Contacts of the helix formed by residues 1002 - 1020 (chain B) in PDB entry 5UNG
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 ASP1002 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1001B ALA* 1.4 77.9 - - - +
1003B LEU* 1.3 55.2 + - - +
1004B GLU* 3.0 34.0 + - - +
1005B ASP* 3.2 26.7 + - - +
1006B ASN* 2.8 37.5 + - - -
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Residues in contact with LEU1003 (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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1001B ALA 4.0 0.8 + - - -
1002B ASP* 1.3 73.4 + - - +
1004B GLU* 1.4 59.0 + - - +
1006B ASN* 3.6 6.7 + - - +
1007B TRP* 3.2 32.9 + - + +
1040B ALA* 3.5 36.1 - - + +
1043B ALA* 3.9 20.2 - - + +
1044B THR 4.6 3.1 - - - +
1045B PRO* 3.8 28.7 - - + -
1046B PRO* 4.1 10.5 - - + -
1061B PHE* 3.9 13.9 - - + -
1101B TYR* 3.4 24.7 - - - +
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Residues in contact with GLU1004 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002B ASP* 3.0 14.1 + - - +
1003B LEU* 1.4 76.2 - - - +
1005B ASP* 1.4 68.6 + - - +
1007B TRP* 3.6 5.0 + - - +
1008B GLU* 3.1 31.4 + - - +
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Residues in contact with ASP1005 (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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1001B ALA 4.9 6.3 + - - +
1002B ASP* 3.2 32.3 + - + +
1004B GLU* 1.4 88.7 - - - +
1006B ASN* 1.4 53.4 + - - +
1008B GLU* 3.5 12.8 + - - +
1009B THR* 2.7 36.8 + - - -
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Residues in contact with ASN1006 (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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1001B ALA 3.4 20.3 + - - -
1002B ASP 2.8 29.3 + - - +
1003B LEU 3.9 5.5 - - - +
1004B GLU 3.4 0.4 - - - -
1005B ASP* 1.4 75.0 - - - +
1007B TRP* 1.4 58.3 + - - +
1009B THR* 3.3 8.6 + - - -
1010B LEU* 3.1 31.7 + - - +
1036B ALA* 3.5 30.5 - - - +
1039B ASP* 3.5 25.1 + - - +
1040B ALA* 3.7 22.1 - - + +
1043B ALA* 5.5 0.4 - - - +
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Residues in contact with TRP1007 (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 LEU* 3.2 29.9 + - + +
1004B GLU* 4.3 4.0 - - - +
1006B ASN* 1.4 73.9 - - - +
1008B GLU* 1.4 58.1 + - - +
1010B LEU* 3.7 28.5 - - + +
1011B ASN* 2.8 51.4 + - - +
1014B LEU* 6.1 0.7 - - + -
1040B ALA* 4.9 2.0 - - + -
1065B PHE* 3.5 35.9 - + - -
1068B LEU* 4.4 14.8 - - + -
1097B THR* 4.8 2.0 - - + -
1098B ARG* 3.6 34.3 - - + -
1101B TYR* 3.2 68.5 - + + -
1102B ILE* 6.5 0.4 - - + -
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Residues in contact with GLU1008 (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 GLU* 3.1 22.6 + - - +
1005B ASP* 3.5 13.0 - - - +
1006B ASN 3.3 0.2 - - - -
1007B TRP* 1.4 75.2 - - - +
1009B THR* 1.4 56.9 + - - +
1011B ASN* 3.6 3.6 + - - +
1012B ASP* 3.0 47.3 + - - +
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Residues in contact with THR1009 (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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1005B ASP 2.7 20.5 + - - -
1006B ASN* 3.3 9.8 + - - -
1008B GLU* 1.4 74.8 - - - +
1010B LEU* 1.4 57.1 + - - +
1012B ASP* 4.1 3.1 - - - -
1013B ASN* 2.8 51.6 + - - +
1032B LYS* 4.1 22.7 - - + +
1033B MET* 4.7 0.6 - - - +
1036B ALA* 4.2 9.0 - - + -
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Residues in contact with LEU1010 (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 ASN* 3.1 25.5 + - + +
1007B TRP* 3.7 46.4 - - + +
1008B GLU 3.4 0.4 - - - -
1009B THR* 1.4 75.7 - - - +
1011B ASN* 1.3 59.6 + - - +
1014B LEU* 3.3 31.1 + - + +
1033B MET* 3.5 53.2 - - + +
1036B ALA* 4.2 6.7 - - + +
1037B ALA* 4.5 13.0 - - - +
1065B PHE* 4.7 2.7 - - + -
1068B LEU* 3.9 24.0 - - + -
1072B ILE* 4.7 0.4 - - + -
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Residues in contact with ASN1011 (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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201B PRO 4.7 3.2 + - - -
202B GLU* 4.0 39.6 + - + +
1007B TRP* 2.8 38.4 + - - +
1008B GLU* 4.1 4.8 - - - +
1009B THR 3.4 0.2 - - - -
1010B LEU* 1.3 73.6 - - - +
1012B ASP* 1.4 65.4 + - - +
1014B LEU* 3.4 18.4 + - - +
1015B LYS* 3.6 20.4 + - - +
1098B ARG* 2.9 39.8 + - - +
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Residues in contact with ASP1012 (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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202B GLU* 6.1 0.7 - - - +
1008B GLU* 3.0 38.3 + - - +
1009B THR* 4.1 4.9 - - - +
1011B ASN* 1.4 77.8 - - - +
1013B ASN* 1.3 62.6 + - - +
1015B LYS* 3.5 15.8 + - - +
1016B VAL* 3.3 24.1 + - - +
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Residues in contact with ASN1013 (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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1009B THR* 2.8 45.5 + - - +
1012B ASP* 1.3 76.3 - - - +
1014B LEU* 1.4 63.1 + - - +
1015B LYS 3.3 0.2 - - - -
1016B VAL* 3.3 14.6 + - - +
1017B ILE* 3.3 29.0 + - - +
1028B ASP* 5.1 0.3 - - - +
1029B ALA* 3.6 32.3 - - - +
1032B LYS* 3.5 31.2 + - - +
1033B MET* 3.8 10.1 - - + -
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Residues in contact with LEU1014 (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 TRP* 6.1 0.2 - - + -
1010B LEU* 3.3 23.6 + - + +
1011B ASN* 3.6 11.9 - - - +
1012B ASP 3.3 0.4 - - - -
1013B ASN* 1.4 76.9 - - - +
1015B LYS* 1.4 61.8 + - + +
1016B VAL 3.6 0.3 + - - -
1017B ILE* 3.6 19.1 + - + +
1018B GLU* 3.6 18.8 + - - +
1033B MET* 3.9 16.6 - - + -
1091B ALA* 3.8 22.7 - - + +
1094B LEU* 3.9 19.5 - - + +
1095B LYS* 4.4 17.8 - - + -
1098B ARG* 4.3 41.7 - - + +
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Residues in contact with LYS1015 (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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202B GLU* 3.1 46.5 + - - +
1011B ASN* 3.6 20.2 + - - +
1012B ASP* 3.5 13.6 + - - +
1013B ASN 3.3 0.4 - - - -
1014B LEU* 1.4 74.6 - - + +
1016B VAL* 1.4 63.3 + - + +
1018B GLU* 3.5 18.0 + - - +
1019B LYS* 3.3 42.4 + - - +
1098B ARG* 5.8 2.4 - - - +
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Residues in contact with VAL1016 (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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1012B ASP 3.3 17.0 - - - +
1013B ASN* 3.3 22.0 + - - +
1014B LEU 3.3 0.8 - - - -
1015B LYS* 1.4 74.8 - - + +
1017B ILE* 1.4 53.6 + - - +
1019B LYS* 3.2 8.3 + - - +
1020B ALA* 2.8 33.3 + - + +
1025B GLN* 4.3 15.0 - - + +
1028B ASP* 5.7 3.1 - - - +
1029B ALA* 3.9 16.8 - - + -
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Residues in contact with ILE1017 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1013B ASN 3.3 17.0 + - - +
1014B LEU* 3.8 13.2 - - + +
1015B LYS 3.4 0.2 - - - -
1016B VAL* 1.4 74.8 - - - +
1018B GLU* 1.3 54.1 + - + +
1020B ALA* 3.4 9.8 + - - +
1026B VAL* 4.0 22.9 - - + +
1029B ALA* 3.7 15.7 - - + -
1030B LEU* 4.1 16.8 - - + -
1033B MET* 3.8 24.5 - - - -
1088B GLN* 2.8 51.9 + - + +
1091B ALA* 3.8 29.4 - - + -
1094B LEU* 4.9 0.2 - - + -
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Residues in contact with GLU1018 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1014B LEU 3.6 14.0 + - - +
1015B LYS* 3.5 21.0 + - - +
1016B VAL 3.3 0.2 - - - -
1017B ILE* 1.3 78.0 - - + +
1019B LYS* 1.3 61.8 + - + +
1020B ALA 3.5 1.3 + - - +
1088B GLN* 4.2 8.8 + - - +
1092B GLU* 4.4 11.6 - - - +
1095B LYS* 3.0 36.6 + - - +
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Residues in contact with LYS1019 (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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1015B LYS* 3.3 30.0 + - - +
1016B VAL* 3.2 8.5 + - - +
1018B GLU* 1.3 78.2 - - + +
1020B ALA* 1.4 63.7 + - - +
1021B ASP* 3.6 11.6 - - - +
1025B GLN* 5.1 2.2 + - - -
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Residues in contact with ALA1020 (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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1016B VAL* 2.8 15.3 + - - +
1017B ILE* 3.4 15.7 + - - +
1018B GLU 4.6 0.7 - - - +
1019B LYS* 1.4 78.8 - - - +
1021B ASP* 1.3 60.4 + - - +
1022B ASN 4.3 0.2 - - - +
1025B GLN* 3.8 29.2 - - + +
1026B VAL* 3.8 22.0 - - + +
1085B LYS* 5.3 3.1 + - - -
1088B GLN* 2.9 21.2 + - - -
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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