Contacts of the helix formed by residues 1112 - 1128 (chain A) in PDB entry 3L2O
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 ILE1112 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023A GLN* 4.3 14.6 - - + +
1024A SER* 3.7 28.9 - - - +
1058A VAL* 3.8 21.5 - - + -
1061A TRP* 3.8 28.7 - - + -
1062A CYS* 3.7 24.7 - - - -
1107A ALA* 3.1 10.9 + - - +
1110A LEU* 3.7 13.9 - - + +
1111A ASP* 1.3 75.5 - - - +
1113A LYS* 1.3 66.6 + - - +
1114A GLY 4.5 1.6 - - - +
1115A LEU* 3.1 15.7 + - + +
1116A LEU* 3.1 21.6 + - - +
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Residues in contact with LYS1113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1079A GLY 6.3 0.2 - - - -
1081A GLY* 4.5 12.5 - - - +
1111A ASP* 3.8 10.5 + - - +
1112A ILE* 1.3 72.0 - - - +
1114A GLY* 1.3 57.3 + - - +
1116A LEU* 3.2 8.3 + - + +
1117A ASP* 2.8 48.0 + - - +
69B TYR* 3.0 28.4 + - + +
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Residues in contact with GLY1114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061A TRP* 3.5 24.5 - - - -
1080A SER* 5.9 4.0 - - - -
1112A ILE* 3.3 3.0 - - - +
1113A LYS* 1.3 78.5 - - - +
1115A LEU* 1.3 61.3 + - - +
1117A ASP* 3.5 9.6 + - - +
1118A VAL* 3.2 21.8 + - - +
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Residues in contact with LEU1115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1058A VAL* 4.3 35.9 - - + -
1061A TRP* 3.4 36.0 - - + -
1092A PHE* 5.1 6.7 - - + -
1103A LEU* 4.8 12.6 - - + +
1107A ALA* 4.0 19.7 - - + +
1112A ILE* 3.1 21.3 + - + +
1114A GLY* 1.3 73.7 - - - +
1116A LEU* 1.3 54.9 + - - +
1118A VAL* 3.5 7.1 + - + +
1119A THR* 2.5 57.7 + - + +
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Residues in contact with LEU1116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104A ILE* 3.5 27.8 - - + +
1107A ALA* 3.7 11.4 - - + +
1108A ASN* 4.0 25.6 - - + +
1112A ILE 3.1 12.2 + - - +
1113A LYS* 3.5 13.5 - - + +
1115A LEU* 1.3 75.3 - - - +
1117A ASP* 1.3 67.5 + - - +
1119A THR* 3.3 2.6 + - - +
1120A CYS* 2.9 51.3 + - - +
66B VAL* 4.8 6.7 - - + -
69B TYR* 4.2 29.6 - - + -
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Residues in contact with ASP1117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1080A SER* 3.9 11.4 - - - -
1081A GLY* 3.4 35.6 + - - +
1113A LYS* 2.8 36.2 + - - +
1114A GLY* 3.7 8.1 - - - +
1116A LEU* 1.3 77.5 - - - +
1118A VAL* 1.3 59.4 + - + +
1120A CYS 3.8 0.2 - - - -
1121A LYS* 2.8 34.1 + - - +
69B TYR* 2.5 38.5 + - - -
73B PHE* 4.0 7.3 - - + -
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Residues in contact with VAL1118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061A TRP* 4.0 21.8 - - + +
1085A ILE* 3.3 45.8 - - + +
1086A PRO* 4.2 7.9 - - + -
1089A ASP* 4.0 12.1 - - + -
1093A LEU* 3.4 20.3 - - + +
1114A GLY 3.2 13.3 + - - +
1115A LEU* 3.9 9.6 - - + +
1116A LEU 3.2 0.4 - - - -
1117A ASP* 1.3 78.7 - - + +
1119A THR* 1.3 59.5 + - + +
1121A LYS* 4.4 2.5 - - - -
1122A THR* 2.7 32.7 + - - -
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Residues in contact with THR1119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093A LEU* 3.8 24.0 - - + -
1100A LEU* 4.2 5.1 - - + +
1103A LEU* 4.1 13.9 - - + -
1104A ILE* 3.6 29.1 - - - +
1107A ALA* 4.7 0.3 - - - +
1115A LEU* 2.5 46.5 + - + +
1116A LEU* 3.3 7.3 + - - +
1118A VAL* 1.3 73.7 - - - +
1120A CYS* 1.3 67.2 + - - +
1122A THR* 2.5 20.3 + - - -
1123A VAL* 3.1 15.8 + - - +
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Residues in contact with CYS1120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104A ILE* 4.1 19.1 - - - -
1116A LEU* 2.9 44.5 + - - +
1117A ASP 4.1 1.1 - - - +
1119A THR* 1.3 76.8 + - - +
1121A LYS* 1.3 58.0 + - - +
1123A VAL* 3.2 4.5 + - - +
1124A ALA* 2.9 27.8 + - - +
66B VAL* 4.6 5.2 - - - -
69B TYR* 4.2 18.8 - - + -
70B ILE* 3.9 31.4 - - + +
73B PHE* 4.3 3.4 - - + -
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Residues in contact with LYS1121 (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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1081A GLY 4.4 4.3 - - - +
1082A THR* 4.0 13.0 + - - +
1083A ASP 3.4 33.5 + - - +
1084A ASP* 3.9 13.3 + - - +
1085A ILE* 4.0 20.2 - - + +
1117A ASP 2.8 20.5 + - - +
1118A VAL* 4.4 0.2 - - - -
1120A CYS* 1.3 77.7 - - - +
1122A THR* 1.3 55.8 + - - +
1124A ALA* 3.2 6.2 + - - +
1125A ASN* 2.9 49.5 + - - +
1128A LYS* 4.8 7.6 - - - +
73B PHE* 3.5 37.3 - - + -
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Residues in contact with THR1122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1085A ILE* 3.2 28.5 - - + -
1090A GLN* 5.5 5.6 - - + -
1093A LEU* 3.5 24.6 - - + +
1100A LEU* 4.0 10.9 - - - +
1118A VAL 2.7 14.9 + - - +
1119A THR* 2.5 24.8 + - - -
1121A LYS* 1.3 74.9 - - - +
1123A VAL* 1.3 59.5 + - - +
1125A ASN* 3.4 9.0 + - - +
1126A MET* 3.3 27.6 + - - +
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Residues in contact with VAL1123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100A LEU* 3.3 19.3 - - + -
1101A PHE* 4.1 8.3 - - + -
1104A ILE* 3.2 26.5 - - + -
1119A THR 3.1 15.4 + - - +
1120A CYS* 3.2 6.5 + - - +
1122A THR* 1.3 72.5 - - - +
1124A ALA* 1.3 67.9 + - - +
1126A MET* 3.1 20.7 + - - +
1127A ILE* 3.3 14.7 + - + +
1139A PHE* 3.9 26.6 - - + -
59B LEU* 4.7 2.9 - - + -
70B ILE* 4.1 23.1 - - + -
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Residues in contact with ALA1124 (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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1120A CYS 2.9 13.4 + - - +
1121A LYS 3.3 9.6 - - - +
1123A VAL* 1.3 76.9 - - - +
1125A ASN* 1.3 64.1 + - - +
1127A ILE* 3.1 13.5 + - - -
1128A LYS* 3.2 17.3 + - - +
70B ILE* 4.0 16.3 - - - +
73B PHE* 3.7 28.9 - - + +
74B LEU* 3.6 18.4 - - + +
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Residues in contact with ASN1125 (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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1085A ILE* 4.1 20.2 - - - +
1121A LYS* 2.9 34.1 + - - +
1122A THR* 3.7 8.3 - - - +
1123A VAL 3.2 0.6 - - - -
1124A ALA* 1.3 71.9 - - - +
1126A MET* 1.3 65.0 + - - +
1128A LYS* 3.2 45.9 + - + +
1130A LYS* 5.3 0.7 + - - -
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Residues in contact with MET1126 (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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1097A GLN* 3.7 28.0 - - + +
1100A LEU* 4.5 14.6 - - + -
1101A PHE* 6.2 0.2 - - + -
1122A THR* 3.3 16.1 + - - +
1123A VAL* 3.1 16.2 + - - +
1125A ASN* 1.3 81.0 - - - +
1127A ILE* 1.3 62.2 + - - +
1128A LYS 3.3 1.2 + - - +
1130A LYS* 3.2 33.6 + - - +
1138A THR* 3.8 11.7 - - + -
1139A PHE* 3.8 22.9 - - + -
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Residues in contact with ILE1127 (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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1123A VAL* 3.6 15.0 - - + +
1124A ALA* 3.1 10.7 + - - +
1126A MET* 1.3 76.3 - - - +
1128A LYS* 1.3 63.8 + - - +
1129A GLY 3.3 2.6 + - - -
1130A LYS* 3.6 14.3 + - - +
1135A ILE* 3.7 35.5 - - + +
1139A PHE* 4.2 20.6 - - + -
59B LEU* 5.0 9.0 - - + -
70B ILE* 4.6 11.4 - - + -
71B LEU* 4.8 1.6 - - + -
74B LEU* 4.3 26.0 - - + -
78B ASP* 4.9 6.8 - - + +
81B GLN* 5.8 0.5 - - - +
82B LEU* 4.4 26.5 - - + +
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Residues in contact with LYS1128 (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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1121A LYS* 4.8 10.5 - - - +
1124A ALA 3.2 15.7 + - - +
1125A ASN* 3.2 36.3 + - - +
1126A MET 3.2 8.1 - - - +
1127A ILE* 1.3 77.6 - - - +
1129A GLY* 1.3 63.3 + - - +
1130A LYS* 4.1 4.7 + - - +
73B PHE* 3.5 27.6 + - - +
74B LEU* 3.8 7.9 - - + +
75B SER* 6.2 0.2 - - - -
78B ASP* 3.4 31.9 - - - +
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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