Contacts of the helix formed by residues 1030 - 1041 (chain B) in PDB entry 4UN5
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 GLY1030 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1031B LYS* 1.3 65.6 + - - +
1032B ALA* 3.2 9.5 - - - +
1033B THR* 2.5 32.9 + - - +
1034B ALA* 3.6 5.4 + - - +
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Residues in contact with LYS1031 (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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1030B GLY* 1.3 76.8 - - - +
1032B ALA* 1.3 60.0 + - - +
1034B ALA* 3.1 13.4 + - + +
1035B LYS* 2.9 28.6 + - - +
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Residues in contact with ALA1032 (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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910B GLU* 3.6 13.0 - - + -
911B LEU* 3.5 45.8 - - + +
914B ALA* 3.3 14.8 - - - +
1030B GLY 3.2 6.4 - - - +
1031B LYS* 1.3 78.7 - - - +
1033B THR* 1.3 57.3 + - - +
1035B LYS* 3.3 2.9 + - - -
1036B TYR* 2.9 26.0 + - - +
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Residues in contact with THR1033 (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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910B GLU* 3.6 28.2 - - + +
1030B GLY* 2.5 31.2 + - - +
1032B ALA* 1.3 77.5 - - + +
1034B ALA* 1.3 57.7 + - - +
1036B TYR* 3.3 8.4 - - - +
1037B PHE* 2.9 32.6 + - - +
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Residues in contact with ALA1034 (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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1030B GLY 4.1 4.7 - - - +
1031B LYS* 3.1 23.5 + - + +
1033B THR* 1.3 82.6 + - - +
1035B LYS* 1.3 56.9 + - - +
1037B PHE* 3.9 3.6 - - - +
1038B PHE* 2.9 32.4 + - - +
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Residues in contact with LYS1035 (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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911B LEU* 6.0 6.6 - - + +
914B ALA* 3.9 16.2 - - + +
915B GLY* 6.2 0.4 - - - -
918B LYS* 3.8 18.1 - - + +
1031B LYS 2.9 12.7 + - - +
1032B ALA* 3.7 8.5 - - - +
1034B ALA* 1.3 75.2 - - - +
1036B TYR* 1.3 62.5 + - - +
1038B PHE* 3.5 6.7 - - + +
1039B TYR* 2.9 64.5 + - + -
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Residues in contact with TYR1036 (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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846B PHE* 4.2 16.0 - + - -
910B GLU* 4.9 8.5 - - + +
913B LYS* 3.6 39.0 - - + +
914B ALA* 3.6 16.7 - - + +
917B ILE* 3.5 32.7 - - + +
1032B ALA 2.9 15.4 + - - +
1033B THR* 3.3 13.9 - - - +
1035B LYS* 1.3 77.5 - - - +
1037B PHE* 1.3 67.4 + + + +
1039B TYR* 3.3 2.2 + - - +
1040B SER* 2.9 36.7 + - - -
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Residues in contact with PHE1037 (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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1033B THR 2.9 18.2 + - - +
1034B ALA* 4.2 3.6 - - - +
1036B TYR* 1.3 82.8 - + + +
1038B PHE* 1.3 63.6 + - - +
1040B SER* 4.3 3.1 - - - -
1041B ASN* 2.3 63.7 + - + +
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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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1001B TYR* 5.5 10.3 - + - -
1004B LEU* 4.1 18.6 - - + -
1034B ALA 2.9 19.8 + - - +
1035B LYS* 3.5 7.6 - - + +
1036B TYR 3.2 0.2 - - - -
1037B PHE* 1.3 81.1 - - - +
1039B TYR* 1.3 102.0 + + - +
1041B ASN* 3.4 2.8 + - - +
1042B ILE* 3.3 43.2 + - + -
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Residues in contact with TYR1039 (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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914B ALA 4.7 2.5 - - - -
917B ILE* 3.8 18.8 - - + +
918B LYS* 3.3 53.2 + - + -
921B LEU* 3.5 25.5 - - + +
922B VAL* 5.3 5.6 - - + -
1004B LEU* 4.6 13.6 - - + +
1007B GLU* 4.0 15.8 + - + +
1008B PHE* 5.7 4.0 - + - -
1035B LYS* 2.9 50.5 + - + +
1036B TYR* 5.3 0.2 - - - -
1038B PHE* 1.3 103.2 - + - +
1040B SER* 1.3 61.6 + - - +
1041B ASN 3.2 0.2 - - - -
1042B ILE* 3.4 27.0 - - + +
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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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917B ILE* 4.0 23.7 - - - +
1036B TYR* 2.9 26.5 + - - -
1037B PHE* 4.1 2.9 - - - -
1038B PHE 3.2 0.4 - - - -
1039B TYR* 1.3 77.9 - - - +
1041B ASN* 1.3 74.1 + - - +
1042B ILE* 3.6 0.7 - - - -
1044B ASN* 4.8 2.1 + - - -
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Residues in contact with ASN1041 (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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1001B TYR* 5.3 2.6 + - - -
1037B PHE* 2.3 74.9 + - + +
1038B PHE* 3.4 3.8 + - - +
1039B TYR 3.2 0.2 - - - -
1040B SER* 1.3 88.3 + - - +
1042B ILE* 1.3 62.4 + - - +
1043B MET 3.2 3.7 + - - +
1044B ASN* 3.2 42.6 + - + +
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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