Contacts of the helix formed by residues 116 - 126 (chain 9) in PDB entry 2J28
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 SER 116 (chain 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1059 MET* 4.3 14.8 - - - +
1129 GLY* 3.2 21.3 - - - -
1139 LYS 4.2 2.9 - - - -
1149 THR 3.5 0.7 - - - -
1159 THR* 1.3 86.6 + - - +
1179 VAL* 1.3 57.6 + - - +
1189 GLY* 2.4 21.0 + - - -
1199 LYS* 3.2 17.5 + - - +
1209 LEU* 3.4 10.1 + - - +
2189 LEU* 5.5 0.2 - - - +
2209 VAL* 4.7 10.2 - - - +
2469 VAL* 4.8 6.8 - - - +
2489 THR* 5.4 5.6 - - - -
2829 LEU* 5.6 0.7 - - - +
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Residues in contact with VAL 117 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059 MET* 4.7 11.2 - - + -
1139 LYS 4.2 2.0 - - - +
1149 THR* 2.9 14.7 + - - +
1159 THR 2.4 8.8 + - - +
1169 SER* 1.3 79.2 + - - +
1189 GLY* 1.3 73.1 + - - +
1209 LEU* 2.7 16.4 - - + +
1219 GLY* 2.5 18.1 + - - -
1349 VAL* 4.0 20.4 - - + -
1889 LEU* 3.9 24.9 - - + +
1909 ASP* 3.8 32.1 - - + +
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Residues in contact with GLY 118 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1159 THR 2.6 11.6 + - - -
1169 SER 2.4 5.8 + - - -
1179 VAL* 1.3 84.0 - - - +
1199 LYS* 1.3 54.8 + - - -
1209 LEU 2.7 0.2 - - - -
1219 GLY* 5.0 0.4 - - - -
1229 LYS* 2.4 35.3 + - - -
1519 LEU* 4.7 19.8 - - - +
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Residues in contact with LYS 119 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1169 SER* 3.2 10.8 + - - +
1189 GLY* 1.3 70.0 - - - -
1209 LEU* 1.3 49.2 + - - +
1229 LYS* 3.1 13.6 - - - +
1239 PHE* 2.3 45.0 + - + +
2749 GLY* 4.0 3.8 + - - -
2769 GLY 2.3 33.2 + - - +
2779 GLU 3.1 0.9 - - - -
2789 LYS 2.8 21.3 - - - +
2799 THR* 3.0 26.5 + - - +
2809 GLU* 4.2 2.2 - - - -
2819 ALA* 2.7 26.0 - - - +
2829 LEU* 3.0 39.9 - - + +
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Residues in contact with LEU 120 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1039 VAL* 4.6 1.8 - - + -
1059 MET* 4.3 19.3 - - + -
1169 SER* 3.4 8.6 + - - +
1179 VAL* 2.7 24.2 - - - +
1189 GLY 2.5 4.2 + - - -
1199 LYS* 1.3 76.3 - - - +
1219 GLY* 1.3 73.4 + - - +
1239 PHE* 2.9 19.9 - - + +
1249 LEU* 3.1 17.9 + - + +
1889 LEU* 3.0 41.3 - - + -
2189 LEU* 5.0 4.3 - - + -
2729 PHE* 5.0 14.8 - - + -
2829 LEU* 3.7 17.8 - - + +
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Residues in contact with GLY 121 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1179 VAL* 2.5 8.0 + - - -
1189 GLY* 2.5 8.7 + - - -
1209 LEU* 1.3 78.9 - - - +
1229 LYS* 1.3 67.1 + - - +
1249 LEU* 2.5 18.7 + - - +
1259 ARG 3.4 3.9 + - - -
1329 VAL* 4.5 16.6 - - - -
1349 VAL* 5.5 3.1 - - - -
1579 VAL* 6.5 0.2 - - - -
1889 LEU* 2.9 23.1 - - - -
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Residues in contact with LYS 122 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1189 GLY* 2.4 25.9 + - - +
1199 LYS* 3.1 10.8 - - - +
1219 GLY* 1.3 73.0 - - - +
1239 PHE* 1.3 66.0 + - - +
1259 ARG* 3.2 16.5 + - + +
1269 GLU* 3.5 37.1 + - + +
1549 GLN 4.5 2.0 + - - -
1559 VAL* 3.3 54.8 + - + +
1579 VAL* 5.9 4.9 - - - +
2799 THR* 3.5 34.3 + - - +
2809 GLU* 5.0 7.9 - - + -
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Residues in contact with PHE 123 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949 ASN* 4.3 17.9 - - + -
1199 LYS* 2.3 34.7 + - + +
1209 LEU* 2.9 16.8 - - + +
1219 GLY 2.5 1.6 + - - -
1229 LYS* 1.3 71.0 - - - +
1249 LEU* 1.3 86.3 + - + -
1269 GLU* 3.2 25.3 + - - +
1279 LYS* 3.7 42.0 - - + +
2729 PHE* 4.7 13.2 - + - -
2829 LEU* 4.7 11.7 - - + -
2849 PRO* 6.0 7.0 - - + -
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Residues in contact with LEU 124 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949 ASN 5.2 7.0 - - - +
959 LEU* 5.0 7.0 - - + -
1039 VAL* 6.0 0.4 - - + -
1209 LEU* 3.1 20.1 + - + +
1219 GLY* 2.5 16.6 + - - +
1239 PHE* 1.3 104.7 - - + +
1259 ARG* 1.3 57.1 + - - +
1279 LYS* 2.1 51.0 - - + +
1289 HIS* 3.9 4.5 - - + +
1309 LYS* 5.1 9.0 - - + +
1329 VAL* 4.7 8.1 - - + -
1869 VAL* 3.8 35.9 - - + -
1889 LEU* 5.1 1.8 - - + -
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Residues in contact with ARG 125 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1219 GLY 3.4 1.6 + - - -
1229 LYS* 3.2 13.0 + - + +
1249 LEU* 1.3 74.1 - - - +
1269 GLU* 1.3 59.0 + - + +
1279 LYS 2.7 14.6 + - - -
1289 HIS 3.7 11.8 + - - +
1299 LYS* 3.9 7.0 + - - +
1309 LYS* 2.3 41.6 + - - -
1319 LYS* 3.6 27.7 - - - +
1329 VAL* 4.0 19.8 - - + +
1559 VAL 5.5 3.4 - - - +
1569 GLY 4.8 9.7 + - - +
1579 VAL* 4.2 21.5 - - + +
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Residues in contact with GLU 126 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1229 LYS* 3.5 37.7 + - + +
1239 PHE* 3.2 13.9 + - - +
1259 ARG* 1.3 76.6 - - + +
1279 LYS* 1.3 59.4 + - - +
2809 GLU* 4.0 20.3 - - - +
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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