Contacts of the helix formed by residues 1007 - 1023 (chain A) in PDB entry 3NC0
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 ASP1007 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1004A LEU* 3.2 11.4 + - + +
1005A ASN 3.7 0.6 - - - -
1006A GLN* 1.3 80.0 - - - +
1008A ILE* 1.3 66.8 + - - +
1009A PRO* 3.2 19.3 - - - +
1010A ALA* 2.9 27.5 + - + +
1011A PHE* 2.8 20.1 + - - +
1045A ALA* 5.9 6.3 - - + +
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Residues in contact with ILE1008 (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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940A THR* 4.6 9.9 - - + +
943A ALA* 4.7 2.9 - - + +
944A SER* 3.3 44.6 - - - +
947A ALA* 4.8 10.8 - - + -
1006A GLN 4.1 0.4 - - - -
1007A ASP* 1.3 71.0 - - - +
1009A PRO* 1.3 62.4 - - + +
1011A PHE* 3.0 8.8 + - - +
1012A LYS* 2.7 53.6 + - + +
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Residues in contact with PRO1009 (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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1007A ASP* 3.2 18.8 - - - +
1008A ILE* 1.3 98.3 - - + +
1010A ALA* 1.3 61.2 + - - +
1012A LYS* 3.2 20.5 + - + +
1013A GLU* 3.2 18.6 + - - +
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Residues in contact with ALA1010 (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 LEU* 4.0 23.2 - - + +
1007A ASP* 2.9 29.4 + - + +
1009A PRO* 1.3 76.7 - - - +
1011A PHE* 1.3 67.5 + - - +
1012A LYS 3.2 0.2 + - - -
1013A GLU* 3.2 10.3 + - - +
1014A HIS* 3.1 21.7 + - - +
1038A ARG* 5.1 2.0 + - - +
1045A ALA* 6.0 1.6 - - + -
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Residues in contact with PHE1011 (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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943A ALA* 3.3 43.1 - - + -
946A LEU* 3.6 19.1 - - + -
947A ALA* 3.6 23.8 - - + -
950A PHE* 3.9 2.9 - + - -
1000A GLY 4.6 0.4 - - - -
1001A LEU* 3.7 48.2 - - + -
1004A LEU* 3.6 33.3 - - + +
1007A ASP 2.8 15.9 + - - +
1008A ILE* 3.3 14.8 - - - +
1010A ALA* 1.3 72.5 - - - +
1012A LYS* 1.3 62.8 + - - +
1014A HIS* 3.2 8.5 - - + +
1015A LEU* 3.1 32.4 + - + +
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Residues in contact with LYS1012 (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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939A LEU* 4.0 31.1 - - + +
940A THR* 2.9 29.6 + - + +
943A ALA* 3.6 23.6 - - + -
1008A ILE* 2.7 33.8 + - + +
1009A PRO* 3.2 14.0 - - + +
1011A PHE* 1.3 69.8 - - - +
1013A GLU* 1.3 70.5 + - - +
1015A LEU* 2.8 18.3 + - - +
1016A ARG* 2.9 18.3 + - - +
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Residues in contact with GLU1013 (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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183A SER* 4.7 8.5 + - - -
188A GLN* 3.2 47.5 + - - +
1009A PRO 3.2 13.0 + - - +
1010A ALA* 3.2 9.6 + - - +
1012A LYS* 1.3 80.1 - - - +
1014A HIS* 1.3 61.0 + - - +
1016A ARG* 2.9 29.4 + - - +
1017A ASP* 2.5 32.7 + - - +
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Residues in contact with HIS1014 (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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188A GLN* 4.8 0.6 + - - -
996A LEU* 4.2 6.7 - - + -
997A PHE* 2.8 72.2 + + - -
1000A GLY* 3.9 11.7 - - - -
1001A LEU* 3.8 18.4 - - + -
1004A LEU* 3.5 26.0 - - + +
1010A ALA 3.1 6.2 + - - +
1011A PHE* 3.2 11.9 - + - +
1013A GLU* 1.3 74.2 - - - +
1015A LEU* 1.3 62.6 + - + +
1017A ASP* 3.1 19.3 + - - +
1018A PHE 3.2 9.7 + - - -
1038A ARG* 4.0 19.9 + - - +
1042A LEU* 5.2 3.6 - - + -
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Residues in contact with LEU1015 (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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927A PHE* 5.5 0.7 - - + -
930A VAL* 4.0 28.7 - - + +
939A LEU* 4.4 15.7 - - + +
942A HIS* 4.7 4.0 - - + -
943A ALA* 3.4 43.1 - - + +
946A LEU* 4.4 18.4 - - + -
997A PHE* 3.9 25.1 - - + -
1001A LEU* 5.0 2.5 - - + -
1011A PHE* 3.1 17.9 + - + +
1012A LYS* 2.8 13.1 + - - +
1014A HIS* 1.3 75.6 - - + +
1016A ARG* 1.3 61.8 + - - +
1018A PHE* 3.0 14.2 + - - +
1019A LEU* 3.1 17.9 + - + +
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Residues in contact with ARG1016 (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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183A SER* 3.5 14.3 + - - -
184A GLY* 3.0 42.5 - - - +
939A LEU* 3.5 38.9 - - + +
1012A LYS* 2.9 20.0 + - - +
1013A GLU* 2.9 36.5 + - - +
1015A LEU* 1.3 74.8 - - - +
1017A ASP* 1.3 61.6 + - - +
1019A LEU* 3.4 15.5 + - + +
1020A VAL* 3.4 22.9 + - - +
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Residues in contact with ASP1017 (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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186A ILE 5.3 0.7 - - - -
187A THR* 2.9 17.2 - - - +
188A GLN* 2.5 49.6 + - - +
189A VAL* 5.9 0.2 - - - +
1013A GLU* 2.5 30.6 + - - +
1014A HIS* 3.4 12.3 + - + +
1016A ARG* 1.3 76.7 - - - +
1018A PHE* 1.3 60.6 + - - +
1019A LEU 3.1 0.2 - - - -
1020A VAL* 3.0 23.1 + - - +
1021A GLN* 3.1 21.0 + - + +
1038A ARG* 5.8 1.7 + - - -
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Residues in contact with PHE1018 (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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927A PHE* 6.0 0.4 - + - -
930A VAL* 6.3 1.3 - - + -
931A THR* 4.3 17.0 - - + -
982A LEU* 4.1 35.2 - - + -
986A PHE* 4.9 3.8 - + - -
989A LEU* 3.6 31.6 - - + -
993A GLN* 5.1 2.5 - - + -
994A VAL* 4.8 8.3 - - + -
997A PHE* 3.3 61.0 - + + -
1014A HIS 3.2 1.6 + - - -
1015A LEU 3.0 6.7 + - - +
1017A ASP* 1.3 78.6 - - - +
1019A LEU* 1.3 61.4 + - + +
1020A VAL 3.2 0.2 - - - -
1021A GLN* 3.9 15.8 - - + +
1022A ILE* 3.0 46.2 + - + +
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Residues in contact with LEU1019 (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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930A VAL* 3.0 38.4 - - + +
931A THR* 3.7 19.5 - - + -
932A ASP 5.9 1.1 - - - +
936A THR* 5.4 12.6 - - + -
939A LEU* 4.7 14.8 - - + -
1015A LEU 3.3 15.5 - - - +
1016A ARG* 3.6 18.4 - - + +
1017A ASP 3.1 0.6 - - - -
1018A PHE* 1.3 80.9 - - + +
1020A VAL* 1.3 59.5 - - - +
1022A ILE* 3.2 25.2 - - + +
1023A LYS* 3.4 24.0 - - - +
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Residues in contact with VAL1020 (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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184A GLY 3.1 29.2 - - - +
185A GLN* 3.8 20.2 - - - +
186A ILE* 4.0 6.7 - - - +
187A THR* 3.8 27.1 - - + +
1016A ARG 3.4 8.4 + - - +
1017A ASP* 3.0 10.5 + - - +
1019A LEU* 1.3 79.2 - - - +
1021A GLN* 1.3 66.6 + - + +
1022A ILE 3.2 0.2 - - - -
1023A LYS* 3.3 17.5 + - + +
1024A GLU* 3.5 32.4 + - - +
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Residues in contact with GLN1021 (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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187A THR* 4.4 13.3 - - + +
989A LEU* 3.5 12.5 - - + +
993A GLN* 3.2 44.5 + - - +
1017A ASP* 3.1 18.9 + - - +
1018A PHE* 3.6 14.1 + - + +
1019A LEU 3.5 0.2 - - - -
1020A VAL* 1.3 82.8 - - + +
1022A ILE* 1.3 55.1 + - - +
1024A GLU* 2.6 34.9 - - - +
1033A LEU* 3.4 37.0 - - - +
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Residues in contact with ILE1022 (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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931A THR* 3.6 29.6 - - - +
933A THR* 6.0 2.7 - - + -
986A PHE* 3.9 37.0 - - + -
988A HIS* 3.1 28.4 + - - -
989A LEU* 4.3 5.8 - - + -
1018A PHE* 3.0 39.9 - - + +
1019A LEU* 3.2 24.9 - - + +
1021A GLN* 1.3 72.5 - - - +
1023A LYS* 1.3 72.4 + - + +
1024A GLU* 3.0 5.1 - - - -
1025A PHE* 5.7 1.9 - - - -
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Residues in contact with LYS1023 (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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88A LYS 4.5 1.2 - - - +
89A THR* 4.2 19.1 + - - +
184A GLY 5.7 2.8 + - - -
933A THR* 3.8 30.3 - - + +
1019A LEU* 3.4 25.6 - - - +
1020A VAL* 3.3 11.3 + - + +
1022A ILE* 1.3 83.6 - - + +
1024A GLU* 1.3 61.9 + - + +
1025A PHE* 4.8 3.0 - - - -
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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