Contacts of the helix formed by residues 1099 - 1113 (chain B) in PDB entry 5DSG
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 THR1099 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1062B GLN* 2.9 33.2 + - - +
1095B TRP* 3.3 18.0 + - - -
1098B GLN* 1.3 88.5 - - + +
1100B PRO* 1.3 64.5 - - - +
1101B ASN 3.5 2.2 - - - -
1102B ARG* 3.8 12.8 + - - +
1103B ALA* 3.1 19.8 + - - +
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Residues in contact with PRO1100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096B TYR* 3.2 23.7 - - + +
1097B ASN 4.1 7.9 - - - +
1098B GLN 3.4 8.7 - - - +
1099B THR* 1.3 87.2 - - - +
1101B ASN* 1.3 69.3 + - - +
1103B ALA* 3.4 2.1 + - - +
1104B LYS* 2.9 44.3 + - - +
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Residues in contact with ASN1101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1099B THR 3.5 0.4 - - - -
1100B PRO* 1.3 84.5 - - - +
1102B ARG* 1.3 66.6 + - - +
1104B LYS* 3.0 22.1 + - - +
1105B ARG* 2.9 44.3 + - - +
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Residues in contact with ARG1102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007B LEU* 4.3 11.7 - - - +
1010B ASP* 3.7 43.0 + - - +
1011B GLU* 5.5 3.8 - - - +
1058B ASN* 2.7 31.9 + - - -
1061B PHE* 4.5 7.5 - - - -
1062B GLN* 3.2 54.0 + - - +
1099B THR* 3.8 14.6 + - - +
1101B ASN* 1.3 77.9 - - - +
1103B ALA* 1.3 57.5 - - - +
1105B ARG* 3.2 20.8 + - - +
1106B VAL* 2.9 38.7 + - + +
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Residues in contact with ALA1103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095B TRP* 3.6 30.4 - - + +
1096B TYR* 3.7 30.5 - - + -
1099B THR 3.1 20.7 + - - +
1100B PRO 3.6 4.0 - - - +
1102B ARG* 1.3 76.8 - - - +
1104B LYS* 1.3 57.5 + - - +
1106B VAL* 3.9 0.7 - - - +
1107B ILE* 2.9 37.5 + - - +
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Residues in contact with LYS1104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096B TYR* 3.2 35.9 - - + +
1100B PRO* 2.9 31.4 + - - +
1101B ASN* 3.0 21.7 + - - +
1103B ALA* 1.3 77.7 - - - +
1105B ARG* 1.3 54.8 + - + +
1107B ILE* 3.8 4.2 - - - +
1108B THR* 2.5 40.0 + - - +
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Residues in contact with ARG1105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LEU* 4.0 27.5 - - - +
1009B ILE* 4.5 10.5 + - - +
1010B ASP* 2.6 38.8 + - - +
1101B ASN* 2.9 26.6 + - - +
1102B ARG* 3.6 27.5 - - - +
1104B LYS* 1.3 78.1 - - + +
1106B VAL* 1.3 57.9 + - - +
1108B THR* 3.4 3.4 + - - -
1109B THR* 2.8 31.7 + - - -
1117B ALA* 3.6 32.1 - - + +
1118B TYR* 3.2 22.9 - - + +
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Residues in contact with VAL1106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006B MET* 4.2 1.3 - - + -
1055B ALA* 3.9 9.0 - - + +
1058B ASN* 3.9 25.8 - - + +
1059B MET* 3.8 10.1 - - + -
1095B TRP* 3.6 29.4 - - + -
1102B ARG* 2.9 25.5 + - + +
1105B ARG* 1.3 75.2 - - - +
1107B ILE* 1.3 58.6 + - - +
1109B THR* 3.2 9.4 + - - -
1110B PHE* 2.9 51.5 + - + -
1118B TYR* 3.8 12.6 - - - +
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Residues in contact with ILE1107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087B ALA* 3.7 29.0 - - + +
1090B LEU* 3.5 48.0 - - + +
1091B ALA* 3.6 12.3 - - + +
1095B TRP* 4.1 10.3 - - + -
1096B TYR* 3.9 15.7 - - + -
1103B ALA 2.9 21.5 + - - +
1104B LYS* 3.8 4.5 - - - +
1106B VAL* 1.3 76.0 - - - +
1108B THR* 1.3 60.3 + - - +
1110B PHE* 3.1 11.1 + - - +
1111B ARG* 2.9 27.7 + - + +
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Residues in contact with THR1108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104B LYS* 2.5 25.3 + - - +
1105B ARG* 3.6 5.1 - - - -
1106B VAL 3.3 0.2 - - - -
1107B ILE* 1.3 78.8 - - - +
1109B THR* 1.3 57.3 + - - +
1111B ARG* 3.1 16.9 + - - +
1112B THR* 2.9 50.3 + - + +
1116B ASP* 5.7 3.6 - - + -
1117B ALA* 4.0 20.9 - - + +
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Residues in contact with THR1109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006B MET* 4.3 7.4 - - + -
1051B VAL* 3.6 30.3 - - + +
1052B ARG* 4.0 2.6 - - - +
1055B ALA* 3.7 21.5 - - + -
1105B ARG 2.8 18.5 + - - -
1106B VAL* 3.3 10.3 - - - -
1108B THR* 1.3 76.3 - - - +
1110B PHE* 1.3 56.4 + - - +
1113B GLY* 3.0 27.2 + - - -
1114B THR 4.0 12.8 + - - +
1115B TRP* 4.8 4.3 - - + -
1117B ALA* 4.4 1.8 - - - +
1118B TYR* 3.2 23.2 - - - -
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Residues in contact with PHE1110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1048B LEU* 4.3 7.9 - - + -
1052B ARG* 2.9 54.5 + - + -
1055B ALA* 3.5 13.7 - - + -
1056B LEU* 3.4 28.3 - - + -
1059B MET* 3.4 29.2 - - - -
1078B LEU* 3.5 42.4 - - + -
1083B TRP* 3.9 11.8 - - - +
1086B ALA* 6.1 0.9 - - + -
1087B ALA* 6.0 2.7 - - + -
1090B LEU* 4.0 18.8 - - + -
1106B VAL* 2.9 29.3 + - + -
1107B ILE* 3.1 8.3 + - - +
1109B THR* 1.3 76.1 - - - +
1111B ARG* 1.3 59.8 + - - +
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Residues in contact with ARG1111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052B ARG* 3.4 9.7 + - - -
1083B TRP* 3.7 25.1 - - + +
1084B ASP* 3.9 23.8 + - - +
1087B ALA* 4.4 16.4 - - + -
1107B ILE* 2.9 12.6 + - - +
1108B THR* 3.1 19.8 + - - +
1110B PHE* 1.3 81.4 - - - +
1112B THR* 1.3 87.3 + - - +
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Residues in contact with THR1112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052B ARG* 3.7 7.3 + - - -
1108B THR* 2.9 27.4 + - + +
1111B ARG* 1.3 107.7 - - - +
1113B GLY* 1.3 64.2 + - - +
1114B THR* 2.8 40.5 + - - +
1116B ASP* 4.7 8.2 - - + +
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Residues in contact with GLY1113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049B ASP* 3.9 4.3 - - - +
1051B VAL* 3.3 25.5 - - - +
1052B ARG* 3.8 26.9 - - - -
1109B THR 3.0 17.0 + - - -
1111B ARG 3.5 1.4 - - - -
1112B THR* 1.3 79.8 + - - +
1114B THR* 1.3 60.6 + - - +
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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