2 - - + -
81C LEU* 3.5 30.5 - - + -
306C HIS 3.1 6.1 + - - +
307C LEU* 3.2 15.8 + - + +
328C GLY* 1.3 69.6 - - - -
330C GLY* 1.3 60.6 + - - +
332C THR* 3.1 20.5 + - + -
333C GLU* 2.9 57.9 + - + +
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Residues in contact with GLY 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C GLY 3.3 0.6 - - - -
329C TRP* 1.3 76.7 - - - +
331C ALA* 1.3 62.8 + - - +
333C GLU* 3.1 11.5 + - - +
334C GLU* 3.0 27.6 + - - +
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Residues in contact with ALA 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C MET* 4.5 8.3 - - + +
309C GLU* 6.1 0.9 - - - +
327C ILE* 3.7 27.0 - - + +
328C GLY 3.4 12.2 + - - +
330C GLY* 1.3 74.3 - - - +
332C THR* 1.3 56.5 + - - +
334C GLU* 3.2 17.8 + - - +
335C LEU* 2.9 30.7 + - - +
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Residues in contact with THR 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ILE* 4.0 11.4 - - + -
74C TYR* 4.3 1.3 - - - +
78C LEU* 4.8 0.7 - - + -
81C LEU* 4.9 0.2 - - + -
305C SER* 2.4 35.4 + - - +
327C ILE* 3.6 8.6 - - - +
328C GLY 2.9 20.3 + - - -
329C TRP* 3.3 33.4 - - + -
330C GLY 3.1 0.4 - - - -
331C ALA* 1.3 73.5 - - - +
333C GLU* 1.3 66.0 + - - +
335C LEU* 3.8 1.9 - - - +
336C LEU* 3.1 44.4 + - + +
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Residues in contact with GLU 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C LEU* 3.9 29.2 - - - +
85C TYR* 4.6 4.0 + - - -
329C TRP* 2.9 52.8 + - + +
330C GLY* 3.4 9.4 - - - +
332C THR* 1.3 75.5 - - - +
334C GLU* 1.3 63.8 + - - +
336C LEU* 4.1 1.7 - - - +
337C ALA* 3.1 23.6 + - - +
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Residues in contact with GLU 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C MET* 4.1 24.4 - - + +
330C GLY 3.0 15.8 + - - +
331C ALA* 3.3 21.1 + - - +
333C GLU* 1.3 77.5 - - + +
335C LEU* 1.3 58.5 + - - +
337C ALA* 3.0 7.9 + - - +
338C LEU* 2.8 28.4 + - - +
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Residues in contact with LEU 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C VAL* 5.5 0.2 - - + -
60C ILE* 5.0 1.1 - - + -
268C CYS* 5.4 0.2 - - - -
280C GLN* 4.2 13.0 - - + +
281C MET* 4.0 25.1 - - - -
284C ALA* 3.9 25.4 - - + -
303C VAL* 3.8 29.4 - - + -
327C ILE* 4.2 18.2 - - + -
331C ALA 2.9 16.4 + - - +
332C THR* 3.8 5.8 - - - +
334C GLU* 1.3 76.7 - - - +
336C LEU* 1.3 72.9 + - + +
338C LEU* 3.3 3.6 - - - +
339C LEU* 3.1 50.7 + - + +
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Residues in contact with LEU 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C VAL* 3.8 29.4 - - + -
60C ILE* 4.1 11.2 - - + -
78C LEU* 4.1 16.4 - - + -
81C LEU* 3.8 26.9 - - + -
85C TYR* 4.0 17.0 - - + -
89C LEU* 3.8 11.5 - - + +
91C ILE* 4.4 15.9 - - + -
332C THR* 3.1 31.7 + - + +
333C GLU* 4.1 2.7 - - - +
335C LEU* 1.3 85.2 - - + +
337C ALA* 1.3 56.8 + - - +
339C LEU* 3.3 3.7 + - + -
340C ALA* 2.8 31.7 + - - +
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Residues in contact with ALA 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C TYR* 3.4 24.5 + - + +
333C GLU 3.1 16.6 + - - +
334C GLU* 3.0 6.5 + - - +
336C LEU* 1.3 73.2 - - - +
338C LEU* 1.3 66.5 + - - +
340C ALA* 3.3 2.0 + - - +
341C GLY* 3.1 20.3 + - - -
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Residues in contact with LEU 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C MET* 3.5 26.7 - - + -
284C ALA* 4.1 13.2 - - + +
285C GLN* 4.0 29.4 - - + +
288C ALA* 3.8 20.4 - - + -
292C GLU* 5.8 2.2 - - - +
334C GLU 2.8 12.7 + - - +
335C LEU* 3.3 9.0 - - - +
337C ALA* 1.3 77.3 - - - +
339C LEU* 1.3 64.6 + - + +
341C GLY* 3.3 1.6 + - - -
342C ALA* 3.0 23.7 + - + +
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Residues in contact with LEU 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 4.3 17.5 - - + -
58C VAL* 4.6 8.3 - - + -
89C LEU* 4.2 7.1 - - + +
268C CYS* 6.0 0.2 - - - -
284C ALA* 3.9 29.8 - - + +
287C ILE* 4.3 18.2 - - + -
288C ALA* 4.4 8.5 - - + +
291C LEU* 4.6 3.1 - - + +
301C VAL* 3.9 26.5 - - + -
335C LEU* 3.1 37.9 + - + +
336C LEU* 3.8 5.2 - - + +
338C LEU* 1.3 80.3 - - + +
340C ALA* 1.3 59.5 + - - +
342C ALA* 3.9 3.9 - - - +
343C ASN* 2.9 32.1 + - - +
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Residues in contact with ALA 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C TYR* 3.3 36.3 - - + -
88C GLU* 3.4 14.0 - - + +
89C LEU* 3.7 19.9 - - + +
336C LEU 2.8 18.1 + - - +
337C ALA 3.8 2.7 - - - +
338C LEU 3.3 0.2 - - - -
339C LEU* 1.3 76.3 - - - +
341C GLY* 1.3 57.9 + - - +
344C LYS* 3.0 29.0 + - - +
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Residues in contact with GLY 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C GLU* 5.3 0.9 - - - -
337C ALA 3.1 13.5 + - - -
338C LEU 3.8 2.9 - - - -
340C ALA* 1.3 75.4 - - - +
342C ALA* 1.3 64.3 + - - +
344C LYS* 3.4 16.3 + - - +
345C LYS* 3.5 19.5 + - - +
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Residues in contact with ALA 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C ALA* 3.7 41.3 - - + +
291C LEU* 4.2 16.5 - - + +
292C GLU* 4.0 19.6 + - - +
338C LEU* 3.0 17.0 + - + +
339C LEU* 3.9 4.5 - - - +
341C GLY* 1.3 78.1 - - - +
343C ASN* 1.3 61.7 + - - +
345C LYS* 3.4 12.6 + - - +
346C ARG* 3.5 6.8 + - - +
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Residues in contact with ASN 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C LYS 3.0 21.1 + - - -
56C LEU* 3.6 14.2 - - + +
88C GLU* 3.1 27.7 + - + +
89C LEU* 4.6 1.1 - - + -
291C LEU* 3.7 13.7 - - + +
339C LEU 2.9 19.0 + - - +
340C ALA 4.3 2.0 - - - +
342C ALA* 1.3 74.5 - - - +
344C LYS* 1.3 65.2 + - - +
346C ARG* 2.8 38.1 + - - -
347C MET* 3.0 32.5 + - - +
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Residues in contact with LYS 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C GLU* 3.8 33.5 + - + +
340C ALA 3.0 18.1 + - - +
341C GLY* 3.5 10.3 - - - +
342C ALA 3.3 0.4 - - - -
343C ASN* 1.3 76.8 - - - +
345C LYS* 1.3 57.7 + - + +
347C MET* 3.7 5.4 + - - +
348C ALA* 3.1 26.3 + - - +
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Residues in contact with LYS 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C GLU* 4.1 36.5 + - + +
341C GLY 3.5 14.5 + - - +
342C ALA 3.4 7.3 + - - +
343C ASN 3.2 0.2 - - - -
344C LYS* 1.3 77.2 - - + +
346C ARG* 1.3 64.8 + - - +
348C ALA* 3.4 8.5 + - - +
349C ARG* 3.2 27.0 + - - +
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Residues in contact with ARG 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C LYS* 2.7 61.8 + - + +
55C ARG 4.1 6.1 + - - -
56C LEU* 4.5 4.4 - - - +
291C LEU* 3.5 31.1 + - - +
294C ASP 3.7 14.4 - - - +
295C GLY 2.6 29.6 + - - -
296C GLY* 4.1 1.7 - - - -
298C ILE 2.9 24.6 + - - -
299C MET* 5.1 0.2 - - - +
342C ALA 3.5 5.3 + - - +
343C ASN* 2.8 30.1 + - - +
345C LYS* 1.3 78.8 - - - +
347C MET* 1.3 64.0 + - - +
349C ARG* 3.1 42.7 - - - +
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Residues in contact with MET 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ASP* 4.4 7.2 - - - +
54C LYS* 3.7 25.8 - - + +
55C ARG* 4.0 16.2 - - + +
87C ASN 3.4 26.7 - - - +
88C GLU* 4.0 10.1 - - - -
343C ASN* 3.0 40.0 + - - +
344C LYS* 3.9 5.2 - - - +
346C ARG* 1.3 78.7 - - - +
348C ALA* 1.3 61.0 + - - +
349C ARG 3.3 6.1 + - - -
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Residues in contact with ALA 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C LYS 3.1 18.8 + - - +
345C LYS* 3.5 9.9 - - - +
347C MET* 1.3 73.8 - - - +
349C ARG* 1.3 64.2 + - - +
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Residues in contact with ARG 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C LEU 3.1 15.1 + - - -
292C GLU* 2.7 28.5 + - - +
293C GLN 3.6 11.3 + - - -
294C ASP* 2.7 35.5 + - - +
345C LYS* 3.2 13.7 + - - +
346C ARG* 3.1 36.5 + - - +
347C MET 3.8 7.9 - - - -
348C ALA* 1.3 82.1 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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