Contacts of the helix formed by residues 1002 - 1019 (chain A) in PDB entry 5UNF
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1001A ALA* 1.4 78.2 - - - +
1003A LEU* 1.4 72.0 + - - +
1004A GLU* 3.4 21.5 + - - +
1005A ASP* 3.3 30.1 + - - +
1006A ASN* 3.0 32.0 + - - -
1043A ALA* 5.6 0.2 - - - -
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Residues in contact with LEU1003 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001A ALA 3.9 1.2 + - - -
1002A ASP* 1.4 79.6 + - - +
1004A GLU* 1.3 56.0 + - - +
1006A ASN* 3.4 5.7 + - - +
1007A TRP* 3.1 53.7 + - + +
1040A ALA* 3.4 39.0 - - + +
1043A ALA* 3.9 15.3 - - + +
1044A THR 4.6 2.7 - - - +
1045A PRO* 3.8 37.0 - - + -
1046A PRO* 4.9 5.6 - - + -
1061A PHE* 3.8 20.6 - - + -
1065A PHE* 4.1 0.7 - - + -
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Residues in contact with GLU1004 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002A ASP* 3.4 16.0 + - - +
1003A LEU* 1.3 77.2 - - - +
1005A ASP* 1.3 61.9 + - - +
1007A TRP* 3.4 8.8 + - - +
1008A GLU* 3.1 28.0 + - - +
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Residues in contact with ASP1005 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001A ALA 5.3 3.4 + - - +
1002A ASP* 3.3 35.2 + - + +
1003A LEU 3.4 0.4 - - - -
1004A GLU* 1.3 80.0 - - - +
1006A ASN* 1.4 56.6 + - - +
1008A GLU* 3.4 18.1 + - - +
1009A THR* 2.8 34.8 + - - -
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Residues in contact with ASN1006 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001A ALA 3.6 14.6 + - - -
1002A ASP 3.0 25.2 + - - +
1003A LEU 3.8 4.9 - - - +
1004A GLU 3.4 0.2 - - - -
1005A ASP* 1.4 76.0 - - - +
1007A TRP* 1.4 59.0 + - - +
1008A GLU 3.2 0.2 - - - -
1009A THR* 3.2 10.4 + - - -
1010A LEU* 2.9 33.4 + - - +
1036A ALA* 3.6 22.7 - - - +
1039A ASP* 3.3 28.7 - - - +
1040A ALA* 3.3 33.2 - - + +
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Residues in contact with TRP1007 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003A LEU* 3.1 53.1 + - + +
1004A GLU* 3.8 7.9 - - - +
1006A ASN* 1.4 72.9 - - - +
1008A GLU* 1.3 58.9 + - - +
1010A LEU* 3.6 25.8 - - + +
1011A ASN* 2.9 45.4 + - - +
1040A ALA* 5.1 1.6 - - + -
1061A PHE* 5.7 1.2 - - - -
1065A PHE* 3.6 26.7 - + - -
1068A LEU* 4.1 20.6 - - + -
1097A THR* 5.1 3.4 - - + -
1098A ARG* 3.4 47.1 - - + -
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Residues in contact with GLU1008 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004A GLU* 3.1 15.9 + - - +
1005A ASP* 3.4 22.4 - - - +
1006A ASN 3.2 0.2 - - - -
1007A TRP* 1.3 76.5 - - - +
1009A THR* 1.4 55.5 + - - +
1011A ASN* 3.4 6.0 + - - +
1012A ASP* 2.9 56.6 + - - +
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Residues in contact with THR1009 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005A ASP 2.8 15.9 + - - -
1006A ASN* 3.2 11.4 + - - -
1008A GLU* 1.4 78.2 - - - +
1010A LEU* 1.4 60.0 + - - +
1012A ASP* 4.2 4.2 - - - +
1013A ASN* 3.0 46.3 + - - +
1032A LYS* 4.4 8.1 - - + +
1036A ALA* 4.0 19.5 - - + -
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Residues in contact with LEU1010 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006A ASN 2.9 20.9 + - - +
1007A TRP* 3.6 43.7 - - + +
1008A GLU 3.3 0.2 - - - -
1009A THR* 1.4 76.8 - - - +
1011A ASN* 1.3 59.3 + - - +
1014A LEU* 3.2 31.4 + - + +
1033A MET* 3.3 58.5 - - + +
1036A ALA* 4.1 6.1 - - + +
1037A ALA* 4.2 14.8 - - + +
1040A ALA* 5.3 0.7 - - + -
1065A PHE* 4.8 2.5 - - + -
1068A LEU* 4.0 16.6 - - + -
1072A ILE* 4.6 3.1 - - + -
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Residues in contact with ASN1011 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A GLY 5.6 3.3 + - - -
288A ASN* 5.3 11.9 - - - +
1007A TRP* 2.9 33.7 + - - +
1008A GLU* 4.0 5.5 - - - +
1010A LEU* 1.3 75.4 - - - +
1012A ASP* 1.4 65.8 + - - +
1014A LEU* 3.3 19.2 + - - +
1015A LYS* 3.3 28.9 + - - +
1098A ARG* 3.2 39.7 + - - +
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Residues in contact with ASP1012 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008A GLU* 2.9 45.6 + - - +
1009A THR* 4.2 5.4 - - - +
1011A ASN* 1.4 78.6 - - - +
1013A ASN* 1.4 65.6 + - - +
1015A LYS* 3.5 23.2 + - - +
1016A VAL* 3.5 11.8 - - - +
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Residues in contact with ASN1013 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009A THR* 3.0 28.3 + - - +
1012A ASP* 1.4 78.5 + - - +
1014A LEU* 1.4 63.4 + - - +
1015A LYS 3.2 0.7 - - - -
1016A VAL* 3.2 23.7 + - - +
1017A ILE* 3.2 18.2 + - - +
1029A ALA* 3.6 17.6 - - + +
1032A LYS* 3.2 38.9 - - - +
1033A MET* 3.6 23.1 - - + +
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Residues in contact with LEU1014 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010A LEU* 3.2 23.8 + - + +
1011A ASN* 3.5 24.7 - - - +
1012A ASP 3.3 0.8 - - - -
1013A ASN* 1.4 75.2 - - - +
1015A LYS* 1.4 63.1 + - + +
1017A ILE* 3.4 13.8 + - + +
1018A GLU* 3.3 34.8 + - - +
1033A MET* 3.7 22.0 - - + -
1091A ALA* 3.6 24.7 - - + +
1092A GLU* 6.0 0.4 - - - +
1094A LEU* 3.9 13.9 - - + -
1095A LYS* 4.8 12.3 - - + +
1098A ARG* 4.3 21.5 - - + +
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Residues in contact with LYS1015 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011A ASN* 3.3 23.8 + - - +
1012A ASP* 3.5 14.3 + - - +
1013A ASN 3.2 0.4 - - - -
1014A LEU* 1.4 74.3 - - + +
1016A VAL* 1.4 62.7 + - + +
1018A GLU* 3.8 21.5 + - - +
1019A LYS* 3.5 36.7 + - + +
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Residues in contact with VAL1016 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012A ASP 3.5 16.2 - - - +
1013A ASN* 3.2 20.1 + - - +
1015A LYS* 1.4 75.9 - - + +
1017A ILE* 1.4 53.9 + - - +
1019A LYS* 3.2 6.1 + - - -
1020A ALA* 2.8 34.7 + - - +
1025A GLN* 4.3 23.1 + - + +
1029A ALA* 4.2 14.6 - - + -
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Residues in contact with ILE1017 (chain A).
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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1013A ASN 3.2 10.9 + - - +
1014A LEU* 3.4 12.5 + - + +
1016A VAL* 1.4 74.0 - - - +
1018A GLU* 1.4 57.5 + - + +
1020A ALA* 3.3 10.3 + - - +
1026A VAL* 4.0 18.8 - - + +
1029A ALA* 3.8 13.2 - - + -
1030A LEU* 3.8 23.3 - - + -
1033A MET* 3.8 28.7 - - - -
1088A GLN* 2.9 51.6 + - + +
1091A ALA* 3.8 27.4 - - + -
1092A GLU* 5.3 2.2 - - - +
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Residues in contact with GLU1018 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014A LEU* 3.3 21.1 + - - +
1015A LYS* 4.0 22.0 - - - +
1016A VAL 3.3 0.2 - - - -
1017A ILE* 1.4 77.5 - - - +
1019A LYS* 1.3 65.6 + - + +
1020A ALA 3.4 1.8 + - - +
1088A GLN* 4.4 11.0 + - - +
1092A GLU* 3.7 20.4 - - - +
1095A LYS* 3.0 35.2 + - - -
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Residues in contact with LYS1019 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015A LYS* 3.5 23.6 + - + +
1016A VAL* 3.2 6.0 + - - +
1018A GLU* 1.3 82.4 - - + +
1020A ALA* 1.4 62.8 + - - +
1021A ASP* 3.6 11.1 - - - +
1025A GLN* 4.4 4.4 + - - -
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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