Contacts of the helix formed by residues 1191 - 1202 (chain I) in PDB entry 6C6U
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 LYS1191 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17I LYS* 4.4 20.3 - - - +
673I HIS* 6.4 0.2 - - - -
1113I LEU* 5.8 0.7 - - - -
1189I GLY 3.5 6.7 + - - +
1190I ALA* 1.3 77.4 - - - +
1192I GLU* 1.3 68.3 + - - +
1193I ALA* 3.4 6.5 - - + +
1194I GLU* 3.5 16.2 + - + +
1195I ILE* 3.3 21.1 + - - +
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Residues in contact with GLU1192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673I HIS* 6.1 0.9 - - + -
1113I LEU* 4.9 13.0 - - + +
1191I LYS* 1.3 75.3 - - - +
1193I ALA* 1.3 59.7 + - - +
1195I ILE* 3.2 13.0 + - + +
1196I LYS* 3.0 41.5 + - + +
641J ILE* 4.4 12.8 - - + +
764J ARG* 2.8 73.0 + - - +
765J GLU* 5.0 2.8 - - - -
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Residues in contact with ALA1193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1191I LYS* 3.4 4.1 - - + +
1192I GLU* 1.3 77.8 - - - +
1194I GLU* 1.3 59.1 + - + +
1196I LYS* 3.4 9.9 + - - +
1197I GLU* 2.9 30.7 + - - +
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Residues in contact with GLU1194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I PHE* 3.2 37.1 - - + -
17I LYS* 2.9 39.1 + - - -
1151I LEU* 4.2 4.4 - - + +
1152I GLY* 5.0 9.2 - - - -
1153I ALA* 3.9 21.7 + - - +
1155I VAL* 5.1 1.4 - - - +
1190I ALA* 3.6 10.4 - - + -
1191I LYS* 3.5 16.9 + - + +
1192I GLU 3.2 0.8 - - - -
1193I ALA* 1.3 76.8 - - + +
1195I ILE* 1.3 59.9 + - - +
1197I GLU* 3.3 9.6 + - - +
1198I LEU* 2.9 30.3 + - - +
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Residues in contact with ILE1195 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I PHE* 6.0 0.4 - - - -
670I PHE* 4.1 14.6 - - + -
1113I LEU* 4.4 23.6 - - + +
1116I HIS* 4.2 14.8 - - + +
1117I LEU* 3.7 51.6 - - + +
1120I ALA* 5.1 0.9 - - + -
1190I ALA* 4.2 6.1 - - + +
1191I LYS 3.3 18.4 - - - +
1192I GLU* 3.2 10.0 + - + +
1194I GLU* 1.3 75.7 - - - +
1196I LYS* 1.3 59.5 + - + +
1198I LEU* 3.3 5.9 + - - +
1199I LEU* 2.9 36.8 + - + +
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Residues in contact with LYS1196 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116I HIS* 5.9 1.1 - - - -
1192I GLU* 3.0 29.5 + - - +
1193I ALA* 3.6 9.9 - - - +
1195I ILE* 1.3 78.7 - - + +
1197I GLU* 1.3 57.2 + - - +
1199I LEU* 3.3 9.3 + - + +
1200I LYS* 2.9 27.8 + - - +
1206I THR* 3.4 45.8 - - + +
1207I SER* 5.0 0.7 - - - +
641J ILE* 4.5 13.9 - - - +
642J ASP* 3.4 29.9 + - - -
764J ARG* 5.3 4.0 - - - +
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Residues in contact with GLU1197 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1151I LEU* 4.1 25.5 - - + +
1152I GLY* 4.9 13.0 + - - -
1193I ALA 2.9 17.9 + - - +
1194I GLU* 3.9 9.6 - - - +
1196I LYS* 1.3 77.6 - - - +
1198I LEU* 1.3 60.7 + - - +
1200I LYS* 3.4 12.6 + - + +
1201I LEU* 3.3 19.6 + - - +
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Residues in contact with LEU1198 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I LYS* 5.8 3.6 - - + -
15I PHE* 4.1 19.1 - - + -
1117I LEU* 5.3 4.0 - - + -
1120I ALA* 3.9 21.7 - - + +
1124I ILE* 4.0 24.7 - - + +
1148I ALA* 5.0 9.0 - - + +
1151I LEU* 3.7 28.2 - - + +
1180I MET* 6.1 1.8 - - - -
1182I ILE* 3.7 29.8 - - + -
1194I GLU 2.9 17.9 + - - +
1195I ILE* 3.9 4.9 - - - +
1196I LYS 3.2 0.2 - - - -
1197I GLU* 1.3 74.6 - - - +
1199I LEU* 1.3 62.0 + - - +
1200I LYS 3.2 1.1 - - - -
1201I LEU* 3.3 10.3 + - + -
1202I GLY* 3.6 9.4 + - - -
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Residues in contact with LEU1199 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116I HIS* 4.1 13.2 - - + +
1119I MET* 4.3 5.6 - - + -
1120I ALA* 3.7 33.2 - - + +
1195I ILE* 2.9 33.0 + - + +
1196I LYS* 3.3 7.6 + - + +
1198I LEU* 1.3 75.7 - - - +
1200I LYS* 1.3 58.3 + - - +
1201I LEU 3.4 0.4 - - - -
1202I GLY* 2.9 16.9 - - - +
1204I LEU* 3.5 41.4 + - + +
1205I PRO 4.1 10.5 - - - +
1206I THR* 3.6 25.8 - - - +
1207I SER 5.2 0.2 - - - -
1208I GLY* 4.4 12.8 - - - -
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Residues in contact with LYS1200 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196I LYS 2.9 17.4 + - - +
1197I GLU* 3.6 13.9 - - + +
1198I LEU 3.2 0.4 - - - -
1199I LEU* 1.3 75.8 - - - +
1201I LEU* 1.3 57.8 + - - +
1202I GLY 2.9 15.2 - - - +
1203I ASP* 4.7 3.3 - - - +
1204I LEU 5.2 1.3 - - - -
1206I THR* 5.5 9.6 - - + +
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Residues in contact with LEU1201 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124I ILE* 3.7 19.7 - - + -
1127I LYS* 5.8 1.0 - - - +
1144I PHE* 4.2 18.7 - - + -
1147I ARG* 3.3 41.5 - - + +
1148I ALA* 3.7 27.4 - - + +
1151I LEU* 3.7 25.6 - - + -
1197I GLU 3.3 11.8 + - - +
1198I LEU* 3.3 11.1 + - + +
1200I LYS* 1.3 76.2 - - - +
1202I GLY* 1.3 64.1 + - - +
1203I ASP* 4.3 5.7 - - - +
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Residues in contact with GLY1202 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120I ALA 6.0 0.2 - - - -
1123I GLY* 4.7 13.9 - - - -
1124I ILE* 3.8 12.3 - - - +
1127I LYS* 5.6 5.8 - - - -
1144I PHE* 5.9 0.2 - - - -
1198I LEU 3.6 9.0 + - - -
1199I LEU 2.9 18.3 - - - +
1200I LYS* 2.9 13.2 - - - +
1201I LEU* 1.3 78.2 - - - +
1203I ASP* 1.3 60.0 + - - -
1204I LEU* 3.2 10.7 - - - +
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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