Contacts of the helix formed by residues 106 - 121 (chain 6) in PDB entry 5U8T
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 VAL 106 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046 ASP* 3.2 37.4 + - + +
1056 ASP* 1.3 77.0 - - - +
1076 THR* 1.3 70.9 + - - +
1096 GLU* 2.9 23.7 + - - +
1106 LYS* 2.9 12.7 + - - +
1766 ARG* 6.2 1.8 - - - +
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Residues in contact with THR 107 (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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1066 VAL* 1.3 87.0 - - - +
1086 GLY* 1.3 57.2 + - - +
1106 LYS* 3.0 24.8 + - - +
1116 VAL* 2.8 46.5 + - + +
1696 ALA* 5.3 6.1 - - + -
1766 ARG* 5.5 6.1 - - - -
1776 PHE* 4.7 12.1 - - + -
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Residues in contact with GLY 108 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1056 ASP 2.4 22.5 + - - -
1076 THR* 1.3 70.2 - - - +
1096 GLU* 1.3 54.1 + - - -
1116 VAL* 3.6 6.5 - - - +
1126 ARG* 2.9 19.1 + - - +
1766 ARG* 5.8 0.2 - - - +
1776 PHE* 3.5 30.3 - - - -
1806 PHE* 3.1 27.5 - - - -
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Residues in contact with GLU 109 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1046 ASP 4.6 4.9 - - - +
1056 ASP* 3.3 18.6 + - + +
1066 VAL* 2.9 19.3 + - - +
1086 GLY* 1.3 71.5 - - - +
1106 LYS* 1.3 62.7 + - - +
1126 ARG* 2.8 58.0 + - - +
1136 GLU* 2.9 17.0 + - + +
1806 PHE* 5.1 3.6 - - - -
1876 ARG* 4.9 4.0 + - - -
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Residues in contact with LYS 110 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1066 VAL 2.9 11.0 + - - +
1076 THR* 3.4 27.9 + - - +
1096 GLU* 1.3 76.4 - - - +
1116 VAL* 1.3 60.1 - - - +
1136 GLU* 3.3 5.2 + - - +
1146 ALA* 2.9 32.1 + - + +
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Residues in contact with VAL 111 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076 THR* 2.8 32.6 + - + +
1086 GLY* 3.6 8.7 - - - +
1106 LYS* 1.3 75.9 - - + +
1126 ARG* 1.3 61.7 + - - +
1146 ALA* 3.8 7.9 - - - -
1156 PHE* 2.9 27.4 + - - +
1666 LEU* 3.8 18.4 - - + -
1696 ALA* 4.6 15.7 - - + -
1706 ILE* 3.6 37.2 - - + -
1776 PHE* 4.8 9.2 - - + -
1816 LEU* 5.6 3.4 - - + -
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Residues in contact with ARG 112 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1086 GLY 2.9 9.8 + - - +
1096 GLU* 2.8 52.1 + - - +
1116 VAL* 1.3 78.5 - - - +
1136 GLU* 1.3 73.2 + - - +
1156 PHE* 3.8 4.5 - - - +
1166 GLU* 2.9 32.0 + - - +
1806 PHE* 3.4 32.2 + - + +
1836 LYS* 3.0 60.9 + - - +
1846 GLY* 3.5 9.7 - - - -
1876 ARG* 3.8 22.8 - - - +
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Residues in contact with GLU 113 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096 GLU* 2.9 19.9 + - + +
1106 LYS* 4.2 3.8 - - - +
1126 ARG* 1.3 86.6 - - - +
1146 ALA* 1.3 59.1 + - - +
1166 GLU* 2.9 37.0 - - - +
1176 GLN* 2.9 25.5 + - - +
1876 ARG* 3.3 25.3 + - - -
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Residues in contact with ALA 114 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1106 LYS* 2.9 20.9 + - + +
1116 VAL* 4.0 0.9 - - - -
1136 GLU* 1.3 76.8 - - - +
1156 PHE* 1.3 60.8 + - - +
1166 GLU 3.1 1.3 - - - -
1176 GLN 3.2 0.9 + - - -
1186 PHE 2.9 21.7 + - - -
1616 ARG* 2.9 33.3 + - - +
1666 LEU* 3.4 22.2 - - + -
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Residues in contact with PHE 115 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116 VAL* 2.9 21.2 + - + +
1126 ARG* 4.2 3.4 - - - +
1146 ALA* 1.3 74.6 - - - +
1166 GLU* 1.3 59.0 + - - +
1186 PHE* 3.7 29.4 - + + -
1196 LEU* 2.8 54.4 + - + +
1516 ILE* 6.4 1.1 - - + -
1536 ILE* 5.2 4.9 - - + -
1586 LEU* 4.3 14.6 - - + -
1666 LEU* 4.0 6.8 - - + +
1706 ILE* 4.3 20.4 - - + -
1816 LEU* 3.5 55.0 - - + -
1846 GLY* 6.3 0.4 - - - -
1856 LEU* 5.4 4.5 - - + -
2656 ILE* 5.5 4.3 - - + -
2676 PHE* 4.3 11.9 - + - -
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Residues in contact with GLU 116 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1126 ARG* 2.9 29.0 + - - +
1136 GLU* 2.9 40.9 - - - +
1156 PHE* 1.3 76.4 - - - +
1176 GLN* 1.3 60.6 + - - +
1196 LEU* 3.2 13.1 - - + +
1206 GLU* 2.9 35.3 + - - +
1846 GLY* 4.0 9.4 - - - +
1876 ARG* 3.5 22.7 + - - +
1886 VAL* 3.4 27.8 + - + +
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Residues in contact with GLN 117 (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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1136 GLU 2.9 13.2 + - - +
1146 ALA 3.2 1.8 + - - +
1166 GLU* 1.3 76.9 - - - +
1186 PHE* 1.3 55.3 + - - +
1206 GLU* 2.8 7.7 + - - -
1216 ASP* 2.2 72.3 + - + +
1616 ARG* 2.6 42.1 + - - +
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Residues in contact with PHE 118 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1146 ALA 2.9 13.7 + - - +
1156 PHE* 3.9 26.0 - + - +
1166 GLU 3.4 0.2 - - - -
1176 GLN* 1.3 76.4 - - - +
1196 LEU* 1.3 59.5 + - - +
1216 ASP 2.7 12.5 - - - +
1226 PHE 4.8 0.2 - - - -
1236 SER* 2.3 60.4 + - - -
1366 TYR* 4.0 21.5 - + - -
1536 ILE* 4.3 7.9 - - + -
1546 ASP 4.4 0.9 - - - -
1576 HIS* 3.4 21.1 - - + -
1586 LEU* 3.4 44.6 - - + -
1616 ARG* 3.5 35.2 - - + +
1666 LEU* 5.9 2.0 - - + -
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Residues in contact with LEU 119 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1156 PHE* 2.8 58.2 + - + +
1166 GLU* 3.2 12.6 - - - +
1186 PHE* 1.3 79.2 - - - +
1206 GLU* 1.3 61.8 + - - +
1236 SER* 4.5 0.5 + - - -
1346 LYS* 5.2 0.3 - - - +
1366 TYR* 3.6 34.9 - - + +
1376 ARG* 5.8 0.9 - - - +
1536 ILE* 6.4 1.1 - - + -
1846 GLY* 4.4 0.9 - - - -
1856 LEU* 3.9 36.8 - - + +
1886 VAL* 3.5 39.0 - - + -
1896 VAL* 5.9 0.2 - - + -
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Residues in contact with GLU 120 (chain 6).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1166 GLU* 2.9 22.0 + - - +
1176 GLN* 2.8 5.9 + - - +
1196 LEU* 1.3 83.6 - - + +
1216 ASP* 1.3 71.6 + - - +
1346 LYS* 3.0 35.9 - - - +
1376 ARG* 4.1 21.0 + - + +
1886 VAL* 4.4 16.8 - - + +
1916 LYS* 3.4 26.1 + - - -
1926 TYR* 3.9 8.4 + - + +
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Residues in contact with ASP 121 (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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1176 GLN* 2.2 64.8 + - + +
1186 PHE* 2.7 27.8 - - - +
1206 GLU* 1.3 83.3 - - - +
1226 PHE* 1.3 66.7 + - + +
1346 LYS* 4.2 7.4 + - - +
1616 ARG* 4.9 2.7 - - - +
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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
------------------------------------------------------------
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