Contacts of the helix formed by residues 1002 - 1010 (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 ASN1002 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225B ARG* 4.2 12.5 + - + +
226B VAL* 1.3 78.1 - - - +
1003B ILE* 1.3 63.7 + - + +
1004B PHE* 3.3 18.6 + - + +
1005B GLU* 2.8 36.2 + - - +
1006B MET* 2.9 27.7 + - - +
1115B TRP* 3.7 13.0 - - - -
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Residues in contact with ILE1003 (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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1002B ASN* 1.3 76.8 - - + +
1004B PHE* 1.3 84.4 + - + +
1006B MET* 3.2 12.5 + - - +
1007B LEU* 2.9 46.8 + - + +
1028B VAL* 4.7 10.5 - - + -
1054B ALA* 3.3 42.6 - - + +
1057B ILE* 3.9 28.3 - - + -
1115B TRP* 3.9 6.6 - - - -
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Residues in contact with PHE1004 (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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1002B ASN* 3.3 16.5 + - - +
1003B ILE* 1.3 90.2 - - + +
1005B GLU* 1.3 57.5 + - - +
1007B LEU* 3.4 6.3 + - - +
1008B ARG* 2.9 26.9 + - - +
1021B GLU* 3.5 29.3 - - + +
1024B PHE* 3.5 25.8 - + + -
1025B ASN* 3.1 58.8 - - - -
1028B VAL* 3.6 25.6 - - + -
1029B ASP* 5.4 1.1 - - - -
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Residues in contact with GLU1005 (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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223B ARG* 3.1 54.8 + - + +
225B ARG 5.1 0.9 - - - +
226B VAL* 4.3 12.3 - - + -
1002B ASN* 2.8 30.0 + - - +
1004B PHE* 1.3 73.6 - - - +
1006B MET* 1.3 60.9 + - - +
1008B ARG* 3.2 15.4 + - - +
1009B ILE* 2.9 50.6 + - + +
1021B GLU* 4.9 3.2 - - - +
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Residues in contact with MET1006 (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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226B VAL* 4.8 1.1 - - - +
1002B ASN 2.9 16.1 + - - +
1003B ILE* 3.2 13.9 + - - +
1005B GLU* 1.3 76.9 - - - +
1007B LEU* 1.3 56.4 + - - +
1009B ILE* 3.3 3.3 + - - +
1010B ASP* 3.1 29.0 + - - +
1054B ALA 3.7 20.4 - - - +
1055B ALA* 3.8 22.0 - - + -
1058B ASN* 3.4 20.6 - - + +
1106B VAL* 4.2 6.5 - - + -
1109B THR* 3.9 10.5 - - + +
1115B TRP* 3.6 20.9 - - + -
1118B TYR* 3.3 51.3 - - + +
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Residues in contact with LEU1007 (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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1003B ILE* 2.9 28.3 + - + +
1004B PHE* 3.8 5.8 - - - +
1006B MET* 1.3 72.8 - - - +
1008B ARG* 1.3 65.2 + - - +
1010B ASP* 3.7 2.9 - - - +
1011B GLU* 3.1 28.6 + - - +
1024B PHE* 4.6 18.0 - - + -
1028B VAL* 3.7 30.5 - - + -
1057B ILE* 5.2 0.9 - - + -
1058B ASN* 3.8 40.2 - - + +
1061B PHE* 3.9 34.3 - - + -
1102B ARG* 4.3 6.1 - - - +
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Residues in contact with ARG1008 (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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1004B PHE 2.9 15.8 + - - +
1005B GLU* 3.3 24.7 - - - +
1007B LEU* 1.3 78.3 - - - +
1009B ILE* 1.3 59.0 + - - +
1011B GLU 2.9 23.6 - - - +
1021B GLU* 4.4 8.7 - - - +
1024B PHE* 4.6 9.4 - - + -
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Residues in contact with ILE1009 (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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137B PRO* 6.1 6.1 - - + -
138B LEU* 3.2 33.5 - - + +
223B ARG* 6.4 0.4 - - + -
226B VAL* 5.4 0.4 - - + -
1005B GLU* 2.9 38.7 + - + +
1006B MET 3.7 4.0 - - - +
1008B ARG* 1.3 75.2 - - - +
1010B ASP* 1.3 60.3 + - - +
1011B GLU 3.1 9.2 + - - -
1105B ARG* 4.5 10.7 + - - +
1117B ALA 5.7 0.4 - - - +
1118B TYR* 3.4 54.3 - - + +
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Residues in contact with ASP1010 (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* 5.3 2.2 - - - -
1006B MET 3.1 13.2 + - - +
1007B LEU* 3.4 3.3 + - - +
1009B ILE* 1.3 75.1 - - - +
1011B GLU* 1.3 60.2 + - - +
1058B ASN* 2.8 21.7 + - - +
1102B ARG* 3.7 46.3 + - - +
1105B ARG* 2.6 41.1 + - - +
1118B TYR* 2.6 27.0 + - - -
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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