Contacts of the helix formed by residues 109 - 127 (chain 4) in PDB entry 1ILL
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 109 (chain 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174 LEU* 6.4 0.2 - - + -
244 CYS* 4.0 2.7 - - + +
254 THR* 2.8 47.3 + - + +
274 LEU 4.5 4.9 + - - +
294 VAL* 3.6 29.4 - - + +
524 LEU* 3.5 31.2 - - + -
554 PHE* 3.5 29.6 - - + -
794 LEU* 4.1 20.6 - - + -
834 LEU* 4.2 6.3 - - + -
1074 SER 3.5 1.4 + - - -
1084 THR* 1.3 68.7 - - - +
1104 GLU* 1.3 64.1 + - - +
1124 PHE* 3.1 15.8 - - - +
1134 LEU* 3.6 10.8 - - + +
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Residues in contact with GLU 110 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174 LEU 3.9 17.5 - - - +
184 THR* 3.5 13.8 - - - +
194 GLU 4.4 0.9 + - - -
214 LYS* 2.6 49.4 + - + +
254 THR* 3.3 28.6 + - + +
264 GLU* 4.1 0.5 - - - +
1084 THR* 3.3 9.2 - - + +
1094 LEU* 1.3 77.6 - - - +
1114 ASN* 1.3 67.6 + - + +
1134 LEU* 3.0 28.4 + - - +
1144 GLU* 3.9 0.3 + - - +
93G GLN* 5.0 1.5 + - - +
179G GLN* 2.9 34.1 + - - +
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Residues in contact with ASN 111 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074 SER* 4.0 5.4 - - - +
1084 THR* 2.9 26.0 + - - +
1104 GLU* 1.3 80.9 - - - +
1124 PHE* 1.3 64.4 - - - +
1144 GLU* 3.0 15.6 + - - +
69G TYR* 2.6 34.7 + - - +
71G THR* 4.5 2.8 + - - -
91G LYS* 2.6 39.8 + - - +
93G GLN* 3.3 28.0 - - - +
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Residues in contact with PHE 112 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294 VAL* 3.3 22.2 - - + -
304 THR 3.3 23.1 - - - -
314 ASP* 4.3 0.4 - - - -
324 ILE* 3.5 32.3 - - + -
334 PHE* 3.1 43.9 - + - -
484 ALA* 4.2 12.3 - - + -
514 VAL* 5.0 0.2 - - + -
524 LEU* 3.3 31.2 - - + -
864 LEU* 5.8 0.9 - - + -
1074 SER* 3.2 21.2 + - - -
1084 THR 2.8 10.1 + - - +
1094 LEU 3.1 17.3 - - - +
1114 ASN* 1.3 74.5 - - - +
1134 LEU* 1.3 75.1 + - + +
1144 GLU 3.1 1.2 + - - -
1154 ARG* 3.1 11.1 + - - +
69G TYR* 4.2 1.5 - - - +
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Residues in contact with LEU 113 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144 LEU* 3.7 11.2 - - + +
174 LEU* 3.2 43.7 - - + -
184 THR* 3.7 16.4 - - + -
524 LEU* 5.2 2.0 - - + -
834 LEU* 4.6 5.4 - - + -
864 LEU* 3.2 39.5 - - + -
1094 LEU* 3.6 11.4 - - + +
1104 GLU* 3.0 13.5 + - - +
1124 PHE* 1.3 87.1 - - + +
1144 GLU* 1.3 60.5 + - - +
1154 ARG 3.1 1.2 + - - -
1164 LEU* 3.1 11.8 + - + +
1174 LYS* 2.8 27.8 + - - +
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Residues in contact with GLU 114 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184 THR* 4.4 2.4 + - + +
1104 GLU 3.9 1.4 + - - +
1114 ASN 3.0 15.6 + - - +
1134 LEU* 1.3 80.3 - - - +
1154 ARG* 1.4 48.9 + - - +
1174 LYS* 2.7 51.6 + - - +
1184 THR* 2.5 45.3 + - - +
1214 ARG* 4.2 3.5 + - - -
68G LEU 3.3 25.1 - - - +
69G TYR* 3.7 4.7 - - - -
93G GLN* 3.0 34.4 + - + +
171G PHE* 3.8 15.4 - - + -
177G SER 3.4 6.4 - - - +
178G ALA* 3.7 9.6 - - - +
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Residues in contact with ARG 115 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334 PHE* 3.6 38.0 - - + +
374 LYS* 3.6 23.6 - - - +
414 GLU* 5.8 0.4 - - - +
444 THR* 3.2 38.1 + - - +
1124 PHE 3.1 3.2 + - - -
1134 LEU 3.1 1.4 - - - -
1144 GLU* 1.4 75.9 - - - +
1164 LEU* 1.3 57.9 + - - +
1184 THR* 3.4 4.7 - - - -
1194 ILE* 2.8 56.2 + - + +
67G HIS* 2.9 35.7 + - + -
69G TYR* 3.2 36.2 - - + +
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Residues in contact with LEU 116 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104 ILE* 4.0 11.0 - - + -
144 LEU* 3.4 23.3 - - + -
334 PHE* 4.7 8.0 - - + -
444 THR* 5.8 3.6 - - + -
454 PHE* 3.7 26.5 - - + -
864 LEU* 3.7 26.2 - - + -
904 LEU* 3.8 21.3 - - + -
1124 PHE 4.4 0.4 + - - -
1134 LEU* 3.1 13.4 + - + +
1154 ARG* 1.3 81.7 - - - +
1174 LYS* 1.4 57.0 - - - +
1204 MET* 3.0 60.7 + - + +
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Residues in contact with LYS 117 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114 ILE* 5.7 1.1 - - + -
144 LEU* 3.6 25.3 - - + +
154 ASN* 4.5 8.7 - - - +
184 THR* 2.7 29.3 + - - -
1134 LEU 2.8 14.7 + - - +
1144 GLU* 2.7 35.9 + - - +
1164 LEU* 1.4 76.3 - - - +
1184 THR* 1.3 62.9 + - - +
1204 MET* 5.4 0.2 - - - -
1214 ARG* 2.6 57.1 + - + +
171G PHE* 4.8 0.2 - - - -
173G PRO* 4.0 7.4 - - + -
176G GLY* 2.6 17.0 + - - +
177G SER 2.4 31.9 + - - -
178G ALA* 4.6 0.2 - - - +
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Residues in contact with THR 118 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1144 GLU* 2.5 33.6 + - - +
1154 ARG* 3.4 7.2 - - - -
1164 LEU 3.1 0.6 - - - -
1174 LYS* 1.3 72.7 - - - +
1194 ILE* 1.3 67.4 + - + +
1204 MET 3.2 0.2 - - - -
1214 ARG* 2.7 32.2 + - - +
1224 GLU 3.3 1.9 + - - -
65G GLU* 3.2 39.5 - - + +
66G ILE 4.2 0.4 - - - +
68G LEU* 3.3 44.5 + - + +
125G HIS 5.5 0.3 - - - +
126G CYS* 5.1 3.7 - - - +
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Residues in contact with ILE 119 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1154 ARG* 2.8 47.5 + - + +
1184 THR* 1.3 83.7 - - + +
1204 MET* 1.4 64.7 + - + +
1224 GLU* 3.2 9.3 + - - +
1234 LYS* 2.5 42.3 + - - +
64G LYS* 5.2 1.3 - - - +
65G GLU* 3.7 12.6 - - - +
66G ILE* 3.1 29.8 - - - +
67G HIS* 3.6 10.1 - - + +
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Residues in contact with MET 120 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74 LEU* 3.6 34.8 - - + +
104 ILE* 5.9 1.3 - - + -
414 GLU* 6.3 0.4 - - - -
454 PHE* 3.6 32.5 - - + -
934 LEU* 4.4 11.2 - - + -
1164 LEU* 3.0 43.7 + - + +
1194 ILE* 1.4 82.2 - - + +
1214 ARG* 1.3 59.7 + - + +
1234 LYS* 3.0 35.9 + - + +
1244 TYR 3.5 2.3 + - - -
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Residues in contact with ARG 121 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74 LEU* 6.3 0.2 - - + -
114 ILE* 3.9 14.8 - - + -
1144 GLU* 4.2 4.8 + - - -
1174 LYS* 2.6 49.2 + - - +
1184 THR* 2.7 15.3 + - - +
1204 MET* 1.3 71.5 - - + +
1224 GLU* 1.4 55.1 + - - -
1234 LYS 2.8 5.9 + - - -
1244 TYR* 3.7 23.8 - - + +
1254 SER* 2.7 60.6 + - - +
125G HIS 2.6 29.9 + - - +
126G CYS* 2.6 30.9 + - - +
128G GLU* 3.6 7.3 - - - +
171G PHE* 3.9 13.5 - - - -
173G PRO* 3.4 25.5 - - - +
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Residues in contact with GLU 122 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1184 THR 3.3 4.2 + - - -
1194 ILE* 3.2 5.1 + - - +
1204 MET 3.1 1.6 - - - -
1214 ARG* 1.4 75.2 - - - +
1234 LYS* 1.4 88.0 + - - +
1264 LYS* 2.6 48.4 + - - +
64G LYS* 2.5 39.8 + - - +
65G GLU* 3.0 21.0 + - - +
125G HIS* 3.5 26.6 - - + -
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Residues in contact with LYS 123 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74 LEU* 4.4 16.2 - - + -
1194 ILE* 2.5 36.0 + - - +
1204 MET* 3.0 24.0 + - + +
1214 ARG 2.8 1.6 - - - -
1224 GLU* 1.4 118.6 + - - +
1244 TYR* 1.4 55.6 + - - +
1254 SER 3.3 0.9 - - - -
1264 LYS* 3.5 4.8 - - + +
1274 CYS* 2.7 39.6 + - - +
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Residues in contact with TYR 124 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14 HIS* 2.7 15.6 + - - -
24 LYS* 3.6 12.1 - - - -
34 CYS* 4.6 11.4 - - + -
74 LEU* 4.8 17.8 - - + +
84 GLN* 5.5 5.8 - - + -
114 ILE* 3.1 44.4 - - + +
1204 MET 3.5 3.1 + - - +
1214 ARG* 3.3 16.5 + - - -
1234 LYS* 1.4 77.7 - - - +
1254 SER* 1.4 68.5 + - - +
1264 LYS 3.1 0.2 - - - -
1274 CYS* 4.4 4.0 - - - -
1284 SER* 2.8 60.4 + - - -
1294 SER 2.9 5.5 + - - -
128G GLU* 2.6 33.6 + - - -
173G PRO* 4.5 5.2 - - + -
174G LEU* 3.7 22.2 + - - +
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Residues in contact with SER 125 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1214 ARG* 2.7 39.4 + - - +
1244 TYR* 1.4 77.6 - - - +
1264 LYS* 1.3 59.8 + - - +
1294 SER 3.2 15.7 - - - -
123G LEU* 4.9 0.5 - - - +
124G ASN 3.2 14.2 - - - +
125G HIS* 3.0 31.5 - - - -
128G GLU* 2.7 26.1 + - - +
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Residues in contact with LYS 126 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1224 GLU* 2.6 49.5 + - - +
1234 LYS* 3.5 6.1 - - - +
1244 TYR 3.1 1.0 + - - -
1254 SER* 1.3 74.6 - - - +
1274 CYS* 1.3 68.7 + - - +
1284 SER 3.6 0.4 - - - -
1294 SER* 3.9 5.2 + - - +
123G LEU* 5.9 2.2 - - - -
125G HIS* 2.6 32.3 + - + +
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Residues in contact with CYS 127 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34 CYS* 2.1 46.8 - - + -
1234 LYS 2.7 19.4 + - - +
1244 TYR* 4.0 0.9 - - - +
1264 LYS* 1.3 82.3 - - - +
1284 SER* 1.3 61.1 + - - +
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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