Contacts of the helix formed by residues 317 - 335 (chain O) in PDB entry 4WNC
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 GLU 317 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13O ARG* 2.8 49.5 + - + +
14O ILE* 4.0 10.3 - - + +
17O LEU* 3.6 13.9 - - + -
52O THR* 3.9 3.3 + - - +
53O HIS* 2.6 30.8 + - - +
238O ALA 4.4 7.3 - - - +
239O ASN* 3.2 20.5 - - - +
315O ASP* 3.0 6.0 + - - +
316O ASN* 1.3 88.3 + - - +
318O PHE* 1.3 59.9 + - - +
319O GLY 3.7 0.2 - - - -
321O SER* 2.8 34.4 + - - -
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Residues in contact with PHE 318 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17O LEU* 4.2 17.7 - - + -
20O ARG* 5.0 10.1 - - + -
21O ALA* 6.3 2.2 - - + -
24O ASN* 5.1 13.0 - - - -
53O HIS* 3.3 43.1 - + + -
288O SER* 3.5 30.3 - - - -
289O ASP 4.0 3.6 - - - +
290O THR* 3.8 12.6 - - + -
315O ASP* 2.8 28.3 + - - +
317O GLU* 1.3 72.7 - - - +
319O GLY* 1.3 65.0 + - - +
321O SER* 4.0 3.3 - - - -
322O ASN* 2.9 53.0 + - - -
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Residues in contact with GLY 319 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289O ASP 3.8 2.6 + - - -
290O THR 3.8 10.5 - - - -
291O HIS 3.5 25.8 - - - -
292O SER* 4.9 3.8 - - - -
315O ASP 3.0 12.1 + - - -
318O PHE* 1.3 75.8 - - - +
320O TYR* 1.3 63.6 + - - +
322O ASN* 3.2 6.8 + - - +
323O ARG* 3.0 28.5 + - - +
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Residues in contact with TYR 320 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14O ILE* 4.2 19.3 - - + -
122O SER* 2.9 39.0 - - - -
123O ALA 3.1 0.9 + - - -
149O ASN* 3.4 31.9 - - - +
150O ALA 2.6 30.5 + - - -
151O SER* 3.7 5.8 - - - -
152O CYS* 3.7 23.1 - - + -
155O ASN* 3.6 15.5 - - - -
292O SER* 5.7 0.4 - - - +
315O ASP 4.1 3.0 + - - -
316O ASN 3.6 20.4 - - - +
317O GLU 4.0 1.1 + - - +
318O PHE 3.4 0.4 - - - -
319O GLY* 1.3 75.8 - - - +
321O SER* 1.3 57.6 + - - +
323O ARG* 3.0 8.7 + - - +
324O VAL* 2.9 44.2 + - + +
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Residues in contact with SER 321 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14O ILE* 3.8 14.9 + - - +
17O LEU* 3.3 39.4 - - - +
18O VAL* 3.7 15.4 + - - +
21O ALA* 4.3 2.5 - - - -
317O GLU 2.8 21.6 + - - -
318O PHE* 4.0 4.9 - - - -
320O TYR* 1.3 77.3 - - - +
322O ASN* 1.3 64.3 + - - +
324O VAL* 3.4 6.2 + - - +
325O VAL* 3.3 24.1 + - - +
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Residues in contact with ASN 322 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21O ALA* 3.7 25.7 - - - +
25O SER* 5.3 6.4 - - - -
290O THR* 3.6 27.8 - - - +
318O PHE* 2.9 33.5 + - - +
319O GLY 3.2 9.2 + - - +
321O SER* 1.3 82.5 - - - +
323O ARG* 1.3 75.7 + - - +
325O VAL* 3.3 4.5 + - - +
326O ASP* 3.0 33.4 + - - +
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Residues in contact with ARG 323 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133O MET* 3.8 29.0 - - + +
149O ASN* 3.9 13.2 + - - +
155O ASN* 3.9 14.6 - - + +
272O GLY 3.7 15.3 + - - -
273O ILE* 4.4 10.4 - - - +
290O THR* 2.8 33.3 + - - -
291O HIS 3.7 0.4 - - - -
292O SER* 2.9 42.4 + - - +
319O GLY 3.0 15.0 + - - +
320O TYR* 3.0 11.2 + - - +
322O ASN* 1.3 86.5 - - - +
324O VAL* 1.3 60.1 + - - +
326O ASP* 2.8 29.8 + - - +
327O LEU* 2.8 32.2 + - - +
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Residues in contact with VAL 324 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18O VAL* 4.0 18.8 - - + -
96O VAL* 3.9 32.3 - - + -
120O ILE* 4.5 12.3 - - + -
122O SER* 4.7 7.6 - - - -
149O ASN* 3.5 21.8 - - + +
320O TYR* 2.9 38.6 + - + +
321O SER 3.6 7.2 - - - +
322O ASN 3.3 0.2 - - - -
323O ARG* 1.3 77.0 - - - +
325O VAL* 1.3 62.6 + - - +
327O LEU* 3.4 5.4 + - - +
328O MET* 3.1 27.1 + - + +
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Residues in contact with VAL 325 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18O VAL* 3.8 30.1 - - + +
21O ALA* 3.9 4.3 - - + -
22O ALA* 3.9 15.7 - - + +
25O SER* 3.8 12.6 - - - +
27O LYS* 3.8 28.9 - - + -
28O VAL* 4.0 14.7 - - + +
321O SER 3.3 12.6 + - - +
322O ASN* 3.6 9.6 - - - +
323O ARG 3.2 0.2 - - - -
324O VAL* 1.3 75.3 - - - +
326O ASP* 1.3 65.3 + - - +
328O MET* 3.2 9.3 + - + +
329O ALA* 3.0 21.5 + - - +
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Residues in contact with ASP 326 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27O LYS* 2.6 36.1 + - - +
133O MET* 4.0 20.5 - - + +
273O ILE* 5.7 1.0 - - - +
322O ASN* 3.0 18.4 + - - +
323O ARG* 2.8 40.7 + - - +
325O VAL* 1.3 77.5 - - - +
327O LEU* 1.3 62.9 + - - +
329O ALA* 3.3 7.1 + - - +
330O HIS* 3.0 23.9 + - - +
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Residues in contact with LEU 327 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120O ILE* 4.0 12.3 - - + -
131O PHE* 4.3 20.0 - - + -
133O MET* 3.7 22.9 - - - -
137O HIS* 4.7 6.5 - - + -
140O TYR* 5.6 3.4 - - + -
147O ILE* 3.9 24.5 - - + -
148O SER 4.7 2.0 - - - +
149O ASN* 3.4 36.3 - - + +
323O ARG 2.8 18.5 + - - +
324O VAL 3.6 4.7 - - - +
325O VAL 3.2 0.2 - - - -
326O ASP* 1.3 78.0 - - - +
328O MET* 1.3 62.1 + - - +
330O HIS* 3.1 8.4 + - + +
331O MET* 2.9 38.6 + - + +
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Residues in contact with MET 328 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4O VAL* 4.3 0.2 - - - +
6O VAL* 3.9 30.3 - - + -
18O VAL* 4.6 3.4 - - + -
28O VAL* 4.1 18.6 - - + -
94O TYR* 3.5 17.6 - - + -
96O VAL* 3.6 33.0 - - + -
120O ILE* 3.8 33.2 - - + -
324O VAL* 3.1 22.0 + - + +
325O VAL* 3.2 18.1 + - + +
327O LEU* 1.3 76.1 - - - +
329O ALA* 1.3 62.8 + - - +
331O MET* 3.3 9.6 + - - +
332O ALA* 2.9 22.2 + - - +
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Residues in contact with ALA 329 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4O VAL* 5.3 0.2 - - - -
27O LYS* 4.2 31.2 - - + +
28O VAL* 4.2 5.8 - - + +
325O VAL 3.0 16.7 + - - +
326O ASP* 3.6 7.4 - - - +
327O LEU 3.2 0.2 - - - -
328O MET* 1.3 77.1 - - - +
330O HIS* 1.3 62.8 + - - +
332O ALA* 3.3 6.2 + - - +
333O SER* 3.1 22.5 + - - -
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Residues in contact with HIS 330 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133O MET* 4.5 10.3 - - + -
137O HIS* 3.5 42.9 + + - +
138O GLU* 3.2 30.9 + - - -
140O TYR* 4.8 7.7 - - + +
326O ASP 3.0 13.8 + - - +
327O LEU* 3.5 10.5 + - + +
329O ALA* 1.3 75.3 - - - +
331O MET* 1.3 69.0 + - - +
333O SER* 2.6 30.7 + - - -
334O LYS* 3.4 24.3 + - + +
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Residues in contact with MET 331 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94O TYR* 3.3 15.7 + - + +
118O ARG* 3.7 29.8 - - + -
120O ILE* 3.8 33.4 - - + -
140O TYR* 3.8 38.5 - - + +
142O ASN* 4.8 0.2 - - - +
144O LEU 5.3 0.7 - - - +
147O ILE* 3.7 26.0 - - + -
327O LEU* 2.9 28.6 + - + +
328O MET* 3.5 12.8 - - - +
330O HIS* 1.3 77.5 - - - +
332O ALA* 1.3 60.6 + - - +
334O LYS* 3.0 17.7 + - - +
335O GLU* 3.4 7.8 + - - +
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Residues in contact with ALA 332 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3O LYS* 5.9 2.9 - - + -
4O VAL* 3.8 32.3 - - + +
94O TYR* 3.2 10.3 + - - +
328O MET 2.9 16.3 + - - +
329O ALA* 3.7 6.5 - - - +
331O MET* 1.3 76.6 - - - +
333O SER* 1.3 61.7 + - - +
334O LYS 3.2 0.9 + - - -
335O GLU* 3.3 20.4 + - + +
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Residues in contact with SER 333 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329O ALA 3.1 12.4 + - - -
330O HIS* 2.6 32.6 + - - -
332O ALA* 1.3 76.4 - - - +
334O LYS* 1.3 60.6 + - - +
335O GLU* 3.5 3.6 - - - +
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Residues in contact with LYS 334 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138O GLU* 4.9 10.0 + - - -
140O TYR* 3.6 36.4 + - + +
141O ASP* 4.5 10.3 - - - +
142O ASN* 3.1 29.6 + - - +
330O HIS* 4.0 26.7 - - + +
331O MET 3.0 11.7 + - - +
333O SER* 1.3 80.5 + - - +
335O GLU* 1.3 66.2 + - - +
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Residues in contact with GLU 335 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93O GLU* 3.9 13.1 - - - +
94O TYR* 2.7 36.8 + - - +
117O LYS* 5.9 0.3 - - - +
118O ARG* 2.7 41.6 + - - -
142O ASN* 4.0 12.2 + - - +
331O MET 3.7 2.9 - - - +
332O ALA* 3.3 16.7 + - - +
333O SER 4.4 3.8 - - - +
334O LYS* 1.3 83.5 - - - +
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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