Contacts of the helix formed by residues 1011 - 1026 (chain M) in PDB entry 6G0L
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 GLY1011 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1009M SER 4.1 1.4 + - - -
1010M ILE* 1.3 72.6 - - - +
1012M GLU* 1.3 63.8 + - - -
1014M GLU* 3.3 21.1 + - - -
1015M VAL* 3.1 32.2 + - - +
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Residues in contact with GLU1012 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011M GLY* 1.3 71.6 - - - -
1013M SER* 1.3 60.5 + - - +
1015M VAL* 3.2 5.6 + - - +
1016M ARG* 2.9 56.7 + - - +
1123M LYS 2.9 29.5 - - - +
1124M GLY* 3.9 6.3 - - - -
1125M VAL* 3.3 18.2 + - - +
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Residues in contact with SER1013 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-70J C 4.0 12.4 + - - -
1012M GLU* 1.3 77.8 - - - +
1014M GLU* 1.3 76.7 + - - +
1016M ARG* 3.5 17.0 - - - +
1017M ALA* 2.9 31.9 + - - +
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Residues in contact with GLU1014 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009M SER 5.3 2.2 - - - +
1010M ILE* 3.6 31.1 - - + +
1011M GLY* 3.3 24.6 + - - +
1012M GLU 3.1 0.2 - - - -
1013M SER* 1.3 89.6 + - - +
1015M VAL* 1.3 60.7 + - - +
1017M ALA* 4.5 3.6 - - - -
1018M LEU* 2.9 32.2 + - - +
1041M LEU* 4.9 2.5 - - + +
1042M PRO* 3.4 40.0 - - + +
1044M LYS* 5.1 6.3 + - + +
1049M TYR* 5.5 4.6 - - + +
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Residues in contact with VAL1015 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010M ILE* 3.6 19.7 - - + +
1011M GLY 3.1 17.0 + - - +
1012M GLU* 3.2 7.1 + - - +
1014M GLU* 1.3 76.9 - - - +
1016M ARG* 1.3 57.7 + - - +
1018M LEU* 3.8 5.5 - - - +
1019M TYR* 2.9 28.2 + - + +
1052M THR* 6.4 0.2 - - + -
1056M MET* 4.5 12.9 - - + +
1122M PHE* 4.2 25.1 - - + +
1123M LYS* 5.0 14.1 - - + +
1125M VAL* 3.6 28.3 - - + -
1128M LEU* 5.1 3.4 - - + -
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Residues in contact with ARG1016 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-71J T 3.5 45.9 + - - -
-70J C 2.7 44.0 + - - +
1012M GLU* 2.9 41.8 + - - +
1013M SER* 3.5 22.2 - - - +
1015M VAL* 1.3 73.8 - - - +
1017M ALA* 1.3 60.3 + - - +
1019M TYR* 3.2 7.0 + - - +
1020M LYS* 2.9 44.3 + - - +
1125M VAL* 3.8 26.0 - - + +
1128M LEU* 6.3 0.2 - - - -
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Residues in contact with ALA1017 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-70J C 4.7 6.0 + - - +
1013M SER 2.9 22.3 + - - +
1014M GLU* 4.3 3.6 - - - +
1016M ARG* 1.3 76.1 - - - +
1018M LEU* 1.3 57.8 + - - +
1020M LYS* 3.4 11.6 + - - +
1021M ALA* 2.9 26.4 + - - +
1040M THR* 3.8 34.2 - - + +
1041M LEU* 4.6 5.2 - - + -
1042M PRO* 6.3 0.4 - - + -
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Residues in contact with LEU1018 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010M ILE* 5.9 5.2 - - + -
1014M GLU 2.9 21.3 + - - +
1015M VAL* 3.9 4.7 - - - +
1017M ALA* 1.3 74.4 - - - +
1019M TYR* 1.3 61.5 + - - +
1021M ALA* 3.1 5.1 + - + +
1022M ILE* 2.9 40.2 + - + +
1028M LEU* 3.6 31.4 - - + -
1041M LEU* 3.9 25.9 - - + +
1049M TYR* 4.0 24.2 - - + +
1052M THR* 3.7 27.4 - - - +
1053M TYR* 5.1 5.2 - - + +
1056M MET* 5.1 11.2 - - + -
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Residues in contact with TYR1019 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I A 5.9 3.8 - - - -
1015M VAL* 2.9 20.3 + - + +
1016M ARG* 3.2 9.2 + - - +
1018M LEU* 1.3 78.2 - - - +
1020M LYS* 1.3 59.9 + - + +
1022M ILE* 3.1 9.0 + - - +
1023M LEU* 2.9 58.2 + - + +
1056M MET* 3.8 23.3 - - + +
1120M PHE* 5.6 0.4 - + - -
1127M SER 5.1 2.2 - - - -
1128M LEU* 3.7 41.3 - - + -
1129M ASN* 2.9 35.5 + - - +
1132M SER* 5.3 1.2 - - - -
1133M LEU* 3.6 33.6 - - + +
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Residues in contact with LYS1020 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73I T 6.4 2.7 - - - -
-71J T 4.2 18.1 + - - -
-70J C 4.4 17.7 + - - -
1016M ARG* 2.9 40.0 + - - +
1017M ALA* 3.7 8.5 - - - +
1019M TYR* 1.3 75.2 - - + +
1021M ALA* 1.3 60.5 + - - +
1023M LEU* 3.1 16.5 + - + +
1024M LYS* 2.9 35.3 + - - +
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Residues in contact with ALA1021 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017M ALA 2.9 14.7 + - - +
1018M LEU* 3.1 17.0 + - + +
1020M LYS* 1.3 75.8 - - - +
1022M ILE* 1.3 57.9 + - - +
1024M LYS* 4.6 5.2 - - - +
1025M PHE* 2.9 40.1 + - + +
1026M GLY 3.6 1.2 + - - +
1028M LEU* 4.3 13.8 - - + +
1035M LEU* 5.1 6.9 - - + +
1040M THR* 5.7 3.1 - - + -
1041M LEU* 5.0 10.3 - - + -
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Residues in contact with ILE1022 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018M LEU* 2.9 24.0 + - + +
1019M TYR* 3.1 7.4 + - - +
1021M ALA* 1.3 75.7 - - - +
1023M LEU* 1.3 61.2 + - - +
1024M LYS 3.1 0.4 - - - -
1026M GLY* 2.9 37.3 + - - +
1028M LEU* 3.8 16.8 - - + -
1053M TYR* 3.6 31.6 - - + +
1056M MET* 3.7 31.6 - - + -
1057M MET* 5.1 6.1 - - - -
1133M LEU* 3.7 27.8 - - + -
1136M ARG* 3.8 7.6 - - + +
1137M VAL* 5.3 3.6 - - + -
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Residues in contact with LEU1023 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I A 3.8 29.4 - - - +
1019M TYR* 2.9 44.5 + - + +
1020M LYS* 3.1 15.5 + - + +
1022M ILE* 1.3 76.1 - - - +
1024M LYS* 1.3 57.4 + - - +
1132M SER* 4.7 17.5 - - - +
1133M LEU* 3.8 24.0 - - + -
1136M ARG* 2.4 45.3 + - + +
1192M TYR* 4.0 7.7 - - - +
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Residues in contact with LYS1024 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1020M LYS* 2.9 18.5 + - - +
1021M ALA* 4.5 1.3 - - - +
1023M LEU* 1.3 79.7 - - - +
1025M PHE* 1.3 87.1 + - + +
1026M GLY 3.8 0.2 - - - -
1140M LEU* 4.2 6.9 - - - +
1190M TYR 4.0 5.8 - - - +
1191M GLY* 3.5 20.3 - - - -
1192M TYR 3.6 20.0 + - - +
1193M GLY* 3.9 6.1 + - - -
1194M SER* 2.6 37.5 + - - +
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Residues in contact with PHE1025 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021M ALA* 2.9 19.1 + - + +
1024M LYS* 1.3 103.5 - - + +
1026M GLY* 1.3 65.2 + - - +
1027M ASN 3.4 9.1 + - - +
1031M ILE* 4.5 16.5 - - + +
1035M LEU* 3.6 46.0 - - + -
1038M ASP* 5.6 4.7 - - - -
1140M LEU* 3.5 15.8 - - - +
1144M LYS* 6.0 2.3 - - - -
1189M LYS 4.8 7.2 - - - -
1190M TYR* 3.7 23.6 - - - -
1191M GLY* 5.6 0.7 - - - -
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Residues in contact with GLY1026 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021M ALA 3.6 1.4 + - - +
1022M ILE* 2.9 38.3 + - - +
1025M PHE* 1.3 73.6 - - - +
1027M ASN* 1.3 64.5 + - - -
1028M LEU* 3.4 7.4 + - - +
1053M TYR* 3.9 14.7 - - - -
1136M ARG* 4.8 1.8 - - - -
1137M VAL* 4.7 10.1 - - - -
1140M LEU* 3.6 13.1 - - - +
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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
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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