Contacts of the helix formed by residues 297 - 312 (chain C) in PDB entry 5D0A
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 LYS 297 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278C ILE* 3.4 30.7 - - + +
279C SER* 4.2 1.1 - - - +
280C ASN* 2.5 38.2 + - - +
283C PHE* 3.5 43.7 - - + -
296C GLY* 1.3 72.3 - - - -
298C LYS* 1.3 67.9 + - - +
299C PRO 3.5 0.4 - - - -
300C ILE* 3.1 5.6 + - - +
301C GLN* 2.9 48.9 + - + +
329C ARG* 3.8 16.4 - - - +
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Residues in contact with LYS 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C LYS* 3.0 43.5 + - + +
295C ARG 4.8 0.6 + - - +
296C GLY* 3.4 0.6 - - - -
297C LYS* 1.3 78.9 - - - +
299C PRO* 1.4 72.7 - - + +
301C GLN* 3.2 3.9 + - - +
302C ARG* 2.9 21.7 + - - +
329C ARG* 3.7 48.9 - - + +
330C PRO* 6.1 1.2 - - - +
331C VAL* 4.0 24.1 - - + +
332C ILE* 4.0 8.9 - - + +
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Residues in contact with PRO 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C THR 3.5 20.2 - - - +
220C GLN* 4.2 6.7 - - - +
221C THR 3.7 21.8 - - - +
222C LYS* 4.3 10.3 - - + -
238C TYR* 6.4 0.7 - - + -
295C ARG* 3.7 29.2 - - + +
296C GLY 3.7 9.9 - - - +
298C LYS* 1.4 95.4 - - + +
300C ILE* 1.3 61.5 + - + +
302C ARG* 3.6 7.2 + - + +
303C ASN* 2.9 37.8 + - - +
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Residues in contact with ILE 300 (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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96C PHE* 3.9 28.7 - - + -
237C LEU* 3.5 27.3 - - + +
238C TYR* 4.1 8.1 - - + -
275C LEU* 4.1 28.5 - - + -
283C PHE* 4.2 19.3 - - + -
287C PHE* 5.7 0.2 - - + -
292C GLY 3.8 19.3 - - - +
296C GLY 3.9 17.5 - - - +
297C LYS* 3.1 8.0 + - + +
299C PRO* 1.3 80.5 - - + +
301C GLN* 1.3 60.1 + - + +
303C ASN* 3.4 3.1 + - - +
304C ALA* 2.9 26.7 + - - +
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Residues in contact with GLN 301 (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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275C LEU* 3.0 30.7 + - + +
276C LEU* 3.6 18.6 + - - +
277C ALA 4.6 0.4 - - - -
278C ILE* 3.8 22.9 + - + +
297C LYS* 2.9 34.0 + - + +
298C LYS 3.7 3.4 - - - +
300C ILE* 1.3 75.0 - - + +
302C ARG* 1.3 64.9 + - - +
304C ALA* 3.2 7.4 + - - +
305C ILE* 3.0 29.0 + - + +
329C ARG* 2.8 41.4 + - - +
332C ILE* 4.0 12.3 - - + -
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Residues in contact with ARG 302 (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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218C LEU 2.9 24.5 + - - -
219C THR* 3.6 12.3 + - - +
221C THR* 2.8 32.4 + - - -
222C LYS 5.9 0.2 - - - -
223C GLY 2.9 27.7 + - - -
225C LEU* 3.7 29.9 - - - +
298C LYS* 2.9 16.9 + - + +
299C PRO* 3.7 4.8 + - + +
301C GLN* 1.3 74.9 - - - +
303C ASN* 1.3 80.9 + - - +
305C ILE* 3.3 9.2 + - - +
306C LEU* 3.1 34.1 + - + +
331C VAL* 4.1 10.1 - - + -
332C ILE* 3.8 13.8 - - + +
335C THR* 3.8 24.2 - - + +
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Residues in contact with ASN 303 (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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219C THR* 3.1 28.5 + - - -
233C ILE* 3.8 17.2 - - + +
236C ARG 3.8 15.5 - - - +
237C LEU* 2.9 30.7 + - - +
299C PRO 2.9 18.5 + - - +
300C ILE 3.7 4.0 - - - +
301C GLN 3.2 0.2 - - - -
302C ARG* 1.3 100.9 + - - +
304C ALA* 1.3 59.8 + - - +
306C LEU* 3.4 8.8 + - - +
307C ALA* 2.8 30.0 + - - +
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Residues in contact with ALA 304 (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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237C LEU* 3.5 16.4 - - + +
272C LEU* 4.0 18.2 - - + +
275C LEU* 4.1 23.3 - - + -
276C LEU* 4.6 5.4 - - + -
300C ILE 2.9 16.1 + - - +
301C GLN* 3.2 6.3 + - - +
303C ASN* 1.3 74.8 - - - +
305C ILE* 1.3 59.8 + - - +
307C ALA* 3.5 2.1 + - - +
308C LEU* 2.9 35.9 + - - +
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Residues in contact with ILE 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C LEU* 3.6 20.9 - - + -
301C GLN* 3.0 19.5 + - + +
302C ARG* 3.4 10.3 - - - +
304C ALA* 1.3 75.8 - - - +
306C LEU* 1.3 63.3 + - - +
308C LEU* 3.1 8.2 + - - +
309C ALA* 2.9 20.1 + - - +
320C LEU* 3.8 11.9 - - + -
323C LEU* 4.3 10.5 - - + -
332C ILE* 4.1 37.9 - - + +
335C THR* 3.6 21.1 - - + +
336C ALA* 3.9 4.7 - - + +
339C ALA* 3.5 25.4 - - + +
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Residues in contact with LEU 306 (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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225C LEU* 3.6 36.3 - - + -
230C ARG* 4.1 21.6 - - + +
233C ILE* 4.2 18.2 - - + -
234C GLY 4.7 1.1 - - - -
302C ARG* 3.1 22.0 + - + +
303C ASN* 3.6 20.0 - - - +
305C ILE* 1.3 76.9 - - - +
307C ALA* 1.3 56.8 + - - +
309C ALA* 3.2 7.1 + - - +
310C HIS* 2.8 28.1 + - - +
335C THR* 3.7 20.9 - - + -
338C TRP* 3.7 27.4 - - + -
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Residues in contact with ALA 307 (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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233C ILE* 5.5 0.2 - - - +
234C GLY 3.5 22.8 + - - +
235C ASN* 3.8 16.8 - - + -
237C LEU* 4.8 0.7 - - + -
272C LEU* 3.8 23.8 - - + -
303C ASN 2.8 20.8 + - - +
304C ALA 3.7 4.7 - - - +
306C LEU* 1.3 73.1 - - - +
308C LEU* 1.3 64.0 + - - +
310C HIS* 3.2 4.0 + - - +
311C PHE* 3.0 27.9 + - - -
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Residues in contact with LEU 308 (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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92C ARG* 4.4 5.2 - - + -
272C LEU* 3.6 31.6 - - + -
273C LYS* 4.3 8.5 - - + -
276C LEU* 3.6 37.9 - - + -
304C ALA 2.9 19.1 + - - +
305C ILE* 3.1 8.9 + - - +
307C ALA* 1.3 76.8 - - - +
309C ALA* 1.3 61.2 + - - +
311C PHE* 3.2 4.6 + - - +
312C LYS 3.0 16.6 + - - -
313C ASP* 3.2 41.1 + - + +
316C ALA* 3.7 18.6 - - + -
320C LEU* 4.9 7.4 - - + -
343C ILE* 4.5 2.7 - - + -
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Residues in contact with ALA 309 (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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305C ILE 2.9 13.0 + - - +
306C LEU 3.5 8.1 - - - +
308C LEU* 1.3 76.2 - - - +
310C HIS* 1.3 61.6 + - - +
312C LYS* 3.0 19.8 + - - +
338C TRP* 3.9 22.4 - - + -
339C ALA* 3.8 23.1 - - + +
342C LYS* 4.1 18.4 - - + +
343C ILE* 3.8 13.3 - - - +
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Residues in contact with HIS 310 (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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230C ARG 5.5 5.6 - - - +
231C THR* 5.0 10.2 + - - -
233C ILE* 6.1 0.2 - - + -
234C GLY* 3.9 39.7 + - - +
235C ASN* 4.3 1.2 + - - +
306C LEU 2.8 13.6 + - - +
307C ALA 3.3 9.4 - - - +
309C ALA* 1.3 76.2 - - - +
311C PHE* 1.3 89.8 + + - +
312C LYS* 3.2 7.0 + - - +
342C LYS* 6.0 0.9 - - - +
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Residues in contact with PHE 311 (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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87C SER* 4.3 9.0 - - - -
92C ARG* 3.4 63.7 + - + +
93C ARG 3.7 14.4 - - - -
235C ASN* 3.7 36.8 - - + -
272C LEU* 3.9 15.0 - - + -
307C ALA 3.0 21.9 + - - +
308C LEU* 3.2 6.0 + - - +
310C HIS* 1.3 93.5 - + - +
312C LYS* 1.3 69.4 + - - +
313C ASP* 3.4 4.1 + - + +
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Residues in contact with LYS 312 (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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308C LEU 3.0 1.9 + - - -
309C ALA 3.0 20.4 + - - +
310C HIS 4.3 5.4 - - - +
311C PHE* 1.3 80.4 - - - +
313C ASP* 1.3 59.2 + - - +
314C ALA* 3.1 10.4 + - - +
342C LYS* 3.4 29.1 + - - +
343C ILE* 3.9 30.5 + - - +
344C GLY* 5.5 0.8 - - - -
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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
------------------------------------------------------------
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