Contacts of the helix formed by residues 1023 - 1039 (chain A) in PDB entry 4FUL
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 HIS1023 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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854A ILE* 3.6 37.9 - - + +
857A THR* 4.4 13.6 + - + -
858A GLU* 4.5 4.2 + - - -
1019A ALA 3.4 18.2 - - - -
1020A LEU 3.0 10.6 + - - +
1022A HIS* 1.3 93.1 + - + +
1024A THR* 1.4 63.5 + - - +
1025A ASN 3.5 2.0 - - - -
1026A LEU* 3.4 23.2 + - + +
1027A LEU* 3.0 23.7 + - - +
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Residues in contact with THR1024 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A ASP* 5.5 1.1 - - + -
1020A LEU 3.4 1.7 + - - -
1021A ARG* 2.6 33.4 + - - +
1022A HIS 3.7 0.6 - - - -
1023A HIS* 1.4 76.4 - - - +
1025A ASN* 1.4 61.3 + - - +
1027A LEU* 3.1 5.2 + - - +
1028A ILE* 2.8 48.5 + - + +
1055A LEU* 3.9 23.5 + - + +
1057A VAL* 3.7 29.6 - - + +
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Residues in contact with ASN1025 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A THR 5.0 6.7 + - - -
562A ASP* 4.4 5.2 - - - +
563A PRO* 3.5 37.2 - - + +
587A LYS* 4.5 25.2 - - - +
591A LYS* 5.8 1.4 - - - +
625A GLY* 5.0 2.7 - - - -
629A GLN* 4.4 12.0 + - - +
1023A HIS 3.5 0.4 - - - -
1024A THR* 1.4 83.1 - - - +
1026A LEU* 1.4 56.8 + - - +
1028A ILE* 3.1 5.5 + - - +
1029A ILE* 2.9 31.7 + - - +
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Residues in contact with LEU1026 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A VAL* 3.6 28.0 - - + -
625A GLY* 3.7 25.0 - - - +
628A MET* 5.2 0.9 - - + -
659A TYR* 3.8 20.9 - - + +
850A ILE* 4.4 6.3 - - + -
854A ILE* 4.3 15.0 - - + -
1023A HIS* 3.4 34.6 + - + +
1024A THR 3.3 0.4 - - - -
1025A ASN* 1.4 74.1 - - - +
1027A LEU* 1.4 59.1 + - - +
1029A ILE* 3.3 4.4 - - + +
1030A LEU* 3.0 54.3 + - + +
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Residues in contact with LEU1027 (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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847A ILE* 4.4 12.8 - - + -
850A ILE* 5.2 1.3 - - + -
851A MET* 4.0 31.0 - - + -
854A ILE* 4.4 14.4 - - + -
941A VAL* 4.7 2.9 - - + -
1020A LEU* 3.4 51.8 - - + +
1023A HIS* 3.0 14.8 + - + +
1024A THR 3.6 3.8 - - - +
1026A LEU* 1.4 75.5 - - + +
1028A ILE* 1.4 60.8 + - - +
1030A LEU* 4.0 12.3 - - + +
1031A PHE* 3.0 26.7 + - - +
1051A ILE* 3.7 11.1 - - + +
1055A LEU* 4.0 20.0 - - + -
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Residues in contact with ILE1028 (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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562A ASP* 4.1 16.2 - - + +
563A PRO* 3.8 37.0 - - + -
564A LEU* 3.8 23.6 - - + +
1024A THR* 2.8 38.6 + - + +
1025A ASN* 3.1 8.3 + - - +
1027A LEU* 1.4 73.0 - - - +
1029A ILE* 1.4 57.1 + - + +
1031A PHE* 3.8 1.7 - - - +
1032A SER* 3.1 30.8 + - - +
1048A ILE* 5.1 0.3 - - - +
1051A ILE* 4.0 21.8 - - + +
1052A ARG* 4.4 16.2 - - + +
1055A LEU* 4.6 4.5 - - + -
1057A VAL* 4.7 0.7 - - + -
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Residues in contact with ILE1029 (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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563A PRO* 5.5 2.9 - - + +
625A GLY* 3.4 25.8 - - - +
628A MET* 3.8 19.3 - - + +
629A GLN* 3.7 36.1 - - + +
632A ASP* 3.4 27.6 - - + +
1025A ASN 2.9 14.2 + - - +
1026A LEU* 3.3 15.3 - - + +
1028A ILE* 1.4 75.5 - - + +
1030A LEU* 1.3 64.3 + - + +
1032A SER* 3.1 24.6 + - - +
1033A MET* 3.1 31.2 + - + +
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Residues in contact with LEU1030 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A MET* 3.7 30.1 - - + -
659A TYR* 4.3 3.6 - - + -
662A GLN* 3.3 31.1 - - + +
847A ILE* 4.1 19.4 - - + +
850A ILE* 3.8 37.7 - - + -
1026A LEU* 3.0 41.1 + - + +
1027A LEU* 4.0 12.1 - - + +
1029A ILE* 1.3 78.8 - - + +
1031A PHE* 1.4 56.7 + - - +
1033A MET* 3.7 2.9 - - - +
1034A MET* 2.9 27.4 + - - +
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Residues in contact with PHE1031 (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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847A ILE* 4.5 2.4 - - - +
942A LEU* 3.3 49.6 - - + -
1027A LEU 3.0 18.6 + - - +
1028A ILE 3.8 3.4 - - - +
1030A LEU* 1.4 74.9 - - - +
1032A SER* 1.3 61.2 + - - +
1034A MET* 3.4 30.4 + - + +
1035A LEU* 2.9 59.0 + - + +
1047A ASP 3.5 15.5 - - - -
1048A ILE* 4.1 6.1 - - + -
1050A TYR* 4.7 8.1 - + + -
1051A ILE* 3.6 37.9 - - + -
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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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1028A ILE* 3.1 15.6 + - - +
1029A ILE* 3.1 25.8 + - - +
1031A PHE* 1.3 75.6 - - - +
1033A MET* 1.3 62.3 + - - +
1035A LEU* 3.3 6.4 + - - +
1036A MET* 3.0 40.7 + - - +
1048A ILE* 3.5 35.6 - - - +
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Residues in contact with MET1033 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A MET* 3.2 45.3 - - + +
631A LEU* 3.8 7.2 - - + +
632A ASP* 3.7 26.7 - - + +
662A GLN* 4.2 22.0 - - + +
665A GLN* 6.4 1.3 - - + -
666A ALA* 4.2 13.7 - - + -
669A PHE* 4.3 12.3 - - + -
1029A ILE* 3.1 34.0 + - + +
1030A LEU* 3.7 5.2 - - - +
1032A SER* 1.3 80.3 + - - +
1034A MET* 1.3 55.9 + - - +
1036A MET* 3.3 8.5 + - + +
1037A THR* 2.9 38.6 + - + +
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Residues in contact with MET1034 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A GLN* 4.2 0.8 + - - +
843A LEU* 3.8 31.2 - - + -
844A ILE* 3.4 34.8 - - + -
847A ILE* 3.7 21.3 - - + -
942A LEU* 4.8 1.3 - - + +
1030A LEU 2.9 18.6 + - - +
1031A PHE* 3.5 39.9 - - + +
1033A MET* 1.3 76.5 - - - +
1035A LEU* 1.3 65.5 + - + +
1037A THR* 4.2 5.4 - - - -
1038A GLY 2.8 27.7 + - - -
1039A MET* 3.4 19.3 - - + +
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Residues in contact with LEU1035 (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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498A ASN* 5.3 0.3 - - - +
1031A PHE* 2.9 53.9 + - + +
1032A SER 3.3 4.7 + - - +
1034A MET* 1.3 81.7 - - + +
1036A MET* 1.3 59.7 + - - +
1039A MET* 3.3 42.5 + - + +
1043A THR* 2.9 28.6 + - + -
1047A ASP* 3.6 32.8 - - + +
1048A ILE* 3.7 14.4 - - + +
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Residues in contact with MET1036 (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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391A GLN* 5.2 5.4 - - - +
497A PHE 4.6 4.9 - - - +
498A ASN* 3.8 19.1 + - - +
499A ALA* 2.9 37.5 + - - +
502A LEU* 6.5 0.2 - - + -
632A ASP* 4.5 11.0 - - + +
633A CYS* 3.6 29.4 - - - -
669A PHE* 3.6 29.6 - - + -
1029A ILE* 6.0 0.2 - - + -
1032A SER* 3.0 28.7 + - - +
1033A MET* 3.5 7.9 - - + +
1034A MET 3.2 0.2 - - - -
1035A LEU* 1.3 77.2 - - - +
1037A THR* 1.3 58.8 + - - +
1039A MET 4.7 2.0 - - - +
1043A THR* 4.3 5.3 - - - -
1048A ILE* 4.9 14.8 - - - -
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Residues in contact with THR1037 (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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499A ALA* 4.1 9.2 - - + -
665A GLN* 3.3 44.5 + - + +
668A LYS* 3.1 30.2 + - + +
669A PHE* 3.5 32.1 - - + -
702A GLU* 4.7 1.4 - - - +
839A ARG* 5.3 4.9 + - - -
843A LEU* 4.2 4.3 - - - +
1033A MET* 2.9 27.5 + - + +
1034A MET* 4.1 3.3 + - - -
1036A MET* 1.3 73.5 - - - +
1038A GLY* 1.3 60.9 + - - +
1039A MET 3.8 2.2 - - - -
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Residues in contact with GLY1038 (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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837A ASP* 4.0 5.5 - - - +
839A ARG* 4.9 14.0 + - - +
840A GLN* 3.7 15.7 - - - +
843A LEU* 3.4 25.8 - - - -
1034A MET 2.8 16.2 + - - -
1037A THR* 1.3 74.5 + - - +
1039A MET* 1.3 68.1 + - - +
1040A PRO* 3.7 3.3 - - - +
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Residues in contact with MET1039 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A ASN* 4.1 8.5 + - - +
500A ASP* 5.4 0.5 - - - +
840A GLN* 3.6 31.4 - - + +
843A LEU* 4.9 1.3 - - + -
844A ILE* 6.1 1.1 - - + -
968A ILE 5.9 4.5 - - - +
1034A MET* 3.4 44.6 - - + +
1035A LEU* 3.3 42.6 + - + +
1036A MET 4.7 3.8 - - - +
1037A THR 4.9 1.2 - - - -
1038A GLY* 1.3 82.2 + - - +
1040A PRO* 1.4 71.5 - - + +
1041A GLN* 3.4 18.8 - - + +
1043A THR* 4.8 2.5 - - - +
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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
------------------------------------------------------------
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