Contacts of the helix formed by residues 314 - 329 (chain C) in PDB entry 5U03
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 TYR 314 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLU* 3.3 5.4 - - - -
303C LEU* 3.6 27.8 - - + -
305C GLY* 4.7 0.7 - - - -
306C LYS 4.5 1.9 + - - -
307C TYR* 3.4 34.5 + - + +
308C THR* 3.0 38.0 + - - -
309C LYS 5.7 0.2 - - - -
311C SER* 4.6 7.2 - - - +
312C ASP* 2.9 1.4 - - - -
313C SER* 1.3 91.9 - - - +
315C ALA* 1.3 52.6 + - - +
316C SER 3.3 0.2 - - - -
317C VAL* 3.0 22.5 + - + -
318C ILE* 2.8 46.4 + - + +
336C TYR* 5.4 2.9 - + + -
370C PRO* 3.6 29.2 - - + +
371C GLY 4.9 5.9 + - - -
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Residues in contact with ALA 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLU* 3.1 5.2 + - - +
69C LEU* 4.3 11.4 - - + -
312C ASP* 3.0 30.6 + - + +
314C TYR* 1.3 75.7 - - - +
316C SER* 1.3 57.6 + - - +
318C ILE* 4.0 7.0 - - - +
319C LYS* 3.0 28.1 + - - +
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Residues in contact with SER 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLU* 2.6 35.3 + - - +
69C LEU* 3.9 25.8 - - - +
76C ARG* 4.2 14.1 + - - +
315C ALA* 1.3 73.0 - - - +
317C VAL* 1.3 58.0 + - - -
319C LYS* 3.6 7.2 - - - +
320C ALA* 2.8 28.1 + - - +
323C HIS* 5.7 0.2 - - - -
528C GLU* 4.0 25.6 - - - +
529C PHE* 4.5 4.3 - - - -
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Residues in contact with VAL 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLU* 4.4 4.9 - - + +
303C LEU* 5.6 0.9 - - + -
313C SER 5.3 0.4 - - - +
314C TYR* 3.0 32.9 + - + +
316C SER* 1.3 77.6 + - - +
318C ILE* 1.3 68.0 + - + +
320C ALA* 3.1 6.2 + - - +
321C LEU* 3.0 24.7 + - + +
368C LEU* 3.8 29.2 - - + -
370C PRO* 6.0 4.3 - - + -
528C GLU* 4.0 29.8 - - + +
540C TYR* 4.2 13.9 - - + +
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Residues in contact with ILE 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C LEU* 5.6 1.1 - - + -
314C TYR* 2.8 34.0 + - + +
315C ALA* 4.1 5.4 - - - +
317C VAL* 1.3 74.0 - - + +
319C LYS* 1.3 58.4 + - - +
321C LEU* 2.9 13.1 + - + +
322C GLU* 2.8 46.5 + - + +
332C LEU* 4.7 1.8 - - + -
334C ILE* 3.9 37.9 - - + -
336C TYR* 3.2 31.2 - - + +
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Residues in contact with LYS 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ARG* 3.6 29.2 - - - +
249C SER* 4.7 10.9 + - - -
250C ILE* 5.4 11.9 - - - +
292C TYR* 6.0 0.6 + - - +
315C ALA 3.0 21.0 + - - +
316C SER* 3.6 9.2 - - - +
317C VAL 3.2 0.2 - - - -
318C ILE* 1.3 77.8 - - - +
320C ALA* 1.3 61.2 + - - +
322C GLU* 2.8 34.8 + - + +
323C HIS* 2.9 51.7 + - + +
533C PRO* 6.1 0.2 - - + -
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Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C SER 2.8 15.4 + - - +
317C VAL 3.1 9.8 + - - +
319C LYS* 1.3 73.3 - - - +
321C LEU* 1.3 62.8 + - - +
323C HIS* 3.0 30.6 + - - +
324C SER* 3.3 9.7 + - - -
528C GLU* 4.0 8.7 - - + +
531C SER* 4.0 15.2 + - - +
536C PRO* 5.2 0.2 - - - +
540C TYR* 3.7 32.2 - - + +
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Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C ILE* 4.1 29.6 - - + -
317C VAL* 3.0 25.2 + - + +
318C ILE* 2.9 14.5 + - + +
320C ALA* 1.3 75.6 - - - +
322C GLU* 1.3 55.8 + - - +
324C SER* 3.0 8.4 + - - +
325C ALA* 2.8 26.5 + - - +
332C LEU* 3.6 18.3 - - + +
334C ILE* 3.7 26.2 - - + -
368C LEU* 5.0 3.4 - - + -
540C TYR* 3.7 38.6 - - + +
543C LEU* 5.0 2.2 - - + -
544C LEU* 4.9 4.1 - - + +
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Residues in contact with GLU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C SER* 5.2 2.9 + - - -
292C TYR* 5.4 14.6 + - + +
318C ILE* 2.8 35.5 + - + +
319C LYS* 2.8 45.7 + - + +
321C LEU* 1.3 72.9 - - - +
323C HIS* 1.3 67.0 + - + +
325C ALA* 3.5 8.5 - - - +
326C LEU* 2.8 26.9 + - - +
332C LEU* 4.4 8.7 - - + -
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Residues in contact with HIS 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ARG* 3.7 14.6 + - - -
292C TYR* 5.7 4.3 - - - -
316C SER 5.7 0.2 - - - -
319C LYS* 2.9 45.6 + - + +
320C ALA* 3.0 11.1 + - - +
322C GLU* 1.3 78.2 - - + +
324C SER* 1.3 62.0 + - - +
326C LEU* 3.4 6.7 + - - +
327C ALA* 3.1 20.3 + - - +
528C GLU 5.8 0.7 - - - -
531C SER* 3.0 39.3 + - - -
532C ARG* 3.3 20.7 - - - +
533C PRO* 3.4 39.4 - - + +
536C PRO* 3.9 12.1 - - + +
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Residues in contact with SER 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C ALA 3.3 7.6 + - - -
321C LEU* 3.0 10.8 + - - -
323C HIS* 1.3 75.6 - - - +
325C ALA* 1.3 64.8 + - - +
327C ALA* 3.0 14.7 + - - +
328C ILE* 3.0 11.6 + - - +
536C PRO* 4.2 7.0 - - - +
537C SER 4.3 0.3 + - - -
540C TYR* 3.6 7.5 - - - +
541C PHE* 3.1 44.9 + - - +
544C LEU* 3.4 22.4 - - - +
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Residues in contact with ALA 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C LEU* 5.3 0.6 - - - +
321C LEU 2.8 13.1 + - - +
322C GLU* 3.1 12.5 + - - +
324C SER* 1.3 76.7 - - - +
326C LEU* 1.3 52.8 + - - +
328C ILE* 4.0 1.8 - - - -
329C ASN* 2.6 30.0 + - - -
330C HIS* 2.9 28.0 + - + +
331C LYS 5.0 0.7 - - - +
332C LEU* 4.2 21.3 - - + -
544C LEU* 3.7 13.2 - - + +
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Residues in contact with LEU 326 (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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288C MET* 4.4 21.1 - - + +
291C ARG* 3.7 39.5 - - + +
292C TYR* 3.5 47.1 - - + +
295C LEU* 5.0 6.5 - - + -
322C GLU 2.8 16.2 + - - +
323C HIS* 3.7 5.6 - - - +
325C ALA* 1.3 74.2 - - - +
327C ALA* 1.3 67.1 + - - +
329C ASN* 2.8 26.3 + - - +
533C PRO* 5.1 15.0 - - + +
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Residues in contact with ALA 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C HIS 3.1 12.7 + - - +
324C SER* 3.0 11.0 + - - +
326C LEU* 1.3 78.5 - - - +
328C ILE* 1.3 61.2 + - - +
329C ASN* 3.3 11.1 + - - -
533C PRO 6.0 0.9 - - - +
536C PRO* 4.7 11.7 - - + -
541C PHE* 3.9 21.3 - - + -
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Residues in contact with ILE 328 (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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324C SER 3.0 7.5 + - - +
325C ALA* 3.4 9.6 - - - +
327C ALA* 1.3 74.1 - - - +
329C ASN* 1.3 73.4 + - - +
330C HIS* 3.4 50.1 + - + +
541C PHE* 4.5 7.6 - - + -
544C LEU* 3.5 26.2 - - + -
545C LEU* 3.8 28.9 - - + -
548C VAL* 4.0 17.0 - - + -
550C ARG* 4.6 7.9 - - + +
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Residues in contact with ASN 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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291C ARG* 3.8 36.2 + - - +
294C ARG 5.2 9.8 - - - +
295C LEU* 4.0 16.1 - - - -
296C LEU* 3.2 14.6 + - + +
325C ALA 2.6 12.0 + - - -
326C LEU* 2.8 22.1 + - - +
327C ALA 3.3 14.8 + - - -
328C ILE* 1.3 78.9 + - - +
330C HIS* 1.3 64.7 + - + +
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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