Contacts of the helix formed by residues 312 - 332 (chain C) in PDB entry 5DO7
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 312 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C SER* 1.3 74.1 - - - +
313C GLU* 1.3 73.8 + - + +
314C ARG 3.5 0.2 - - - -
315C GLU* 2.7 31.9 - - - +
316C ILE* 3.0 19.7 - - + +
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Residues in contact with GLU 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C SER* 4.3 4.5 - - - -
312C LYS* 1.3 91.0 - - + +
314C ARG* 1.3 53.2 + - - +
316C ILE* 2.8 33.0 + - + +
317C GLU* 2.8 19.3 + - - +
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Residues in contact with ARG 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C ASP 4.8 0.4 - - - -
310C GLN* 4.0 13.7 - - - +
311C SER* 4.3 10.3 - - - +
312C LYS 3.5 0.4 - - - -
313C GLU* 1.3 77.5 - - - +
315C GLU* 1.3 63.1 + - - +
317C GLU* 3.6 17.1 + - - +
318C THR* 2.9 30.5 + - + +
246D PHE* 3.6 38.2 + - + -
249D HIS* 4.4 19.2 + - - -
250D ASN* 4.0 20.2 + - - +
253D LYS* 5.9 1.8 - - - +
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Residues in contact with GLU 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C VAL* 4.2 7.3 - - + +
308C ASP 3.6 25.1 + - - +
309C THR* 4.1 18.1 + - - -
310C GLN 3.9 4.8 + - - -
311C SER 4.0 10.4 - - - +
312C LYS* 2.7 30.1 + - - +
313C GLU 3.2 0.2 - - - -
314C ARG* 1.3 77.5 - - - +
316C ILE* 1.3 63.5 + - + +
318C THR* 2.2 28.2 + - - -
319C SER* 2.7 27.0 + - - -
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Residues in contact with ILE 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C LYS* 3.0 36.6 - - + +
313C GLU* 2.8 19.2 + - + +
315C GLU* 1.3 84.4 - - + +
317C GLU* 1.3 67.5 + - - +
319C SER* 2.8 20.5 + - - -
320C LYS* 3.2 10.8 + - + +
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Residues in contact with GLU 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C GLU 2.8 14.0 + - - +
314C ARG* 3.6 25.2 - - - +
316C ILE* 1.3 75.9 - - - +
318C THR* 1.3 61.1 + - - +
320C LYS* 3.3 15.8 + - - +
321C ARG* 3.3 27.6 + - - +
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Residues in contact with THR 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C SER 5.5 0.7 - - - +
307C VAL* 3.0 30.4 - - - +
314C ARG* 2.9 21.1 - - + +
315C GLU* 2.2 34.1 + - - -
317C GLU* 1.3 73.8 - - - +
319C SER* 1.3 67.2 + - - +
321C ARG* 2.8 51.4 + - - +
322C VAL* 2.8 12.5 + - - +
246D PHE* 4.4 21.8 - - + -
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Residues in contact with SER 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C VAL* 3.3 21.2 - - - +
315C GLU* 2.7 19.7 + - - -
316C ILE* 2.8 14.1 + - - -
318C THR* 1.3 73.0 + - - +
320C LYS* 1.3 57.1 + - - +
322C VAL* 3.0 6.9 - - - +
323C GLN* 2.8 30.5 + - - +
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Residues in contact with LYS 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C ILE* 3.2 7.0 + - + +
317C GLU* 3.4 10.8 - - - +
318C THR 3.1 0.4 - - - -
319C SER* 1.3 75.1 - - - +
321C ARG* 1.3 68.0 + - - +
323C GLN* 3.1 8.6 + - - +
324C MET* 2.8 53.6 + - + +
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Residues in contact with ARG 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C TYR* 4.4 17.0 + - + +
303C ASP 4.2 5.7 + - - -
304C LEU* 3.4 56.9 + - - +
306C SER 5.5 1.6 + - - -
317C GLU* 3.3 20.4 + - - +
318C THR* 2.8 45.2 + - - +
320C LYS* 1.3 73.9 - - - +
322C VAL* 1.3 63.5 + - - +
324C MET* 2.8 8.9 + - - +
325C ILE* 2.8 37.1 + - + +
246D PHE* 6.0 2.2 - - - -
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Residues in contact with VAL 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C SER* 4.3 9.9 - - - +
272C ILE* 3.5 21.1 - - + -
304C LEU 4.9 3.6 - - - +
305C THR* 2.9 30.7 - - - +
307C VAL* 3.3 26.9 - - + -
318C THR 2.8 12.0 + - - +
319C SER* 3.0 23.1 - - - +
321C ARG* 1.3 73.9 - - - +
323C GLN* 1.3 56.1 + - - +
325C ILE* 3.7 7.7 - - + -
326C GLU* 2.8 28.7 + - + +
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Residues in contact with GLN 323 (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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270C GLU* 3.3 19.9 - - - +
319C SER 2.8 18.8 + - - +
320C LYS* 3.3 11.7 - - - +
322C VAL* 1.3 73.5 - - + +
324C MET* 1.3 64.7 + - + +
326C GLU* 2.8 22.5 + - - +
327C SER* 2.8 41.3 + - - -
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Residues in contact with MET 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C LYS* 2.8 51.2 + - + +
321C ARG* 2.8 11.9 + - - +
323C GLN* 1.3 78.1 - - + +
325C ILE* 1.3 56.1 + - + +
327C SER* 3.0 10.0 + - - -
328C ALA* 2.8 35.8 + - - +
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Residues in contact with ILE 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ILE* 4.1 16.7 - - + +
283C PHE* 4.4 3.4 - - + -
284C PHE* 4.0 25.1 - - + -
287C CYS* 3.5 34.1 - - + +
289C TYR* 3.8 27.4 - - + -
304C LEU* 5.0 8.7 - - + +
305C THR* 5.6 4.5 - - + -
321C ARG* 2.8 34.1 + - + +
322C VAL* 3.9 7.0 - - - +
324C MET* 1.3 79.0 - - + +
326C GLU* 1.3 61.1 + - - +
328C ALA* 3.4 5.7 - - - +
329C TYR* 3.4 16.5 + - - +
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Residues in contact with GLU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C GLU* 3.0 33.3 - - + +
271C LEU 3.3 24.7 - - - +
272C ILE* 4.2 15.7 - - + +
322C VAL* 2.8 19.0 + - + +
323C GLN* 2.8 27.4 + - - +
325C ILE* 1.3 70.3 - - - +
327C SER* 1.3 66.8 - - - +
329C TYR* 2.8 16.9 + - + +
330C LYS* 3.0 47.2 + - + +
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Residues in contact with SER 327 (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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323C GLN* 2.8 26.7 + - - +
324C MET* 3.0 19.5 + - - -
326C GLU* 1.3 79.7 - - - +
328C ALA* 1.3 77.5 + - - +
329C TYR 3.1 0.7 + - - -
330C LYS* 3.2 11.1 + - - +
331C LYS* 3.3 15.9 + - - +
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Residues in contact with ALA 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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283C PHE* 4.3 2.9 - - + -
287C CYS* 3.8 25.8 - - + -
324C MET 2.8 15.3 + - - +
325C ILE* 3.4 9.9 - - - +
327C SER* 1.3 85.6 + - - +
329C TYR* 1.3 60.2 + - - +
331C LYS* 3.7 5.4 + - - +
332C SER* 3.4 18.2 + - - -
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Residues in contact with TYR 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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73C SER* 4.8 5.1 + - - -
271C LEU* 4.4 13.9 - - + +
272C ILE* 3.1 33.7 - - - +
273C PHE* 3.7 23.1 - + - +
274C CYS* 3.7 32.2 + - + +
283C PHE* 3.4 21.5 - + + -
325C ILE 3.4 5.3 + - - +
326C GLU 2.8 15.0 + - - +
328C ALA* 1.3 70.6 - - - +
330C LYS* 1.3 79.5 + - + +
331C LYS 3.0 2.5 - - - -
332C SER 2.8 13.2 + - - -
334C ILE* 5.0 1.3 - - + -
335C CYS* 2.4 67.2 + - + +
338C THR* 3.8 10.7 + - - +
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Residues in contact with LYS 330 (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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42C HIS* 4.8 11.1 + - - -
71C ASP* 3.4 28.4 + - - +
73C SER* 4.1 13.3 + - - -
270C GLU* 6.4 0.2 - - + -
271C LEU* 4.9 11.9 - - + +
326C GLU* 3.0 33.8 + - + +
327C SER* 3.2 5.7 + - - +
329C TYR* 1.3 100.2 - - + +
331C LYS* 1.3 58.2 + - - +
335C CYS* 4.1 8.7 - - - +
336C HIS 5.1 0.3 + - - -
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Residues in contact with LYS 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C SER 3.3 15.5 + - - +
328C ALA* 3.9 4.7 - - - +
329C TYR 3.0 0.6 - - - -
330C LYS* 1.3 78.4 - - - +
332C SER* 1.3 67.3 + - - +
333C ALA 3.8 0.2 + - - -
336C HIS* 4.8 5.0 + - - +
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Residues in contact with SER 332 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C PHE* 4.0 16.2 - - - -
286C ASP* 4.2 11.6 + - - -
328C ALA 3.4 11.4 + - - -
329C TYR 2.8 18.5 + - - -
331C LYS* 1.3 75.9 - - - +
333C ALA* 1.3 78.5 + - - +
334C ILE* 3.2 14.3 + - - +
335C CYS* 2.8 22.2 + - - +
336C HIS* 2.8 10.6 + - - -
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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
------------------------------------------------------------
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