Contacts of the helix formed by residues 114 - 126 (chain 5) in PDB entry 3J9X
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 ASN 114 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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765 TYR* 2.9 21.0 + - - +
1125 ASN 3.7 2.5 + - - +
1135 ALA* 1.3 69.8 - - - +
1155 PRO* 1.3 61.7 - - - +
1165 GLN* 2.8 23.5 + - - +
1175 VAL* 2.7 45.7 + - + +
1185 LEU* 3.0 10.6 + - - +
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Residues in contact with PRO 115 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045 LYS* 5.0 3.0 - - - +
1085 ILE* 3.9 32.3 - - + -
1135 ALA 3.2 10.0 - - - +
1145 ASN* 1.3 89.4 - - - +
1165 GLN* 1.3 56.8 + - - +
1185 LEU* 3.2 14.4 + - + +
1195 ASP* 2.9 37.3 + - - +
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Residues in contact with GLN 116 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665 TYR* 2.9 44.9 + - - -
1145 ASN* 2.8 18.7 + - - +
1155 PRO* 1.3 74.6 - - - +
1175 VAL* 1.3 70.3 + - - +
1195 ASP* 3.3 9.7 + - - +
1205 ALA* 3.1 16.7 + - - +
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Residues in contact with VAL 117 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625 VAL* 5.3 0.7 - - + -
635 LEU* 4.1 13.5 - - + -
665 TYR* 4.1 28.0 - - + -
685 ILE* 4.9 8.1 - - + -
765 TYR* 3.7 37.2 - - + +
1145 ASN* 2.7 28.0 + - + +
1165 GLN* 1.3 83.3 - - - +
1185 LEU* 1.3 66.2 + - - +
1205 ALA* 3.0 16.8 + - + +
1215 VAL* 3.0 15.2 + - + +
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Residues in contact with LEU 118 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765 TYR* 3.6 23.8 - - + -
795 PHE* 3.3 52.0 - - + -
1045 LYS* 4.4 12.1 - - + +
1075 TYR* 4.4 8.1 - - + -
1085 ILE* 3.3 35.4 - - + -
1135 ALA* 3.8 17.7 - - + -
1145 ASN 3.0 10.9 + - - +
1155 PRO* 3.4 13.0 - - + +
1175 VAL* 1.3 76.7 - - - +
1195 ASP* 1.3 61.4 + - - +
1215 VAL* 3.1 3.8 + - - -
1225 VAL* 3.0 20.3 + - - +
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Residues in contact with ASP 119 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1045 LYS* 2.7 37.3 + - - +
1155 PRO* 2.9 19.0 + - - +
1165 GLN* 3.6 11.0 - - - +
1175 VAL 3.2 0.2 - - - -
1185 LEU* 1.3 73.3 - - - +
1205 ALA* 1.3 60.5 + - - +
1225 VAL* 3.2 7.8 + - - +
1235 ASN* 2.8 30.8 + - - +
1295 PRO* 4.3 26.4 - - + +
1305 THR 5.6 0.7 + - - -
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Residues in contact with ALA 120 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625 VAL* 4.0 9.3 - - + +
665 TYR* 3.5 39.9 - - + +
1165 GLN* 3.1 10.6 + - - +
1175 VAL 3.0 12.7 + - - +
1195 ASP* 1.3 77.6 - - - +
1215 VAL* 1.3 60.0 + - - +
1235 ASN* 3.3 19.6 + - - +
1245 ILE* 3.4 14.4 - - - +
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Residues in contact with VAL 121 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595 VAL* 4.0 26.5 - - + -
625 VAL* 5.0 8.7 - - + -
635 LEU* 5.1 0.7 - - + -
765 TYR* 4.4 20.6 - - + +
795 PHE* 3.8 13.7 - - + -
805 GLY* 3.6 31.4 - - - -
1175 VAL* 3.0 22.1 + - + +
1185 LEU* 3.1 8.3 + - - +
1205 ALA* 1.3 76.3 - - - +
1225 VAL* 1.3 63.5 + - - +
1245 ILE* 3.0 17.6 + - - +
1255 ILE* 3.2 19.0 + - + +
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Residues in contact with VAL 122 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795 PHE* 3.6 23.1 - - + -
835 VAL* 4.5 7.0 - - + -
1005 ILE* 4.2 21.8 - - + -
1045 LYS* 5.0 1.1 - - + -
1185 LEU 3.0 15.6 + - - +
1195 ASP* 3.6 13.5 - - - +
1215 VAL* 1.3 75.5 - - - +
1235 ASN* 1.3 54.8 + - - +
1245 ILE 2.9 1.4 + - - -
1255 ILE* 4.6 5.2 - - - +
1265 THR* 2.6 52.5 + - + +
1285 SER 3.2 20.6 - - - +
1295 PRO* 3.9 10.1 - - + -
1305 THR 4.1 6.3 - - - +
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Residues in contact with ASN 123 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1195 ASP 2.8 17.7 + - - +
1205 ALA* 3.4 11.6 + - - +
1215 VAL 3.2 0.4 - - - -
1225 VAL* 1.3 74.5 - - - +
1245 ILE* 1.3 68.4 + - - +
1275 GLY* 3.1 33.7 + - - +
1285 SER* 3.4 16.6 - - - +
1295 PRO* 3.5 11.8 - - + +
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Residues in contact with ILE 124 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585 ASN* 3.7 37.5 - - + +
595 VAL* 5.0 3.8 - - + +
625 VAL* 3.6 26.0 - - + -
1205 ALA 3.4 14.1 - - - +
1215 VAL* 3.0 7.1 + - - +
1225 VAL 3.0 0.8 - - - -
1235 ASN* 1.3 94.8 - - - +
1255 ILE* 1.3 70.9 + - + +
1265 THR 3.4 0.4 - - - -
1275 GLY* 3.6 6.2 + - - -
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Residues in contact with ILE 125 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555 VAL* 3.9 25.1 - - + -
595 VAL* 4.4 4.9 - - + -
805 GLY* 3.2 42.0 - - - +
835 VAL* 3.7 26.2 - - + -
845 ALA* 4.5 15.0 - - + +
875 LEU* 4.8 16.9 - - + +
1215 VAL* 3.2 21.1 + - + +
1225 VAL* 4.2 1.6 - - - +
1245 ILE* 1.3 81.3 - - + +
1265 THR* 1.3 62.0 + - + +
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Residues in contact with THR 126 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835 VAL* 4.3 12.3 - - + -
875 LEU* 6.1 3.4 - - + -
965 LEU* 4.6 12.6 - - + -
1005 ILE* 4.1 18.4 - - + -
1225 VAL* 2.6 29.0 + - + +
1245 ILE 4.2 0.2 - - - -
1255 ILE* 1.3 79.9 - - + +
1275 GLY* 1.3 57.2 + - - +
1285 SER* 2.4 34.9 + - - -
1305 THR* 6.3 0.2 - - - -
1345 SER* 5.1 6.2 - - - +
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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