Contacts of the helix formed by residues 114 - 126 (chain 6) 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 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766 TYR* 2.9 22.1 + - + +
1126 ASN 3.7 2.5 + - - +
1136 ALA* 1.3 70.9 - - - +
1156 PRO* 1.4 63.4 - - - +
1166 GLN* 2.8 26.5 + - - +
1176 VAL* 2.7 39.8 + - + +
1186 LEU* 3.0 10.8 + - - +
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Residues in contact with PRO 115 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046 LYS* 4.5 8.5 - - - +
1086 ILE* 3.9 28.5 - - + -
1136 ALA 3.3 9.8 - - - +
1146 ASN* 1.4 89.5 - - - +
1166 GLN* 1.3 56.2 + - - +
1186 LEU* 3.3 14.2 + - + +
1196 ASP* 2.9 37.7 + - - +
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Residues in contact with GLN 116 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666 TYR* 3.2 36.5 + - + -
1146 ASN* 2.8 23.3 + - - +
1156 PRO* 1.3 74.6 - - - +
1176 VAL* 1.3 62.0 + - + +
1196 ASP* 3.4 10.5 + - - +
1206 ALA* 3.1 17.7 + - - +
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Residues in contact with VAL 117 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626 VAL* 5.5 0.7 - - + -
636 LEU* 3.6 30.7 - - + -
666 TYR* 3.9 29.4 - - + -
686 ILE* 4.3 15.0 - - + -
766 TYR* 3.7 29.2 - - + +
1146 ASN* 2.7 22.0 + - + +
1166 GLN* 1.3 73.1 - - + +
1186 LEU* 1.3 66.6 - - - +
1206 ALA* 3.0 9.5 + - + +
1216 VAL* 2.9 22.3 + - + +
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Residues in contact with LEU 118 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766 TYR* 3.7 20.6 - - + -
796 PHE* 3.3 53.6 - - + -
1046 LYS* 4.0 18.8 - - + +
1076 TYR* 4.4 1.8 - - + -
1086 ILE* 3.3 35.7 - - + +
1136 ALA* 3.8 17.9 - - + -
1146 ASN 3.0 12.2 + - - +
1156 PRO* 3.5 14.8 - - + +
1166 GLN 3.2 0.2 - - - -
1176 VAL* 1.3 77.3 - - - +
1196 ASP* 1.3 62.7 + - - +
1216 VAL* 3.2 2.9 + - - -
1226 VAL* 3.1 20.2 + - - +
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Residues in contact with ASP 119 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046 LYS* 2.7 37.0 + - - +
1156 PRO* 2.9 23.0 + - - +
1166 GLN* 3.6 11.7 - - - +
1186 LEU* 1.3 72.9 - - - +
1206 ALA* 1.3 60.9 + - - +
1226 VAL* 3.1 9.2 + - - +
1236 ASN* 2.8 43.0 + - - +
1296 PRO* 5.4 13.4 - - + +
1306 THR* 5.2 3.8 - - - +
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Residues in contact with ALA 120 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626 VAL* 3.8 11.6 - - + +
666 TYR* 3.5 39.5 - - + +
1166 GLN* 3.1 5.7 + - - +
1176 VAL* 3.0 10.6 + - - +
1196 ASP* 1.3 79.8 - - - +
1216 VAL* 1.3 63.2 + - - +
1236 ASN* 3.1 20.3 + - - +
1246 ILE* 3.3 18.0 + - - +
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Residues in contact with VAL 121 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596 VAL* 4.1 27.6 - - + -
626 VAL* 5.4 4.5 - - + -
636 LEU* 5.0 2.5 - - + -
766 TYR* 4.2 21.8 - - + +
796 PHE* 3.8 13.2 - - + -
806 GLY* 3.5 32.5 - - - +
1176 VAL* 2.9 21.4 + - + +
1186 LEU* 3.5 8.3 - - - +
1206 ALA* 1.3 76.8 - - + +
1226 VAL* 1.3 62.4 + - - +
1246 ILE* 3.0 17.3 + - - +
1256 ILE* 3.2 18.9 + - + +
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Residues in contact with VAL 122 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796 PHE* 3.7 24.0 - - + -
836 VAL* 4.6 7.9 - - + -
1006 ILE* 4.3 20.6 - - + -
1046 LYS* 6.0 1.3 - - + -
1186 LEU 3.1 14.0 + - - +
1196 ASP* 3.5 12.3 - - - +
1216 VAL* 1.3 76.2 - - - +
1236 ASN* 1.3 55.0 + - - +
1246 ILE 3.0 0.3 + - - -
1256 ILE* 4.6 4.9 - - - +
1266 THR* 2.5 52.9 + - + +
1286 SER 3.2 22.0 - - - +
1296 PRO* 4.3 7.4 - - + -
1306 THR* 4.4 8.7 - - + +
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Residues in contact with ASN 123 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1196 ASP* 2.8 29.0 + - - +
1206 ALA* 3.1 12.5 + - - +
1226 VAL* 1.3 74.9 - - - +
1246 ILE* 1.3 58.7 + - + +
1276 GLY* 3.2 26.0 - - - +
1286 SER* 3.1 1.1 - - - -
1296 PRO* 3.0 45.2 - - - +
123a ASN* 3.8 21.0 + - - +
124a ILE* 3.9 0.7 - - - +
127a GLY 5.3 5.2 - - - +
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Residues in contact with ILE 124 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556 VAL* 5.6 1.3 - - - +
586 ASN* 3.6 38.8 - - + +
596 VAL* 4.7 6.1 - - + +
626 VAL* 3.7 25.6 - - + -
1206 ALA 3.3 14.8 - - - +
1216 VAL* 3.0 8.9 + - - +
1226 VAL 3.0 0.6 - - - -
1236 ASN* 1.3 85.6 - - + +
1256 ILE* 1.3 73.4 + - + +
1266 THR 4.4 0.2 - - - -
1276 GLY 3.9 3.9 + - - -
58a ASN* 4.7 6.5 + - - +
124a ILE* 4.1 27.3 - - + +
126a THR 5.0 0.9 - - - +
127a GLY* 3.4 34.5 - - - +
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Residues in contact with ILE 125 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556 VAL* 4.0 25.4 - - + -
596 VAL* 4.6 1.8 - - + -
806 GLY* 3.1 43.1 - - - +
836 VAL* 3.9 25.8 - - + -
846 ALA* 4.4 14.1 - - + +
876 LEU* 4.5 19.4 - - + +
1216 VAL* 3.2 18.7 + - + +
1226 VAL 4.2 1.1 - - - +
1246 ILE* 1.3 83.9 - - + +
1266 THR* 1.3 63.2 + - + +
58a ASN* 4.8 11.1 - - - +
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Residues in contact with THR 126 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836 VAL* 4.5 4.3 - - + -
876 LEU* 6.0 2.9 - - + -
966 LEU* 4.8 10.1 - - + -
1006 ILE* 4.1 20.4 - - + -
1226 VAL* 2.5 36.7 + - + +
1246 ILE 4.4 0.4 - - - -
1256 ILE* 1.3 85.1 - - + +
1276 GLY* 1.3 58.2 + - - +
1286 SER* 2.5 29.6 + - - +
61a ALA* 5.7 4.3 - - - +
62a VAL* 5.4 4.2 - - - +
65a GLN* 3.9 22.8 + - - +
124a ILE* 4.8 1.9 - - - +
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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
------------------------------------------------------------
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