Contacts of the helix formed by residues 1030 - 1040 (chain B) in PDB entry 4TU6
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 ASP1030 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009B PHE* 3.5 12.6 - - - +
1010B THR 2.9 17.2 - - - +
1011B LYS 3.1 15.9 - - - +
1012B PRO* 3.5 25.5 - - + +
1029B MET* 1.3 79.4 - - - +
1031B LEU* 1.3 62.4 + - - +
1032B SER* 2.7 26.8 + - - -
1033B SER* 3.0 31.7 + - - -
1034B VAL* 3.1 14.0 + - - +
1056B ILE* 3.9 13.5 - - - -
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Residues in contact with LEU1031 (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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997B THR* 4.3 17.2 - - + +
1000B LEU* 4.4 13.5 - - + +
1001B ALA* 4.2 32.5 - - + +
1006B PHE* 4.4 14.1 - - + -
1009B PHE* 2.9 36.8 + - + +
1010B THR* 4.1 8.1 - - + -
1030B ASP* 1.3 73.1 - - - +
1032B SER* 1.3 57.1 + - - +
1034B VAL* 3.2 5.4 + - + +
1035B ILE* 2.9 33.9 + - - +
1053B ILE* 4.0 18.2 - - + -
1056B ILE* 3.8 19.3 - - + -
1081B LEU* 4.5 6.5 - - + -
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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
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1010B THR 3.3 15.2 + - - -
1012B PRO* 3.7 12.6 - - - +
1030B ASP* 2.7 22.5 + - - -
1031B LEU* 1.3 77.5 - - - +
1033B SER* 1.3 59.9 + - - +
1035B ILE* 3.5 10.4 + - - +
1036B SER* 3.0 26.7 + - - -
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Residues in contact with SER1033 (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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1012B PRO* 5.1 2.8 - - - +
1029B MET* 3.6 21.5 - - - -
1030B ASP* 3.0 24.8 + - - -
1032B SER* 1.3 78.7 + - - +
1034B VAL* 1.3 60.1 + - - +
1036B SER* 3.4 5.7 + - - +
1037B LYS* 2.9 38.1 + - - +
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Residues in contact with VAL1034 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997B THR* 4.2 12.3 - - + +
1029B MET* 3.9 14.1 - - - -
1030B ASP 3.1 16.1 + - - +
1031B LEU* 3.2 9.8 + - + +
1033B SER* 1.3 75.6 - - - +
1035B ILE* 1.3 56.5 - - - +
1037B LYS* 3.1 3.1 + - - +
1038B ILE* 2.9 30.0 + - + +
1043B TYR* 3.7 24.2 - - + +
1049B TYR* 3.7 30.7 - - + -
1052B ASP* 4.3 8.7 - - + -
1053B ILE* 4.4 8.5 - - + -
1056B ILE* 4.2 14.1 - - + -
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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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994B ARG* 5.9 5.4 - - + +
997B THR* 3.5 27.8 - - + +
998B HIS* 5.2 3.8 - - - +
1001B ALA* 4.5 18.4 - - + -
1031B LEU* 2.9 22.3 + - + +
1032B SER* 3.8 9.4 - - - +
1034B VAL* 1.3 77.0 - - - +
1036B SER* 1.3 63.6 + - - +
1038B ILE* 3.4 11.5 + - + +
1039B ASP* 3.3 30.2 + - - +
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Residues in contact with SER1036 (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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1032B SER 3.0 16.5 + - - -
1033B SER* 3.4 6.2 + - - -
1035B ILE* 1.3 75.9 - - - +
1037B LYS* 1.3 66.5 + - - +
1039B ASP* 3.3 8.8 + - - +
1040B LEU* 3.0 37.2 + - - +
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Residues in contact with LYS1037 (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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1029B MET* 4.0 17.5 - - + +
1033B SER* 2.9 23.2 + - - +
1034B VAL 3.1 5.4 + - - +
1036B SER* 1.3 74.3 - - - +
1038B ILE* 1.3 65.5 + - - +
1040B LEU* 3.2 8.2 + - + -
1042B LYS* 3.1 58.8 + - + +
1043B TYR* 3.6 22.0 - - + +
1052B ASP* 2.7 28.6 + - - +
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Residues in contact with ILE1038 (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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990B ARG* 3.4 47.9 - - + +
993B LEU* 3.7 24.7 - - + +
994B ARG* 3.9 19.1 - - + +
997B THR* 3.6 27.4 - - - +
1034B VAL* 2.9 23.8 + - + +
1035B ILE* 3.5 12.3 - - + +
1037B LYS* 1.3 76.1 - - - +
1039B ASP* 1.3 61.1 + - - +
1041B HIS* 3.0 18.0 + - - -
1042B LYS 5.0 0.4 - - - +
1043B TYR* 3.7 22.0 - - + +
1049B TYR* 4.4 1.1 - - + -
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Residues in contact with ASP1039 (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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990B ARG* 5.0 0.7 - - - +
994B ARG* 2.9 40.4 + - - +
1035B ILE* 3.3 23.9 + - - +
1036B SER* 3.3 10.5 + - - +
1038B ILE* 1.3 80.6 - - - +
1040B LEU* 1.3 60.3 + - + +
1041B HIS* 3.2 18.8 + - - -
1201B SO4 5.5 0.3 + - - -
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Residues in contact with LEU1040 (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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1036B SER* 3.0 28.2 + - - +
1037B LYS* 3.2 5.6 + - + +
1038B ILE 3.1 0.4 - - - -
1039B ASP* 1.3 79.8 - - + +
1041B HIS* 1.3 71.2 + - - +
1042B LYS* 3.2 26.5 + - + +
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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
------------------------------------------------------------
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