Contacts of the helix formed by residues 304 - 323 (chain C) in PDB entry 1PQ3
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 SER 304 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C ALA* 3.4 9.3 - - - +
303C THR* 1.3 88.4 - - - +
305C GLU* 1.3 76.1 + - - +
306C GLU* 3.1 26.7 - - - +
307C GLU* 3.3 14.9 + - - +
308C ALA* 3.3 16.6 + - - +
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Residues in contact with GLU 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C THR 5.1 0.2 - - - +
304C SER* 1.3 84.2 - - - +
306C GLU* 1.3 57.9 + - - +
308C ALA* 3.2 9.3 + - - +
309C LYS* 3.0 33.6 + - - +
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Residues in contact with GLU 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A THR* 5.7 1.4 + - - -
304C SER* 3.1 17.5 - - - +
305C GLU* 1.3 78.7 + - - +
307C GLU* 1.3 84.2 + - - +
309C LYS* 3.0 10.3 + - - +
310C THR* 2.7 46.8 + - - +
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Residues in contact with GLU 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C PRO* 3.8 33.9 - - + +
262C ALA* 4.4 0.4 - - - +
302C ALA* 4.0 8.0 - - + -
303C THR* 3.0 36.3 + - - -
304C SER* 3.3 22.8 + - - +
305C GLU 3.4 0.2 - - - -
306C GLU* 1.3 96.1 + - - +
308C ALA* 1.3 61.1 + - - +
310C THR* 3.4 4.9 + - - -
311C THR* 2.9 28.6 + - - -
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Residues in contact with ALA 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ALA* 5.8 0.7 - - - +
262C ALA* 4.3 6.9 - - - +
297C VAL* 5.8 0.7 - - - +
299C PRO* 4.2 21.1 - - + +
302C ALA* 3.5 20.8 - - + +
304C SER 3.3 4.2 + - - +
305C GLU* 3.2 11.8 + - - +
306C GLU 3.1 0.4 - - - -
307C GLU* 1.3 80.9 - - - +
309C LYS* 1.3 61.7 + - - +
311C THR* 3.2 4.7 + - - -
312C ALA* 3.0 23.5 + - - +
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Residues in contact with LYS 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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52C ALA* 6.2 1.3 - - + -
305C GLU* 3.0 19.7 + - - +
306C GLU* 3.5 11.9 - - - +
308C ALA* 1.3 78.4 - - - +
310C THR* 1.3 56.6 + - - +
312C ALA* 3.3 8.2 + - + +
313C ASN* 2.9 50.2 + - - +
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Residues in contact with THR 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 5.7 9.4 - - + -
258C THR 5.2 2.5 - - - +
259C LEU* 3.4 24.5 - - + +
261C PRO* 5.0 3.8 - - + -
306C GLU* 2.7 32.6 + - - +
307C GLU* 3.6 8.5 - - - -
308C ALA 3.2 0.2 - - - -
309C LYS* 1.3 73.4 - - - +
311C THR* 1.3 57.8 + - - +
313C ASN* 3.8 7.2 - - - +
314C LEU* 3.0 27.0 + - + +
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Residues in contact with THR 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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252C ILE* 4.0 13.7 - - + +
259C LEU 4.4 3.6 - - - -
260C ALA* 4.0 22.9 - - + -
261C PRO* 3.5 8.1 - - - +
262C ALA* 3.2 40.7 + - - +
297C VAL* 4.3 11.8 - - + +
307C GLU 2.9 15.0 + - - -
308C ALA 3.2 6.5 + - - -
310C THR* 1.3 73.7 - - - +
312C ALA* 1.3 66.6 + - - +
314C LEU* 3.3 6.6 + - - +
315C ALA* 3.0 22.0 + - - +
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Residues in contact with ALA 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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48C ALA* 3.8 25.6 - - + +
49C ILE* 4.7 3.4 - - - +
52C ALA* 3.8 19.7 - - + -
297C VAL* 5.0 6.7 - - + +
308C ALA 3.0 17.0 + - - +
309C LYS* 3.6 8.1 - - - +
311C THR* 1.3 77.0 - - - +
313C ASN* 1.3 62.9 + - - +
315C ALA* 3.1 17.5 + - - +
316C VAL* 3.1 16.1 + - - +
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Residues in contact with ASN 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ALA* 3.7 25.0 - - - +
57C ARG* 5.6 2.9 + - - +
309C LYS* 2.9 39.3 + - - +
310C THR* 3.8 6.0 - - - +
312C ALA* 1.3 77.2 - - - +
314C LEU* 1.3 62.6 + - - +
316C VAL* 3.2 5.8 + - - +
317C ASP* 3.0 34.8 + - - +
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Residues in contact with LEU 314 (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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252C ILE* 4.1 3.1 - - + -
255C PHE* 3.5 50.5 - - + -
259C LEU* 3.5 28.9 - - + +
260C ALA* 3.8 13.7 - - + -
273C TYR* 3.4 35.7 - - + -
277C MET* 5.4 0.7 - - + -
310C THR* 3.0 18.1 + - + +
311C THR 3.6 4.9 - - - +
313C ASN* 1.3 76.9 - - - +
315C ALA* 1.3 63.5 + - - +
317C ASP* 3.2 8.0 + - + +
318C VAL* 3.0 28.3 + - + +
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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
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49C ILE* 3.8 20.9 - - + -
252C ILE* 4.0 11.9 - - + +
294C LEU* 3.6 27.8 - - + +
297C VAL* 4.2 3.8 - - + -
311C THR 3.0 12.5 + - - +
312C ALA* 3.1 9.8 + - - +
314C LEU* 1.3 77.6 - - - +
316C VAL* 1.3 62.3 + - - +
318C VAL* 3.3 3.9 + - - +
319C ILE* 3.2 27.8 + - - +
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Residues in contact with VAL 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 3.5 32.3 - - + +
52C ALA* 3.6 19.1 - - + +
54C LEU* 4.0 23.6 - - + +
57C ARG* 3.3 36.3 - - + +
312C ALA 3.1 12.2 + - - +
313C ASN* 3.6 7.4 - - - +
315C ALA* 1.3 74.1 - - - +
317C ASP* 1.3 53.7 + - - +
319C ILE* 3.1 9.5 + - - +
320C ALA* 2.7 33.3 + - - +
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Residues in contact with ASP 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 4.1 6.6 - - - +
57C ARG* 2.4 39.3 + - - +
273C TYR* 2.5 36.9 + - + +
277C MET* 3.7 11.9 - - + -
313C ASN* 3.0 24.1 + - - +
314C LEU* 3.2 9.8 + - - +
316C VAL* 1.3 74.5 - - - +
318C VAL* 1.3 55.8 + - - +
320C ALA* 3.7 1.1 - - - +
321C SER* 2.7 37.6 + - - -
325C GLN* 4.2 2.9 - - - +
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Residues in contact with VAL 318 (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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250C PHE* 3.8 36.1 - - + -
252C ILE* 5.2 0.7 - - + -
255C PHE* 3.5 35.9 - - + -
277C MET* 3.4 15.0 - - + +
280C ALA* 3.9 5.9 - - + +
292C LEU* 5.4 2.9 - - + -
294C LEU* 4.2 11.4 - - + -
314C LEU* 3.0 16.8 + - + +
315C ALA* 3.6 8.1 - - - +
317C ASP* 1.3 76.8 - - - +
319C ILE* 1.3 57.8 + - + +
321C SER* 3.8 0.9 - - - -
322C SER* 2.8 41.2 + - - +
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Residues in contact with ILE 319 (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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49C ILE* 4.3 7.2 - - + -
54C LEU* 3.8 29.2 - - + -
58C LEU* 4.3 5.6 - - + -
114C VAL* 4.2 16.6 - - + -
116C LEU* 3.6 30.7 - - + -
292C LEU* 4.2 13.5 - - + -
294C LEU* 4.0 19.3 - - + -
315C ALA 3.3 14.8 - - - +
316C VAL 3.1 6.5 + - - +
318C VAL* 1.3 75.7 - - - +
320C ALA* 1.3 67.3 + - - +
322C SER* 3.1 13.6 + - - -
323C PHE* 3.3 35.9 + - + -
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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
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54C LEU* 5.2 0.6 - - - +
57C ARG* 3.9 22.7 - - + +
58C LEU* 4.4 6.9 - - - +
61C LEU* 3.5 13.6 - - + +
316C VAL* 2.7 21.0 + - + +
317C ASP 3.7 1.3 - - - +
319C ILE* 1.3 72.3 - - - +
321C SER* 1.3 58.9 + - - +
323C PHE* 2.9 18.9 + - - -
324C GLY 3.3 1.0 + - - -
325C GLN* 3.1 44.5 + - + +
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Residues in contact with SER 321 (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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277C MET* 3.7 16.7 + - - +
280C ALA* 3.6 18.9 - - - +
281C GLU* 3.4 28.6 + - - +
284C HIS* 3.8 9.4 - - - +
317C ASP 2.7 22.5 + - - -
320C ALA* 1.3 75.0 - - - +
322C SER* 1.3 61.1 + - - +
323C PHE 3.0 1.4 + - - -
324C GLY* 3.2 9.5 + - - -
325C GLN* 3.6 23.0 + - - +
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Residues in contact with SER 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C LEU* 3.9 11.8 - - - +
280C ALA* 3.5 21.9 - - - +
283C ILE* 5.2 1.1 - - - -
284C HIS* 3.5 18.4 + - - +
289C LEU* 3.6 23.0 - - - +
292C LEU* 3.5 30.6 - - - +
318C VAL* 2.8 24.2 + - - +
319C ILE 3.1 3.8 + - - -
321C SER* 1.3 74.9 - - - +
323C PHE* 1.3 60.3 + - - +
324C GLY 3.6 0.2 - - - -
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Residues in contact with PHE 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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24C HIS* 6.2 3.4 - - + -
26C VAL* 3.8 26.2 - - + -
58C LEU* 4.2 9.0 - - + -
61C LEU* 3.7 18.2 - - + +
63C CYS* 4.3 16.1 - - - -
112C SER* 3.9 21.1 - - - -
114C VAL* 3.3 34.8 - - + -
284C HIS* 3.4 11.7 - - - -
289C LEU* 3.7 29.4 - - + -
291C ALA 6.1 0.4 - - - -
292C LEU* 4.5 9.0 - - + -
319C ILE* 3.3 29.5 + - + +
320C ALA 2.9 10.8 + - - +
322C SER* 1.3 80.5 - - - +
324C GLY* 1.3 54.7 + - - +
325C GLN 3.8 0.2 - - - -
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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