Contacts of the helix formed by residues 1075 - 1091 (chain A) in PDB entry 5LUQ
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 ARG1075 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011A GLU* 4.2 12.7 + - - +
1012A ALA* 5.2 5.9 - - - +
1014A LEU 4.8 0.2 - - - -
1015A ASP* 3.7 31.8 + - - +
1018A VAL* 3.5 9.5 - - - +
1066A LEU* 3.8 45.4 - - - +
1069A HIS* 4.1 22.7 + - - +
1070A PRO* 3.3 34.8 - - + -
1073A PHE* 2.5 6.8 + - + -
1074A LYS* 1.3 81.3 - - - +
1076A LEU* 1.3 64.5 + - - +
1077A GLY 3.5 1.6 - - - -
1078A ALA* 3.0 23.2 - - - +
1079A SER* 3.6 3.1 + - - -
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Residues in contact with LEU1076 (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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1067A ALA* 3.4 23.1 - - - +
1070A PRO* 5.2 0.2 - - - +
1072A ALA* 3.4 24.2 - - + +
1073A PHE 2.7 10.6 + - - +
1075A ARG* 1.3 73.8 - - - +
1077A GLY* 1.3 53.6 + - - +
1078A ALA 2.5 17.0 + - - -
1079A SER* 2.9 14.1 + - - -
1080A LEU* 3.5 13.4 + - - +
1111A LEU* 3.5 23.9 - - + +
1114A ALA* 3.5 16.8 - - + -
1115A HIS* 3.3 35.7 - - + +
1124A ILE* 3.5 32.5 - - + -
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Residues in contact with GLY1077 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017A ILE* 3.6 29.4 - - - +
1018A VAL* 3.9 13.2 - - - +
1073A PHE 4.4 0.2 + - - -
1075A ARG 3.5 0.6 - - - -
1076A LEU* 1.3 75.5 - - - +
1078A ALA* 1.3 55.6 + - - +
1080A LEU* 3.1 33.3 - - - +
1081A ALA* 3.8 6.6 - - - +
1124A ILE* 4.5 10.6 - - - +
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Residues in contact with ALA1078 (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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1014A LEU* 3.1 64.4 - - + +
1066A LEU* 4.4 6.3 - - + -
1075A ARG* 3.0 21.0 - - - +
1076A LEU 2.5 6.3 + - - -
1077A GLY* 1.3 73.0 - - - +
1079A SER* 1.3 63.0 + - - +
1080A LEU 3.3 1.1 + - - -
1081A ALA* 3.4 3.1 + - - +
1082A PHE 3.0 17.2 + - - -
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Residues in contact with SER1079 (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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1063A LEU* 3.9 8.6 + - - +
1066A LEU* 4.3 10.2 - - - +
1067A ALA* 3.0 34.6 - - - +
1075A ARG 3.6 0.8 + - - -
1076A LEU 2.9 8.1 + - - -
1078A ALA* 1.3 78.7 - - - +
1080A LEU* 1.3 62.7 + - - +
1082A PHE* 3.0 14.6 + - - +
1083A ASN 3.0 6.9 + - - -
1107A TYR* 2.3 48.7 + - - -
1111A LEU* 3.8 6.1 - - - -
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Residues in contact with LEU1080 (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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597A ALA* 5.1 3.1 - - + -
1076A LEU 3.5 10.1 + - - +
1077A GLY* 3.1 36.3 - - - +
1079A SER* 1.3 78.8 - - - +
1081A ALA* 1.3 80.2 + - + +
1083A ASN* 3.2 2.8 + - - -
1084A ASN* 2.4 33.4 + - - -
1107A TYR* 3.7 2.0 - - - -
1111A LEU* 3.6 5.7 - - + +
1124A ILE* 3.8 9.9 - - + +
1127A CYS* 3.3 37.5 - - + +
1128A CYS* 3.3 28.0 - - - -
1131A ILE* 3.4 28.3 - - + -
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Residues in contact with ALA1081 (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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593A ASN 6.1 0.9 - - - -
594A GLY* 5.1 6.7 - - - +
597A ALA* 5.7 1.8 - - + -
1014A LEU* 5.3 0.7 - - + -
1025A LEU* 4.1 12.3 - - + -
1029A CYS* 3.7 22.9 - - - -
1077A GLY 3.8 13.2 - - - +
1078A ALA* 3.6 9.0 - - - +
1079A SER 3.3 0.2 - - - -
1080A LEU* 1.3 86.7 - - + +
1082A PHE* 1.3 66.6 + - - +
1084A ASN* 3.1 4.9 + - - +
1085A ILE* 2.8 30.6 + - + +
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Residues in contact with PHE1082 (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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1014A LEU* 4.6 9.5 - - + +
1028A PHE* 5.9 3.1 - + + -
1029A CYS* 4.9 2.0 - - - -
1032A CYS* 4.7 10.3 - - + -
1036A PHE* 3.0 42.8 - + - -
1059A LEU* 4.3 4.5 - - + -
1060A PHE* 4.6 11.4 - + - -
1063A LEU* 3.1 55.0 - - + -
1066A LEU* 5.1 2.0 - - + -
1078A ALA 3.0 11.6 + - - +
1079A SER* 3.0 14.4 + - - +
1081A ALA* 1.3 74.6 - - - +
1083A ASN* 1.3 81.3 + - + +
1085A ILE* 2.9 18.3 + - + +
1086A TYR* 2.9 27.4 + + + +
1107A TYR* 5.0 2.7 - + - -
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Residues in contact with ASN1083 (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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1060A PHE* 5.7 2.8 - - - -
1079A SER 3.0 4.2 + - - -
1080A LEU 3.2 4.0 + - - +
1082A PHE* 1.3 92.9 - - - +
1084A ASN* 1.3 58.4 + - - +
1086A TYR* 3.2 2.5 + - - +
1087A ARG* 2.9 29.3 + - - +
1090A ARG* 4.8 13.3 - - - +
1100A VAL* 6.1 0.9 - - - +
1104A LEU* 3.1 30.8 - - - +
1107A TYR* 3.1 39.0 - - + +
1131A ILE* 4.3 4.8 - - + +
1134A LEU* 3.5 18.6 - - + +
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Residues in contact with ASN1084 (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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590A GLU* 4.0 13.1 - - - +
593A ASN* 4.2 26.7 + - + +
1080A LEU* 2.4 39.2 + - - +
1081A ALA* 3.5 7.6 - - - +
1083A ASN* 1.3 76.0 - - - +
1085A ILE* 1.3 64.1 + - + +
1087A ARG* 3.4 15.9 + - - +
1127A CYS* 3.9 5.8 + - - +
1130A ALA* 3.5 17.3 - - - +
1131A ILE* 3.3 19.8 - - - +
1134A LEU* 3.2 33.0 - - + +
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Residues in contact with ILE1085 (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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590A GLU* 3.1 38.6 - - + +
591A GLN* 4.3 1.8 - - + +
593A ASN* 4.7 2.0 - - + -
594A GLY* 3.8 12.6 - - - +
1029A CYS* 3.0 60.6 - - + +
1030A GLY* 5.1 0.2 - - - -
1032A CYS* 5.1 3.1 - - + -
1033A ILE* 3.1 39.4 - - + +
1036A PHE* 5.4 1.1 - - + -
1081A ALA* 2.8 30.4 + - - +
1082A PHE* 2.9 6.5 + - + +
1084A ASN* 1.3 74.8 - - + +
1086A TYR* 1.3 59.4 + - - +
1087A ARG 3.5 0.2 - - - -
1089A PHE* 4.4 0.7 - - - -
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Residues in contact with TYR1086 (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 PHE* 3.1 57.1 + + + +
1040A SER* 5.6 1.0 - - - -
1059A LEU* 5.9 2.7 - - + -
1060A PHE* 4.6 7.2 - + - -
1082A PHE* 2.9 30.9 + + + +
1083A ASN* 3.6 3.4 - - - +
1085A ILE* 1.3 77.0 - - - +
1087A ARG* 1.3 66.4 + - - +
1088A GLU 3.3 2.2 - - - -
1089A PHE* 2.8 41.8 + + + +
1090A ARG* 3.0 55.0 + - + -
1093A GLU* 3.3 24.3 + - - -
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Residues in contact with ARG1087 (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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593A ASN* 5.5 4.6 + - - -
1083A ASN 2.9 12.4 + - - +
1084A ASN 3.4 16.1 + - - +
1085A ILE 3.5 0.2 - - - -
1086A TYR* 1.3 76.4 - - - +
1088A GLU* 1.3 66.2 + - - +
1090A ARG* 2.8 21.9 + - + +
1091A GLU* 3.1 31.7 + - + +
1133A HIS* 5.0 13.7 + - - -
1134A LEU* 3.2 45.9 - - + +
1137A ILE* 3.4 28.5 - - + +
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Residues in contact with GLU1088 (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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586A GLN* 3.7 45.0 + - - +
587A THR* 4.7 5.8 - - - +
590A GLU* 3.8 25.4 - - + +
1084A ASN 4.9 0.8 + - - -
1086A TYR 3.3 0.8 - - - -
1087A ARG* 1.3 80.0 - - - +
1089A PHE* 1.3 80.9 + - + +
1091A GLU* 3.3 34.0 - - - +
1092A GLU* 4.5 7.8 + - - +
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Residues in contact with PHE1089 (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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1033A ILE* 3.1 49.1 - - + -
1034A ARG* 6.1 2.0 - - - -
1036A PHE 5.9 0.2 - - - -
1037A LEU* 4.2 33.7 - - + -
1040A SER* 6.3 2.2 - - - -
1085A ILE 4.4 0.7 - - - -
1086A TYR* 2.8 49.0 + + + +
1088A GLU* 1.3 95.7 - - + +
1090A ARG* 1.3 63.4 + - - +
1091A GLU 2.9 6.4 + - - -
1092A GLU* 3.1 23.1 + - - +
1093A GLU* 4.1 9.4 - - - +
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Residues in contact with ARG1090 (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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1056A THR* 6.3 0.4 - - - +
1060A PHE* 3.5 26.1 - - + -
1083A ASN* 4.8 12.1 - - - +
1086A TYR* 3.0 53.0 + - + +
1087A ARG* 2.8 18.8 + - + +
1089A PHE* 1.3 70.9 - - - +
1091A GLU* 1.3 60.9 + - - +
1092A GLU 3.3 1.0 + - - -
1093A GLU* 4.1 10.6 + - - +
1096A VAL* 2.8 59.1 + - - +
1097A GLU* 3.8 12.6 - - - +
1100A VAL* 3.0 27.4 - - + +
1101A PHE* 3.7 29.2 - - + -
1104A LEU* 6.2 2.2 - - + -
1137A ILE* 5.5 2.9 - - + -
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Residues in contact with GLU1091 (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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586A GLN* 5.5 1.0 + - - +
1087A ARG* 3.1 36.6 + - - +
1088A GLU* 3.3 34.2 - - - +
1089A PHE 2.9 0.4 - - - -
1090A ARG* 1.3 78.3 - - - +
1092A GLU* 1.3 75.4 + - + +
1097A GLU* 4.1 9.6 - - - +
1101A PHE* 5.1 1.3 - - - -
1137A ILE* 4.0 34.1 - - + +
1140A LYS* 5.6 4.0 + - - +
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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
------------------------------------------------------------
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