Contacts of the helix formed by residues 1029 - 1044 (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 THR1029 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006B SER 5.4 0.2 - - - +
1007B GLN* 2.7 59.9 + - - +
1027B LEU* 2.8 15.1 + - + +
1028B ASP* 1.3 81.7 + - - +
1030B PRO* 1.3 71.1 - - - +
1031B GLU* 3.5 13.2 - - - -
1032B SER* 2.9 20.1 + - - -
1033B ALA* 3.0 20.1 + - - +
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Residues in contact with PRO1030 (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 GLN* 4.5 3.6 - - - +
1028B ASP* 5.9 0.2 - - - +
1029B THR* 1.3 81.5 - - - +
1031B GLU* 1.3 80.5 + - - +
1033B ALA* 3.4 9.3 + - + +
1034B ARG* 3.0 41.0 + - - +
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Residues in contact with GLU1031 (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* 3.6 34.0 + - - +
1007B GLN* 3.3 19.8 - - + +
1008B VAL* 3.7 22.0 - - + +
1029B THR* 3.5 3.7 - - - +
1030B PRO* 1.3 96.4 - - - +
1032B SER* 1.3 65.5 + - - +
1034B ARG* 3.1 22.2 + - - +
1035B ILE* 3.0 23.4 + - - +
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Residues in contact with SER1032 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007B GLN 3.8 10.2 + - - -
1008B VAL* 4.6 4.8 + - - -
1025B PRO 3.6 7.4 + - - -
1026B GLU* 4.0 0.5 - - - -
1027B LEU* 3.3 32.8 + - - +
1029B THR* 2.9 22.3 + - - -
1031B GLU* 1.3 75.6 - - - +
1033B ALA* 1.3 59.5 + - - +
1035B ILE* 3.2 10.0 + - - +
1036B ILE* 2.8 49.8 + - - +
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Residues in contact with ALA1033 (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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1027B LEU 4.8 1.4 + - - +
1029B THR 3.0 13.1 + - - +
1030B PRO* 3.5 13.0 - - + +
1032B SER* 1.3 75.7 - - - +
1034B ARG* 1.3 56.6 + - - +
1036B ILE* 3.9 5.9 - - - +
1037B ALA* 3.0 29.3 + - - +
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Residues in contact with ARG1034 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952B LEU* 3.3 42.9 + - + +
953B SER* 3.9 23.5 + - - +
954B ASP* 4.6 7.9 + - - -
964B THR* 6.1 3.8 - - + -
966B PRO* 3.7 15.6 - - + +
1030B PRO* 3.0 19.8 + - - +
1031B GLU* 3.4 32.7 - - - +
1032B SER 3.1 0.2 - - - -
1033B ALA* 1.3 75.0 - - + +
1035B ILE* 1.3 65.8 + - - +
1037B ALA* 3.2 7.3 + - - +
1038B PHE* 3.0 18.5 + - - +
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Residues in contact with ILE1035 (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* 3.7 38.8 - - + +
952B LEU* 4.0 18.6 - - + +
985B LEU* 5.9 0.9 - - + -
994B LEU* 4.3 8.3 - - + -
1004B PHE* 4.2 4.0 - - + -
1008B VAL* 3.9 21.1 - - + -
1024B LEU* 3.9 27.6 - - + -
1031B GLU 3.0 15.0 + - - +
1032B SER* 3.3 17.5 - - - +
1034B ARG* 1.3 77.0 - - - +
1036B ILE* 1.3 69.1 + - + +
1038B PHE* 3.3 2.9 + - + +
1039B ILE* 3.0 42.6 + - + +
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Residues in contact with ILE1036 (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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1023B ASP* 5.7 1.8 - - - +
1024B LEU* 4.4 17.7 - - + +
1025B PRO 4.2 11.4 - - - +
1026B GLU* 3.8 38.4 - - + +
1032B SER* 2.8 37.9 + - - +
1033B ALA* 4.0 4.7 - - - +
1035B ILE* 1.3 84.3 - - + +
1037B ALA* 1.3 58.5 + - - +
1039B ILE* 4.1 7.0 - - + +
1040B SER* 3.0 31.7 + - - -
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Residues in contact with ALA1037 (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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963B ARG* 5.6 9.2 - - + +
964B THR 5.4 2.0 - - - +
965B ILE* 4.2 31.7 - - + +
1033B ALA 3.0 20.3 + - - +
1034B ARG* 3.3 7.9 - - - +
1035B ILE 3.1 0.2 - - - -
1036B ILE* 1.3 77.9 - - - +
1038B PHE* 1.3 64.4 + - - +
1040B SER* 3.2 8.4 + - - -
1041B TRP* 3.1 23.9 + - - +
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Residues in contact with PHE1038 (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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947B TYR* 3.6 41.3 - + + -
949B VAL* 4.2 18.4 - - + -
952B LEU* 4.3 4.5 - - + -
965B ILE* 4.7 1.3 - - + -
966B PRO* 3.3 37.8 - - + +
967B GLN* 4.5 1.3 - - - -
968B PRO* 3.5 32.3 - - + -
985B LEU* 4.3 4.3 - - + -
1034B ARG 3.0 7.3 + - - +
1035B ILE* 3.3 7.8 + - + +
1037B ALA* 1.3 77.5 - - - +
1039B ILE* 1.3 68.0 + - + +
1041B TRP* 3.3 26.2 + + - +
1042B LEU* 3.1 41.8 + - + +
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Residues in contact with ILE1039 (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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985B LEU* 4.1 23.1 - - + -
992B LEU* 4.0 13.5 - - + -
994B LEU* 5.4 0.4 - - + -
1024B LEU* 3.8 28.9 - - + -
1035B ILE* 3.0 26.3 + - + +
1036B ILE* 4.1 9.0 - - + +
1038B PHE* 1.3 80.0 - - + +
1040B SER* 1.3 60.1 + - - +
1042B LEU* 3.1 10.8 + - - +
1043B ARG* 2.9 57.5 + - - +
1052B LEU* 4.0 18.2 - - + -
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Residues in contact with SER1040 (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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963B ARG* 4.0 10.7 + - - -
1036B ILE* 3.0 20.4 + - - -
1037B ALA* 3.2 13.3 + - - -
1039B ILE* 1.3 77.1 - - - +
1041B TRP* 1.3 63.5 + - - +
1043B ARG* 3.7 12.9 + - - +
1044B GLU* 3.1 43.7 + - - +
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Residues in contact with TRP1041 (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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364B PRO* 5.8 8.3 - - + -
947B TYR* 5.7 2.2 - + - -
957B ALA* 5.7 4.1 - - + +
960B ILE* 5.8 3.0 - - + +
963B ARG* 4.9 1.3 - - - +
965B ILE* 3.6 37.4 - - + +
967B GLN* 3.5 37.7 - - - -
1037B ALA 3.1 14.8 + - - +
1038B PHE* 3.6 16.2 - + - +
1040B SER* 1.3 79.1 + - - +
1042B LEU* 1.3 82.4 + - + +
1044B GLU* 3.5 16.8 + - - -
1045B GLN* 2.9 65.4 + - + +
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Residues in contact with LEU1042 (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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947B TYR* 4.0 20.4 - - + +
985B LEU* 3.9 21.3 - - + -
987B ASP* 3.6 20.9 - - - +
992B LEU* 4.4 13.5 - - + -
1038B PHE* 3.1 44.1 + - + +
1039B ILE* 3.1 12.3 + - - +
1041B TRP* 1.3 92.7 - - + +
1043B ARG* 1.3 58.3 + - - +
1045B GLN* 3.0 30.0 + - + +
1046B ARG* 3.3 19.6 + - - +
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Residues in contact with ARG1043 (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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992B LEU* 4.3 4.9 - - + +
1023B ASP* 4.1 15.0 + - - -
1039B ILE* 2.9 34.6 - - + +
1040B SER* 3.7 14.8 - - - +
1042B LEU* 1.3 70.5 - - - +
1044B GLU* 1.3 55.1 + - - +
1045B GLN 3.1 5.2 - - - -
1046B ARG* 3.0 33.4 - - - +
1049B PHE* 3.4 43.6 - - + -
1050B PRO* 2.6 48.3 + - + +
1052B LEU* 3.7 24.9 - - - +
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Residues in contact with GLU1044 (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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963B ARG* 3.3 29.2 + - - -
1040B SER* 3.1 31.7 + - - +
1041B TRP* 3.7 14.1 - - - +
1042B LEU 3.1 0.4 - - - -
1043B ARG* 1.3 74.4 - - - +
1045B GLN* 1.3 64.1 + - - +
1046B ARG 3.1 11.7 + - - +
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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