Contacts of the helix formed by residues 2215 - 2236 (chain A) in PDB entry 5KW2
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 THR2215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1158A TRP 4.0 14.6 - - - -
1159A ASP* 3.7 23.3 + - - +
1161A TYR 3.0 9.3 + - - -
1903A GLY* 3.2 23.6 - - - +
1904A SER 3.7 0.4 - - - -
2214A LEU* 1.3 81.3 - - - +
2216A HIS* 1.3 68.0 + - - +
2217A ARG* 3.5 14.1 + - + +
2218A ARG* 3.3 30.1 + - + +
2219A LYS* 3.4 12.9 + - - +
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Residues in contact with HIS2216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LEU* 3.6 33.5 - - + +
1157A THR* 6.4 1.8 - - - -
1158A TRP* 5.3 3.6 - - - +
1159A ASP* 4.8 8.5 + - - +
2214A LEU 3.7 2.1 + - - -
2215A THR* 1.3 74.8 + - - +
2217A ARG* 1.3 63.9 + - + +
2219A LYS* 3.2 12.5 + - + +
2220A LEU* 2.9 44.0 + - + +
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Residues in contact with ARG2217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1159A ASP* 6.1 2.8 - - - +
2215A THR* 3.3 11.7 + - + +
2216A HIS* 1.3 80.3 - - - +
2218A ARG* 1.3 60.0 + - - +
2220A LEU* 3.0 16.9 + - + +
2221A ARG* 2.8 59.9 + - - +
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Residues in contact with ARG2218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG* 5.0 7.0 + - - +
107A GLY* 2.8 45.0 + - - -
108A ALA* 5.2 2.4 - - - +
114A TYR* 5.3 1.8 - - - -
115A GLN* 2.8 28.7 + - - -
118A ARG* 5.5 3.8 - - - +
1903A GLY 4.1 7.5 + - - +
1904A SER* 3.5 31.5 + - - +
2214A LEU 5.4 0.2 - - - -
2215A THR* 3.3 26.7 + - + +
2217A ARG* 1.3 77.9 - - - +
2219A LYS* 1.3 61.8 + - + +
2221A ARG* 3.6 12.6 + - - +
2222A ALA* 3.3 21.5 + - - +
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Residues in contact with LYS2219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLY 5.4 0.2 + - - -
108A ALA* 3.3 43.3 + - + +
109A ALA 5.5 0.2 + - - -
111A PRO* 4.1 15.8 - - - +
205A CYS 4.7 3.3 - - - +
208A ALA 3.4 20.2 - - - +
209A LEU* 3.8 22.0 - - + +
901A GLY* 3.3 27.2 + - - -
902A SER* 3.6 18.4 + - - -
1005A GLU* 5.4 1.2 + - - -
1904A SER 4.9 0.8 + - - -
2214A LEU* 3.8 11.9 + - - +
2215A THR 3.4 11.1 + - - +
2216A HIS* 3.2 13.4 + - + +
2217A ARG 3.2 0.4 - - - -
2218A ARG* 1.3 79.8 - - + +
2220A LEU* 1.3 62.3 + - - +
2222A ALA* 3.6 3.1 + - - +
2223A ALA* 3.2 21.7 + - - +
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Residues in contact with LEU2220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LEU* 3.7 26.0 - - + +
2216A HIS* 2.9 29.9 + - + +
2217A ARG* 3.0 19.7 + - + +
2219A LYS* 1.3 75.8 - - - +
2221A ARG* 1.3 64.8 + - + +
2223A ALA* 3.3 4.3 + - + +
2224A TRP* 3.1 49.4 + - + +
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Residues in contact with ARG2221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG* 4.1 15.7 - - - +
2217A ARG* 2.8 50.0 + - + +
2218A ARG* 3.9 11.5 - - - +
2220A LEU* 1.3 70.9 - - + +
2222A ALA* 1.3 60.4 + - - +
2224A TRP* 3.4 6.5 + - - +
2225A VAL* 2.9 37.1 + - + +
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Residues in contact with ALA2222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG* 3.6 45.7 - - + +
108A ALA* 3.8 12.3 - - + +
205A CYS* 3.8 6.6 - - - -
2218A ARG 3.3 12.4 + - - +
2219A LYS 3.7 9.4 - - - +
2220A LEU 3.3 0.6 - - - -
2221A ARG* 1.3 78.3 - - - +
2223A ALA* 1.3 56.5 + - - +
2225A VAL* 3.4 0.9 + - - +
2226A ALA* 2.9 32.9 + - - +
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Residues in contact with ALA2223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A PHE* 3.4 13.4 - - + -
205A CYS* 3.8 19.6 - - + +
206A LEU* 4.5 13.2 - - + -
209A LEU* 4.0 21.3 - - + -
2219A LYS 3.2 12.4 + - - +
2220A LEU* 3.5 9.9 - - + +
2222A ALA* 1.3 78.7 - - - +
2224A TRP* 1.3 58.5 + - + +
2227A GLY* 2.9 23.2 + - - -
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Residues in contact with TRP2224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2220A LEU* 3.1 51.8 + - + +
2221A ARG* 3.8 6.1 - - - +
2222A ALA 3.3 0.2 - - - -
2223A ALA* 1.3 77.5 - - + +
2225A VAL* 1.3 60.1 + - + +
2227A GLY* 5.0 0.4 - - - -
2228A GLY* 2.9 28.1 + - - -
2275A VAL* 5.8 0.2 - - - +
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Residues in contact with VAL2225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU* 3.8 31.9 - - + +
101A SER* 5.3 0.9 - - - -
104A ARG* 3.9 37.9 - - + +
2221A ARG* 2.9 23.4 + - + +
2222A ALA 3.9 2.7 - - - +
2224A TRP* 1.3 77.9 - - + +
2226A ALA* 1.3 57.6 + - - +
2228A GLY* 3.4 1.0 + - - -
2229A ALA* 2.8 28.8 + - + +
2275A VAL* 3.6 26.1 - - + +
2276A THR* 4.7 7.0 - - - +
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Residues in contact with ALA2226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A SER* 4.1 28.7 - - - +
104A ARG* 5.4 0.2 - - + -
198A THR* 4.1 3.3 - - - +
201A CYS 4.5 0.4 - - - +
202A PHE* 3.9 27.8 - - + +
205A CYS* 4.2 10.5 - - - -
2222A ALA 2.9 17.7 + - - +
2223A ALA 4.0 2.9 - - - +
2225A VAL* 1.3 75.9 - - - +
2227A GLY* 1.3 53.7 + - - +
2229A ALA* 3.3 2.1 + - - +
2230A LEU* 2.8 34.3 + - - +
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Residues in contact with GLY2227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A PHE* 3.4 28.9 - - - -
2223A ALA 2.9 13.6 + - - -
2224A TRP* 3.9 1.3 - - - -
2226A ALA* 1.3 73.2 - - - +
2228A GLY* 1.3 64.4 + - - +
2230A LEU* 3.4 4.5 + - - +
2231A LEU* 3.0 26.2 + - - +
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Residues in contact with GLY2228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2224A TRP* 2.9 18.6 + - - -
2225A VAL 3.7 1.3 - - - -
2227A GLY* 1.3 73.9 - - - +
2229A ALA* 1.3 57.1 + - - +
2231A LEU* 3.5 5.9 + - - +
2232A THR* 3.0 36.8 + - - +
2275A VAL* 3.6 17.7 - - - -
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Residues in contact with ALA2229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 3.9 36.9 - - + +
100A LEU* 5.8 1.3 - - + -
101A SER* 4.5 1.1 - - - -
198A THR* 4.1 7.0 - - + -
2225A VAL* 2.8 21.0 + - + +
2226A ALA* 3.4 7.9 - - - +
2228A GLY* 1.3 74.3 - - - +
2230A LEU* 1.3 64.9 + - - +
2232A THR* 3.2 7.9 + - - -
2233A LEU* 3.0 30.4 + - - +
2275A VAL* 4.1 5.5 - - + +
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Residues in contact with LEU2230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LEU* 4.0 20.4 - - + +
198A THR* 3.8 11.1 - - + +
199A ALA* 3.7 36.8 - - + +
202A PHE* 3.8 33.9 - - + -
2226A ALA 2.8 20.3 + - - +
2227A GLY* 3.7 4.9 - - - +
2229A ALA* 1.3 71.7 - - - +
2231A LEU* 1.3 58.8 + - - +
2233A LEU* 3.3 5.5 + - - +
2234A LEU* 3.0 40.2 + - + +
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Residues in contact with LEU2231 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2227A GLY 3.0 17.5 + - - +
2228A GLY* 3.9 6.1 - - - +
2230A LEU* 1.3 77.5 - - - +
2232A THR* 1.3 61.0 + - + +
2234A LEU* 3.1 17.5 + - + +
2235A LEU* 2.9 56.9 + - + +
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Residues in contact with THR2232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU* 3.5 18.2 - - - +
2228A GLY* 3.0 18.8 + - - +
2229A ALA* 3.2 9.2 + - - -
2231A LEU* 1.3 76.3 - - + +
2233A LEU* 1.3 60.3 + - - +
2235A LEU* 4.0 3.8 - - + +
2236A CYS* 3.1 35.3 + - - +
2237A VAL* 4.0 1.7 + - - +
2268A SER* 5.4 0.2 - - - -
2271A LEU* 3.6 44.0 - - + -
2272A ASN* 4.0 6.0 + - - +
2275A VAL* 3.8 16.7 - - + +
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Residues in contact with LEU2233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLY* 3.8 28.7 - - - +
97A LEU* 4.2 14.1 - - + -
191A PHE* 3.4 17.7 - - + -
194A PRO* 4.8 4.5 - - + +
195A LEU* 4.2 20.0 - - + +
198A THR* 3.4 36.1 - - + +
2229A ALA 3.0 22.6 + - - +
2230A LEU* 3.4 6.1 - - - +
2232A THR* 1.3 76.5 + - - +
2234A LEU* 1.3 58.9 + - - +
2235A LEU 3.5 0.2 + - - -
2237A VAL* 3.3 27.3 - - + +
2238A GLY* 2.9 28.2 + - - -
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Residues in contact with LEU2234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A PHE* 5.7 1.6 - - + -
195A LEU* 4.2 26.4 - - + +
2230A LEU* 3.0 30.4 + - + +
2231A LEU* 3.5 19.7 - - + +
2233A LEU* 1.3 77.7 - - - +
2235A LEU* 1.3 61.7 + - + +
2238A GLY* 3.4 6.8 - - - -
2239A PRO* 3.2 21.7 - - - +
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Residues in contact with LEU2235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2231A LEU* 2.9 47.1 + - + +
2232A THR* 4.8 1.8 - - + -
2234A LEU* 1.3 81.0 - - + +
2236A CYS* 1.3 67.5 + - - +
2239A PRO* 3.3 11.5 - - + +
2264A THR* 3.2 21.7 - - - +
2271A LEU* 6.2 5.4 - - + -
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Residues in contact with CYS2236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2232A THR* 3.1 20.2 + - - +
2235A LEU* 1.3 82.4 - - - +
2237A VAL* 1.3 66.2 + - + +
2238A GLY 3.3 0.7 - - - -
2239A PRO* 3.4 2.8 - - - +
2240A TYR* 4.8 0.5 + - - +
2261A GLY 3.8 2.8 - - - +
2264A THR* 3.1 39.2 + - - +
2265A GLY* 3.1 13.6 + - - -
2267A TRP* 4.2 1.8 - - - -
2268A SER* 3.8 29.2 - - - -
2271A LEU* 3.9 31.9 - - - -
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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
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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