Contacts of the helix formed by residues 304 - 319 (chain Y) in PDB entry 5A31
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 LEU 304 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271Y VAL* 3.0 38.6 - - + +
294Y PHE* 6.4 0.4 - - + -
297Y ALA* 3.1 46.9 - - + +
298Y GLN* 3.9 3.1 - - - +
301Y ASP* 3.6 15.3 - - + +
303Y TYR* 1.3 87.9 - - - +
305Y ILE* 1.3 66.4 + - - +
306Y LYS* 3.3 3.7 + - - -
307Y GLY* 3.5 8.1 + - - +
308Y MET* 3.1 39.8 - - + +
331Y LEU* 5.4 0.8 - - - +
334Y ILE* 4.9 1.4 - - - +
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Residues in contact with ILE 305 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92X GLU* 4.6 22.6 - - + +
303Y TYR* 4.0 2.9 - - + -
304Y LEU* 1.3 72.8 - - - +
306Y LYS* 1.3 62.5 + - - +
308Y MET* 3.4 7.6 + - - +
331Y LEU* 4.3 10.5 - - + -
334Y ILE* 3.8 22.4 - - + -
335Y SER* 3.2 26.0 - - - +
338Y HIS* 3.7 41.1 - - + +
340Y GLU* 2.1 63.2 - - + +
341Y PRO* 4.6 1.1 - - + -
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Residues in contact with LYS 306 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54X ARG* 5.3 11.2 - - - +
272Y ASP* 5.5 8.3 + - - +
304Y LEU* 3.3 1.1 - - + -
305Y ILE* 1.3 78.3 - - - +
307Y GLY* 1.3 65.3 + - - +
308Y MET 3.4 0.2 + - - -
309Y ASP* 4.0 12.3 - - - +
310Y VAL* 4.7 5.0 + - - +
340Y GLU* 4.4 8.3 - - - +
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Residues in contact with GLY 307 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275Y GLY* 5.9 7.0 - - - -
279Y ASP* 6.0 2.0 - - - -
294Y PHE* 3.4 21.4 - - - -
304Y LEU* 3.5 10.0 + - - +
305Y ILE 3.4 0.6 - - - -
306Y LYS* 1.3 82.2 - - - +
308Y MET* 1.3 63.4 + - - +
310Y VAL* 3.1 19.8 + - - +
311Y TYR 3.3 7.6 + - - -
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Residues in contact with MET 308 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294Y PHE* 3.1 37.2 - - - -
298Y GLN* 3.7 36.3 - - + +
302Y PRO 5.1 4.0 - - - +
304Y LEU* 3.1 46.0 - - + +
305Y ILE 3.4 4.6 + - - +
306Y LYS 3.3 1.4 - - - -
307Y GLY* 1.3 73.5 - - - +
309Y ASP* 1.3 66.9 - - - +
311Y TYR* 4.1 1.1 - - - -
312Y GLY* 2.7 24.4 + - - -
327Y LEU* 3.9 21.3 - - + +
331Y LEU* 3.6 33.4 - - + -
340Y GLU* 4.9 1.1 - - + -
344Y VAL* 5.1 2.4 - - - +
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Residues in contact with ASP 309 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305Y ILE 4.0 0.2 + - - -
306Y LYS 4.0 8.7 - - - +
308Y MET* 1.3 79.5 - - - +
310Y VAL* 1.3 68.0 + - + +
312Y GLY* 3.6 5.5 + - - -
313Y TYR* 3.8 6.2 + - - +
340Y GLU* 3.5 38.2 - - + +
343Y VAL* 3.1 23.8 - - - +
344Y VAL* 5.7 2.0 + - - +
347Y CYS* 4.7 1.7 - - - -
372Y SER* 4.0 16.5 - - - -
374Y GLN* 3.0 43.7 + - - +
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Residues in contact with VAL 310 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278Y ALA 5.8 0.9 - - - +
279Y ASP* 4.5 17.7 - - - +
282Y PHE* 3.7 46.8 - - + -
294Y PHE* 5.8 1.8 - - + -
306Y LYS 4.8 4.5 - - - +
307Y GLY* 3.1 10.2 + - - +
309Y ASP* 1.3 88.0 - - + +
311Y TYR* 1.3 63.4 + - + +
313Y TYR* 3.2 20.3 + - - +
314Y LEU* 3.6 9.8 + - + +
374Y GLN* 4.1 15.0 - - + +
406Y ARG* 5.7 5.2 - - - +
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Residues in contact with TYR 311 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291Y VAL* 3.9 19.3 - - + -
294Y PHE* 2.7 73.1 - + + -
295Y GLU* 3.3 26.6 + - - +
298Y GLN* 4.0 14.9 + - - -
307Y GLY 3.3 0.4 + - - -
308Y MET 3.1 3.3 + - - +
310Y VAL* 1.3 78.9 - - - +
312Y GLY* 1.3 64.1 + - - +
314Y LEU* 3.4 19.8 + - + +
315Y LEU* 3.3 48.7 + - + +
320Y ARG* 5.0 0.2 + - - -
323Y ASP* 5.5 1.9 + - - +
327Y LEU* 3.4 24.0 - - + -
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Residues in contact with GLY 312 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308Y MET 2.7 19.1 + - - -
309Y ASP 3.6 2.4 + - - -
310Y VAL 3.4 0.2 - - - -
311Y TYR* 1.3 73.6 - - - +
313Y TYR* 1.3 62.2 + - - +
315Y LEU* 3.2 16.1 + - - +
316Y ALA* 3.2 12.1 + - - +
324Y VAL* 3.9 7.0 - - - +
327Y LEU* 4.3 13.7 - - - -
344Y VAL* 4.5 11.7 - - - -
347Y CYS* 3.8 12.3 - - - +
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Residues in contact with TYR 313 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282Y PHE* 4.7 12.8 - + + -
309Y ASP 3.8 1.2 + - - -
310Y VAL 3.2 12.0 + - - +
312Y GLY* 1.3 75.5 - - - +
314Y LEU* 1.3 64.3 + - + +
316Y ALA* 3.2 15.6 + - + +
317Y ARG* 3.2 21.9 + - + -
347Y CYS* 3.5 19.7 - - - -
350Y PHE* 5.1 13.0 - + - -
351Y TYR* 4.1 20.1 + + - -
374Y GLN* 3.6 29.4 - - - +
377Y LEU* 4.7 13.0 - - + -
378Y LEU* 6.2 0.4 - - + -
408Y ASP* 2.9 38.6 + - - -
411Y GLU* 4.2 6.9 + - - -
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Residues in contact with LEU 314 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278Y ALA* 6.5 0.4 - - + -
282Y PHE* 3.9 29.6 - - + -
287Y ASN* 3.3 40.5 - - - +
290Y SER* 3.8 17.9 - - - -
291Y VAL* 3.4 29.5 - - + +
294Y PHE* 5.6 2.5 - - + -
310Y VAL* 3.6 9.8 + - + +
311Y TYR* 3.4 26.4 + - + +
312Y GLY 3.3 0.6 - - - -
313Y TYR* 1.3 80.1 - - + +
315Y LEU* 1.3 58.7 + - - +
317Y ARG* 3.4 7.1 + - + +
318Y GLU* 2.9 27.4 + - - +
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Residues in contact with LEU 315 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291Y VAL* 4.2 8.5 - - + -
311Y TYR* 3.3 55.6 - - + +
312Y GLY* 3.2 2.7 + - - +
314Y LEU* 1.3 77.2 - - - +
316Y ALA* 1.3 51.2 + - - +
318Y GLU* 3.1 7.2 + - + -
319Y GLY 2.8 29.8 + - - -
320Y ARG* 3.1 41.7 + - + +
323Y ASP* 3.5 34.8 - - + +
324Y VAL* 3.5 20.9 - - + +
327Y LEU* 4.5 4.7 - - + -
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Residues in contact with ALA 316 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312Y GLY 3.2 10.4 + - - +
313Y TYR* 3.2 13.9 + - + +
315Y LEU* 1.3 76.8 - - - +
317Y ARG* 1.3 61.0 + - - +
319Y GLY* 3.1 13.5 + - - -
320Y ARG 5.1 0.7 - - - +
321Y LEU* 5.7 3.6 - - + -
324Y VAL* 4.3 5.3 - - + +
347Y CYS* 4.4 8.5 - - + +
351Y TYR* 3.2 61.1 - - + +
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Residues in contact with ARG 317 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287Y ASN* 4.6 17.5 - - - +
313Y TYR* 3.2 23.6 + - + +
314Y LEU* 3.4 8.9 + - - +
316Y ALA* 1.3 74.9 - - - +
318Y GLU* 1.3 60.0 + - - +
319Y GLY* 3.5 0.9 + - - -
351Y TYR* 4.2 7.9 + - - +
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Residues in contact with GLU 318 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287Y ASN* 6.0 1.1 - - - +
291Y VAL* 6.2 2.2 - - + -
314Y LEU 2.9 17.7 + - - +
315Y LEU* 3.5 11.7 - - + +
317Y ARG* 1.3 75.8 - - - +
319Y GLY* 1.3 60.8 + - - +
320Y ARG* 3.5 23.2 + - + +
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Residues in contact with GLY 319 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315Y LEU 2.8 6.8 + - - -
316Y ALA* 3.1 15.0 + - - -
317Y ARG 3.2 1.2 - - - -
318Y GLU* 1.3 77.6 - - - +
320Y ARG* 1.3 56.0 + - - -
321Y LEU* 3.1 14.2 + - - +
351Y TYR* 5.8 1.3 - - - -
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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