Contacts of the helix formed by residues 1015 - 1034 (chain D) in PDB entry 4XHT
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 PHE1015 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1010D LEU* 3.0 50.9 + - + +
1011D HIS 4.2 0.2 + - - -
1013D GLU* 3.9 23.1 - - + -
1014D GLY* 1.3 78.7 - - - +
1016D SER* 1.3 64.1 + - - +
1017D ILE 3.3 2.9 - - - -
1018D PRO* 3.2 10.5 - - + +
1019D LEU* 2.9 28.5 + - + +
1050D GLU* 5.7 1.3 - - + -
1053D GLU 5.6 0.7 - - - -
1054D ALA* 4.1 30.5 - - + -
1057D ASN* 3.5 36.6 - - + -
1059D GLN* 4.7 4.5 - - - -
1060D PHE* 4.3 9.0 - + + -
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Residues in contact with SER1016 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011D HIS* 2.7 45.3 + - - +
1014D GLY 3.4 5.0 + - - -
1015D PHE* 1.3 76.2 - - - +
1017D ILE* 1.3 61.5 + - - +
1019D LEU* 3.3 1.6 + - - +
1020D LEU* 2.9 40.7 + - - +
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Residues in contact with ILE1017 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014D GLY 5.0 0.2 + - - -
1016D SER* 1.3 80.6 - - - +
1018D PRO* 1.3 73.1 - - + +
1020D LEU* 3.1 17.9 + - + +
1021D TRP* 3.0 20.5 + - + +
1048D THR* 5.8 0.9 - - - +
1050D GLU* 4.0 21.5 + - + +
1051D ASN* 4.2 11.4 - - - +
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Residues in contact with PRO1018 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015D PHE* 3.2 19.5 - - + +
1017D ILE* 1.3 95.5 - - + +
1019D LEU* 1.3 57.2 + - - +
1021D TRP* 3.3 8.1 + - + +
1022D LEU* 2.9 29.3 + - - +
1050D GLU* 3.6 28.5 - - + +
1051D ASN* 3.3 22.4 - - - +
1054D ALA* 3.6 30.5 - - + -
1060D PHE* 3.8 12.1 - - + -
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Residues in contact with LEU1019 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007D GLY* 3.6 25.6 - - - +
1010D LEU* 3.7 10.3 - - + -
1011D HIS* 3.6 39.3 - - + +
1015D PHE* 2.9 22.7 + - + +
1016D SER 3.6 3.6 - - - +
1018D PRO* 1.3 75.5 - - - +
1020D LEU* 1.3 58.7 + - - +
1022D LEU* 3.4 7.7 + - + +
1023D GLN* 2.9 28.5 + - - +
1060D PHE* 3.8 14.8 - - + -
1063D LEU* 3.5 31.9 - - + -
1098D LEU* 4.3 20.9 - - + +
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Residues in contact with LEU1020 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011D HIS* 5.2 6.1 - - + -
1016D SER* 2.9 29.6 + - - +
1017D ILE* 3.1 18.4 + - + +
1019D LEU* 1.3 73.4 - - - +
1021D TRP* 1.3 64.7 + - - +
1023D GLN* 3.4 24.2 + - - +
1024D ASN* 3.0 33.1 + - - +
1098D LEU* 5.1 7.2 - - + -
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Residues in contact with TRP1021 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017D ILE* 3.0 11.7 + - + +
1018D PRO* 3.5 20.4 - - + +
1020D LEU* 1.3 74.2 - - - +
1022D LEU* 1.3 72.7 + - + +
1024D ASN* 3.2 9.3 + - + +
1025D CYS* 3.0 44.9 + - - -
1044D LEU* 4.3 12.1 - - + -
1045D VAL 3.6 17.9 + - - -
1046D PRO* 3.6 36.7 - - + +
1047D LEU 5.4 0.8 - - - +
1051D ASN* 3.4 41.2 - - + +
1055D MET* 3.8 34.5 - - + -
1060D PHE* 4.6 7.6 - + - -
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Residues in contact with LEU1022 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018D PRO 2.9 16.5 + - - +
1019D LEU* 3.6 6.5 - - + +
1020D LEU 3.4 0.2 - - - -
1021D TRP* 1.3 82.4 - - + +
1023D GLN* 1.3 63.3 + - - +
1025D CYS* 3.1 6.1 + - - +
1026D LEU* 2.9 46.9 + - + +
1044D LEU* 3.9 24.0 - - + -
1060D PHE* 4.1 16.4 - - + -
1063D LEU* 4.3 12.1 - - + -
1064D LEU* 3.7 33.4 - - + -
1067D LEU* 3.9 20.0 - - + -
1069D VAL* 5.0 2.9 - - + -
1098D LEU* 4.5 5.8 - - - +
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Residues in contact with GLN1023 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1019D LEU 2.9 14.0 + - - +
1020D LEU* 3.4 32.3 - - - +
1022D LEU* 1.3 77.0 - - - +
1024D ASN* 1.3 63.2 + - - +
1026D LEU* 3.2 5.1 + - - +
1027D ILE* 3.0 38.2 + - + +
1095D ALA* 3.0 39.8 + - + +
1096D ALA* 4.6 3.4 - - - +
1098D LEU* 4.0 31.4 - - - +
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Residues in contact with ASN1024 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1020D LEU* 3.0 23.8 + - - +
1021D TRP* 3.6 10.3 - - + +
1023D GLN* 1.3 78.4 - - - +
1025D CYS* 1.3 57.3 + - - +
1027D ILE* 3.9 13.3 - - - +
1028D ARG* 3.0 35.4 + - - +
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Residues in contact with CYS1025 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021D TRP* 3.0 49.9 + - - +
1022D LEU 3.1 8.0 + - - +
1024D ASN* 1.3 75.6 - - - +
1026D LEU* 1.3 63.9 + - - +
1028D ARG* 3.4 10.7 + - - +
1029D ALA* 3.1 24.3 + - - +
1044D LEU* 3.6 29.6 - - + -
1045D VAL 5.6 1.3 - - - -
1082D ILE* 4.1 5.1 - - + +
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Residues in contact with LEU1026 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1022D LEU* 2.9 42.3 + - + +
1023D GLN* 3.6 6.3 - - - +
1025D CYS* 1.3 74.6 - - - +
1027D ILE* 1.3 59.1 + - - +
1029D ALA* 3.4 3.5 + - - +
1030D ALA* 2.9 28.1 + - - +
1067D LEU* 4.3 12.3 - - + +
1069D VAL* 4.8 10.3 - - + -
1082D ILE* 4.1 22.2 - - + -
1086D LEU* 5.9 0.9 - - + -
1091D LEU* 3.8 31.8 - - + +
1094D ALA* 4.2 13.2 - - + +
1095D ALA* 4.0 32.5 - - + +
1098D LEU* 4.6 1.3 - - - +
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Residues in contact with ILE1027 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023D GLN* 3.0 30.4 + - + +
1024D ASN* 3.9 13.9 - - - +
1026D LEU* 1.3 74.1 - - - +
1028D ARG* 1.3 60.4 + - - +
1030D ALA* 3.2 6.8 + - - +
1031D ASP* 2.9 44.0 + - - +
1092D ARG* 4.4 15.5 - - + +
1095D ALA* 3.8 19.3 - - + -
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Residues in contact with ARG1028 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011A HIS* 3.7 43.4 + - + -
1016A SER* 6.0 1.3 - - - -
1023A GLN* 5.3 6.7 + - - +
1098A LEU* 3.9 24.9 - - - +
1024D ASN* 3.0 23.8 + - - +
1025D CYS* 3.8 11.8 - - - +
1027D ILE* 1.3 76.9 - - - +
1029D ALA* 1.3 63.4 + - - +
1031D ASP* 3.4 8.4 + - + +
1032D ASP* 3.0 37.6 + - - +
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Residues in contact with ALA1029 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1025D CYS 3.1 16.6 + - - +
1026D LEU 3.7 4.5 - - - +
1028D ARG* 1.3 76.9 - - - +
1030D ALA* 1.3 62.6 + - - +
1032D ASP* 3.3 9.7 + - - +
1033D ARG* 3.1 34.5 + - - +
1042D VAL* 4.2 15.5 - - + -
1082D ILE* 4.0 20.4 - - + -
1091D LEU* 3.9 13.0 - - + -
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Residues in contact with ALA1030 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026D LEU 2.9 15.4 + - - +
1027D ILE* 3.4 10.5 - - - +
1029D ALA* 1.3 77.4 - - - +
1031D ASP* 1.3 61.5 + - - +
1033D ARG 3.3 8.3 + - - -
1034D GLU* 3.4 15.6 - - - +
1088D PRO* 3.5 31.6 - - + +
1091D LEU* 3.6 16.3 - - + +
1092D ARG* 3.9 21.5 - - + -
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Residues in contact with ASP1031 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027D ILE* 2.9 28.6 + - - +
1028D ARG* 3.7 8.6 - - - +
1030D ALA* 1.3 75.0 - - - +
1032D ASP* 1.3 65.3 + - - +
1034D GLU* 3.4 21.7 + - - +
1092D ARG* 2.8 35.7 + - - +
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Residues in contact with ASP1032 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011A HIS* 5.6 5.0 - - - +
1016A SER* 6.0 1.7 - - - -
1028D ARG* 3.0 33.7 + - - +
1029D ALA* 3.3 12.2 + - - +
1031D ASP* 1.3 80.4 - - - +
1033D ARG* 1.3 62.3 + - + +
1034D GLU 3.2 9.1 + - - +
1042D VAL* 5.9 2.9 - - - +
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Residues in contact with ARG1033 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029D ALA* 3.1 21.0 + - - +
1030D ALA 4.0 0.2 - - - +
1031D ASP 3.3 0.8 - - - -
1032D ASP* 1.3 75.0 - - + +
1034D GLU* 1.3 64.9 + - - +
1039D SER* 3.5 34.0 + - - +
1040D GLN 3.1 24.4 + - - +
1042D VAL* 4.2 7.1 - - - +
1082D ILE* 2.9 39.5 + - - +
1083D PRO 2.7 23.0 + - - -
1084D ALA* 3.7 7.5 + - - -
1086D LEU* 2.9 33.2 + - - +
1088D PRO* 3.9 23.2 - - + +
1091D LEU* 3.8 12.2 - - - +
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Residues in contact with GLU1034 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030D ALA 3.4 12.3 - - - +
1031D ASP* 3.6 13.0 - - - +
1032D ASP 3.2 9.8 - - - +
1033D ARG* 1.3 84.0 - - - +
1088D PRO* 3.8 16.5 - - + +
1092D ARG* 2.9 33.7 + - - -
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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