Contacts of the helix formed by residues 1030 - 1040 (chain A) in PDB entry 4TU4
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1009A PHE* 3.5 10.1 - - - +
1011A LYS* 3.5 21.4 - - - +
1012A PRO* 3.4 24.8 - - + +
1028A PRO 5.6 0.2 - - - -
1029A MET* 1.3 78.7 - - - +
1031A LEU* 1.3 60.2 + - - +
1032A SER* 2.3 41.6 + - - -
1033A SER* 2.6 26.5 + - - -
1034A VAL* 3.0 27.2 + - - +
1056A ILE* 3.8 11.7 - - - -
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Residues in contact with LEU1031 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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997A THR* 3.9 20.4 - - + +
1000A LEU* 4.1 14.1 - - + +
1001A ALA* 3.9 36.3 - - + +
1006A PHE* 4.7 2.2 - - + +
1009A PHE* 2.8 31.5 + - + +
1010A THR* 4.2 9.4 - - + +
1030A ASP* 1.3 71.0 - - - +
1032A SER* 1.3 61.9 + - - +
1034A VAL* 3.4 6.0 + - + +
1035A ILE* 3.1 27.9 + - - +
1053A ILE* 4.3 16.2 - - + -
1056A ILE* 3.8 19.5 - - + -
1081A LEU* 4.4 17.0 - - + -
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Residues in contact with SER1032 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010A THR 3.3 17.7 + - - -
1011A LYS* 4.1 17.9 - - - -
1012A PRO* 3.4 15.4 - - - +
1030A ASP* 2.3 31.3 + - - -
1031A LEU* 1.3 72.4 - - - +
1033A SER* 1.3 57.1 + - - +
1035A ILE* 3.3 9.6 + - - +
1036A SER* 3.0 29.1 + - - -
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Residues in contact with SER1033 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012A PRO* 4.3 6.6 - - - +
1028A PRO 5.8 0.2 - - - -
1029A MET* 3.9 17.9 - - - -
1030A ASP* 2.6 29.9 + - - -
1032A SER* 1.3 77.1 + - - +
1034A VAL* 1.3 62.6 + - - +
1036A SER* 3.3 9.3 + - - -
1037A LYS* 2.9 35.9 + - - +
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Residues in contact with VAL1034 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997A THR* 3.9 12.8 - - + +
1029A MET* 3.9 17.0 - - + -
1030A ASP 3.0 20.5 + - - +
1031A LEU* 3.6 10.1 - - - +
1032A SER 3.3 0.2 - - - -
1033A SER* 1.3 76.8 - - - +
1035A ILE* 1.3 57.3 + - - +
1037A LYS* 3.1 3.8 + - - +
1038A ILE* 2.9 30.1 + - + +
1043A TYR* 3.6 22.6 - - + +
1049A TYR* 3.5 34.3 - - + +
1052A ASP* 4.3 7.4 - - + -
1053A ILE* 4.8 7.2 - - + -
1056A ILE* 4.3 9.4 - - + -
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Residues in contact with ILE1035 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994A ARG* 4.3 21.3 - - + +
997A THR* 3.6 29.8 - - + -
998A HIS* 4.8 4.9 - - + +
1031A LEU 3.1 15.6 + - - +
1032A SER* 3.3 10.9 + - - +
1034A VAL* 1.3 73.5 - - - +
1036A SER* 1.3 64.9 + - - +
1038A ILE* 3.2 14.5 + - + +
1039A ASP* 3.1 38.2 + - - +
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Residues in contact with SER1036 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032A SER 3.0 14.4 + - - -
1033A SER* 3.4 13.3 - - - -
1035A ILE* 1.3 77.7 - - - +
1037A LYS* 1.3 57.6 + - - +
1039A ASP* 3.2 9.1 + - - +
1040A LEU* 2.9 42.1 + - - +
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Residues in contact with LYS1037 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029A MET* 4.3 16.9 - - + +
1033A SER* 2.9 21.4 + - - +
1034A VAL 3.1 4.2 + - - +
1036A SER* 1.3 75.3 - - - +
1038A ILE* 1.3 67.0 + - - +
1040A LEU* 3.3 6.0 + - + -
1041A HIS 3.3 3.5 + - - -
1042A LYS* 3.0 57.6 + - + +
1043A TYR* 3.6 20.0 - - + +
1052A ASP* 2.7 34.8 + - - +
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Residues in contact with ILE1038 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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990A ARG* 3.2 57.5 - - + +
993A LEU* 3.7 38.6 - - + +
994A ARG* 3.8 20.4 - - + +
997A THR* 3.8 10.8 - - - +
1034A VAL* 2.9 23.3 + - + +
1035A ILE* 3.2 13.9 + - + +
1037A LYS* 1.3 74.8 - - - +
1039A ASP* 1.3 59.4 + - - +
1041A HIS* 2.9 17.3 + - - -
1042A LYS 5.0 0.2 - - - +
1043A TYR* 3.6 24.2 + - + +
1049A TYR* 4.4 0.2 - - + -
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Residues in contact with ASP1039 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994A ARG* 2.8 41.1 + - - +
1035A ILE* 3.1 28.9 + - - +
1036A SER* 3.6 10.1 - - - +
1038A ILE* 1.3 76.4 - - - +
1040A LEU* 1.3 59.0 - - + +
1041A HIS* 3.2 17.8 + - - -
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Residues in contact with LEU1040 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036A SER* 2.9 29.4 + - - +
1037A LYS* 3.9 10.3 - - + +
1038A ILE 3.2 0.4 - - - -
1039A ASP* 1.3 77.8 - - + +
1041A HIS* 1.3 70.4 + - - +
1042A LYS* 3.3 31.0 + - + +
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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