Contacts of the helix formed by residues 1001 - 1008 (chain B) in PDB entry 2NUP
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 THR1001 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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950B ASP* 3.8 19.3 - - + +
981B ASP 3.4 17.5 + - - +
999B ASN 3.5 1.8 + - - -
1000B CYS* 1.3 78.8 - - - +
1002B GLN* 1.3 64.1 + - - +
1003B ASN* 3.1 18.4 + - - +
1004B PHE* 3.5 22.0 + - + +
1005B LEU* 3.4 20.1 + - - +
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Residues in contact with GLN1002 (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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1000B CYS 3.8 0.8 + - - -
1001B THR* 1.3 69.7 + - - +
1003B ASN* 1.3 67.6 + - - +
1004B PHE 3.1 1.8 - - - -
1005B LEU* 3.0 24.8 + - + +
1006B SER* 3.1 18.6 + - - -
1011B VAL 4.5 1.0 - - - +
1012B GLN* 2.8 45.0 + - - +
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Residues in contact with ASN1003 (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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950B ASP 5.6 3.8 + - - -
1001B THR* 3.1 8.8 + - - +
1002B GLN* 1.3 77.7 - - - +
1004B PHE* 1.3 59.1 + - - +
1006B SER* 4.5 4.5 - - - -
1007B GLN* 3.0 48.1 + - - +
1008B VAL* 4.7 0.6 - - - +
1031B GLU* 3.6 36.8 + - - +
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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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949B VAL* 4.0 8.1 - - + -
950B ASP* 3.6 35.4 - - + +
983B ALA* 3.5 24.0 - - + -
994B LEU* 4.6 10.3 - - + -
996B VAL* 4.4 6.5 - - + -
1000B CYS* 3.5 20.0 - - - -
1001B THR* 3.5 24.4 + - + +
1002B GLN 3.1 0.6 - - - -
1003B ASN* 1.3 79.7 - - - +
1005B LEU* 1.3 60.3 + - - +
1008B VAL* 3.1 47.6 + - + +
1009B LEU* 3.0 47.5 + - + -
1035B ILE* 4.2 9.9 - - + -
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Residues in contact with LEU1005 (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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1000B CYS* 4.5 17.0 - - + +
1001B THR 3.4 15.0 + - - +
1002B GLN* 3.0 22.8 + - + +
1004B PHE* 1.3 78.1 - - - +
1006B SER* 1.3 51.8 + - - +
1009B LEU* 3.1 15.6 + - + +
1010B GLY 2.7 31.7 + - - -
1011B VAL* 2.9 19.0 + - + +
1013B ASN* 3.6 12.6 - - - +
1014B TYR* 3.4 31.9 - - + +
1017B ILE* 3.6 34.3 - - + -
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Residues in contact with SER1006 (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 GLN* 3.1 15.8 + - - -
1003B ASN* 3.9 1.9 + - - -
1005B LEU* 1.3 79.6 - - - +
1007B GLN* 1.3 77.7 + - - +
1010B GLY* 3.3 18.2 + - - -
1011B VAL 3.0 16.6 + - - +
1012B GLN* 3.6 20.8 + - - +
1027B LEU* 3.8 5.4 - - - +
1029B THR* 5.4 0.5 - - - +
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Residues in contact with GLN1007 (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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1003B ASN* 3.0 31.9 + - - +
1006B SER* 1.3 91.6 + - - +
1008B VAL* 1.3 60.6 + - - +
1027B LEU* 3.2 11.0 - - - +
1029B THR* 2.7 52.6 + - + +
1030B PRO* 4.5 2.6 - - - +
1031B GLU* 3.3 28.2 - - + +
1032B SER* 3.8 1.4 - - - -
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Residues in contact with VAL1008 (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 ASN* 5.7 0.2 - - - +
1004B PHE* 3.1 58.7 + - + +
1007B GLN* 1.3 83.3 - - + +
1009B LEU* 1.3 62.6 + - - +
1010B GLY 3.5 0.4 - - - -
1024B LEU* 4.3 11.1 - - + +
1025B PRO* 3.7 16.1 - - - +
1027B LEU* 3.6 8.0 - - - +
1031B GLU* 3.7 31.6 - - + +
1032B SER* 4.9 3.9 + - - -
1035B ILE* 3.9 26.9 - - + -
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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