Contacts of the helix formed by residues 1034 - 1051 (chain C) in PDB entry 2NB1
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 GLN1034 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1029C MET* 3.3 37.9 - - + +
1032C LEU* 2.8 45.2 + - + +
1033C PRO* 1.3 65.4 - - - +
1035C HIS* 1.3 62.4 + - - +
1036C THR* 3.4 3.8 + - - -
1037C ILE* 3.4 38.2 + - + +
1038C GLU* 3.2 20.3 + - - +
1122D MET* 5.5 6.5 - - - +
1125D VAL* 3.7 28.2 - - - +
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Residues in contact with HIS1035 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1033C PRO* 2.8 15.3 + - + +
1034C GLN* 1.3 69.6 - - - +
1036C THR* 1.3 65.3 + - - +
1038C GLU* 3.2 11.1 + - + +
1039C THR* 3.0 36.3 + - - -
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Residues in contact with THR1036 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034C GLN* 3.4 2.0 - - - -
1035C HIS* 1.3 77.9 - - - +
1037C ILE* 1.3 56.5 + - - +
1039C THR* 3.4 5.0 + - - -
1040C TYR* 2.8 37.3 + - + +
1121D LEU* 5.9 0.9 - - + -
1124D LEU* 5.6 9.0 - - + -
1125D VAL* 4.1 24.9 - - + -
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Residues in contact with ILE1037 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029C MET* 3.8 21.8 - - + -
1034C GLN* 3.4 51.5 + - + +
1035C HIS 3.3 0.6 - - - -
1036C THR* 1.3 76.2 - - - +
1038C GLU* 1.3 57.4 + - - +
1040C TYR* 3.5 7.4 - - + +
1041C ARG* 2.9 38.9 + - + +
1121D LEU* 3.5 49.8 - - + -
1125D VAL* 4.3 5.8 - - + -
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Residues in contact with GLU1038 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1034C GLN 3.2 12.7 + - - +
1035C HIS* 3.2 17.1 + - + +
1037C ILE* 1.3 76.7 - - - +
1039C THR* 1.3 66.2 + - - +
1041C ARG* 3.5 4.6 + - - +
1042C GLN* 3.1 41.6 + - + +
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Residues in contact with THR1039 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035C HIS* 3.0 34.5 + - - -
1036C THR* 4.1 3.8 - - - -
1038C GLU* 1.3 77.4 - - - +
1040C TYR* 1.3 56.2 + - - +
1042C GLN* 3.5 6.8 + - + +
1043C GLN* 2.8 40.1 + - + +
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Residues in contact with TYR1040 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036C THR* 2.8 28.6 + - + +
1037C ILE* 3.5 5.6 - - + +
1039C THR* 1.3 70.1 - - - +
1041C ARG* 1.3 78.0 + - - +
1043C GLN* 3.2 9.5 + - + +
1044C GLN* 3.0 53.6 + - + +
1120D GLU* 5.3 5.0 + - - -
1121D LEU* 3.7 40.2 - - + -
1124D LEU* 5.1 14.8 - - + -
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Residues in contact with ARG1041 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037C ILE* 2.9 25.1 + - + +
1038C GLU* 3.8 5.8 - - - +
1040C TYR* 1.3 89.4 - - - +
1042C GLN* 1.3 62.8 + - + +
1044C GLN* 3.5 8.0 + - - +
1045C GLN* 3.0 45.4 + - + +
1113D MET* 4.6 11.1 - - - +
1117D GLU* 3.5 39.3 + - - +
1121D LEU* 6.0 1.8 - - - -
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Residues in contact with GLN1042 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038C GLU* 3.1 34.9 + - + +
1039C THR* 3.5 9.2 - - + +
1041C ARG* 1.3 73.8 - - + +
1043C GLN* 1.3 65.8 + - - +
1045C GLN* 3.0 7.3 + - - +
1046C GLN* 2.8 62.3 + - - +
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Residues in contact with GLN1043 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1039C THR* 2.8 28.5 + - + +
1040C TYR* 3.7 9.6 - - + +
1042C GLN* 1.3 72.1 - - - +
1044C GLN* 1.3 57.0 + - - +
1046C GLN* 3.3 8.3 + - - +
1047C GLN* 2.8 54.0 + - + +
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Residues in contact with GLN1044 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040C TYR* 3.0 48.4 + - + +
1041C ARG* 3.9 8.0 + - - +
1043C GLN* 1.3 76.4 - - - +
1045C GLN* 1.3 64.1 + - + +
1047C GLN* 3.4 14.2 + - + +
1048C HIS* 3.2 23.6 + - - +
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Residues in contact with GLN1045 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041C ARG* 3.0 40.1 + - + +
1042C GLN* 3.0 9.7 + - - +
1044C GLN* 1.3 77.3 - - + +
1046C GLN* 1.3 70.7 + - - +
1048C HIS* 3.6 14.9 + - - +
1049C GLN* 3.9 7.1 + - - +
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Residues in contact with GLN1046 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1042C GLN* 2.8 69.6 + - - +
1043C GLN* 3.7 7.3 + - - +
1045C GLN* 1.3 80.4 - - - +
1047C GLN* 1.3 64.8 + - - +
1049C GLN* 3.0 20.4 + - - +
1050C HIS* 3.2 28.9 + - + -
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Residues in contact with GLN1047 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1043C GLN* 2.8 43.0 + - + +
1044C GLN* 3.4 15.2 + - + +
1046C GLN* 1.3 71.7 - - - +
1048C HIS* 1.3 63.0 + - - +
1050C HIS* 2.9 12.7 + - - +
1051C LEU* 2.9 27.9 + - + +
1058C ILE* 6.4 0.2 - - - +
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Residues in contact with HIS1048 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044C GLN 3.2 14.7 + - - +
1045C GLN* 3.9 9.2 - - - +
1046C GLN 3.3 0.4 + - - -
1047C GLN* 1.3 78.2 - - - +
1049C GLN* 1.3 60.5 + - - +
1051C LEU* 3.3 34.6 - - + +
1052C LEU 4.8 0.7 + - - -
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Residues in contact with GLN1049 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045C GLN 3.9 5.8 + - - +
1046C GLN* 3.0 13.9 + - - +
1048C HIS* 1.3 80.1 - - - +
1050C HIS* 1.3 72.2 + - + +
1052C LEU* 4.3 11.4 + - - +
1054C LYS* 5.9 0.7 - - - +
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Residues in contact with HIS1050 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046C GLN* 3.2 35.2 + - + +
1047C GLN* 2.9 10.3 + - - +
1049C GLN* 1.3 88.8 + - + +
1051C LEU* 1.3 56.7 + - - +
1052C LEU* 2.9 13.2 + - - +
1053C GLN* 3.3 9.2 + - - -
1054C LYS* 3.9 20.6 + - + +
1055C GLN* 5.2 13.2 + - - +
1058C ILE* 5.8 2.1 - - - +
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Residues in contact with LEU1051 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1047C GLN* 2.9 11.9 + - + +
1048C HIS* 3.3 38.8 - - + +
1049C GLN 3.4 0.8 - - - -
1050C HIS* 1.3 69.9 - - - +
1052C LEU* 1.3 53.7 + - - +
1053C GLN* 2.9 25.0 + - - +
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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