Contacts of the helix formed by residues 1107 - 1128 (chain A) in PDB entry 4DDG
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 ASP1107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1103A ALA 4.5 7.9 - - - +
1104A LEU* 3.6 14.5 + - - +
1106A ASP* 1.3 88.5 + - - +
1108A SER* 1.3 78.5 + - - +
1109A LYS* 3.2 26.2 + - - +
1110A GLU* 3.3 29.5 + - + +
1111A LEU* 3.6 14.9 + - - +
1256A LYS* 5.1 9.0 + - - +
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Residues in contact with SER1108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1106A ASP 3.9 8.0 + - - -
1107A ASP* 1.3 78.3 + - - +
1109A LYS* 1.3 70.7 + - - +
1111A LEU* 3.8 6.2 - - - +
1112A GLN* 3.6 21.0 + - - +
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Residues in contact with LYS1109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107A ASP* 3.4 14.3 + - - +
1108A SER* 1.3 85.2 - - - +
1110A GLU* 1.3 68.9 + - - +
1111A LEU 3.2 0.7 - - - -
1112A GLN* 3.0 11.3 + - - +
1113A ARG* 2.9 28.1 + - - +
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Residues in contact with GLU1110 (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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1104A LEU* 3.8 22.4 - - + -
1107A ASP* 3.3 28.9 + - + +
1109A LYS* 1.3 83.2 - - - +
1111A LEU* 1.3 61.8 + - - +
1113A ARG* 2.3 44.6 + - - +
1114A PHE* 2.9 34.2 + - + +
1229A VAL* 5.0 9.3 - - + +
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Residues in contact with LEU1111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104A LEU* 3.5 32.4 - - + +
1105A LEU 5.5 0.4 - - - -
1106A ASP 5.8 0.4 - - - +
1107A ASP 3.6 15.1 + - - +
1108A SER* 3.8 7.0 - - - +
1110A GLU* 1.3 79.1 - - - +
1112A GLN* 1.3 58.2 + - + +
1114A PHE* 3.8 1.2 - - - +
1115A LYS* 2.9 37.0 + - + +
1146A ILE* 4.1 20.4 - - + +
1149A VAL* 3.2 34.5 - - + +
1150A GLU* 3.4 35.9 - - + +
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Residues in contact with GLN1112 (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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1108A SER 3.8 11.7 - - - +
1109A LYS* 3.0 13.9 + - - +
1111A LEU* 1.3 81.7 - - + +
1113A ARG* 1.3 58.2 + - - +
1115A LYS* 3.3 8.6 + - - +
1116A ALA* 2.9 28.8 + - - +
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Residues in contact with ARG1113 (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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1109A LYS 2.9 14.0 + - - +
1110A GLU* 2.3 43.1 + - - +
1112A GLN* 1.3 74.5 - - - +
1114A PHE* 1.3 65.2 + - - +
1116A ALA* 3.1 8.1 + - + +
1117A VAL* 2.9 28.7 + - + +
1227A LEU 4.4 2.4 + - - -
1228A SER* 3.1 39.6 + - - +
1229A VAL* 4.9 1.4 - - - +
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Residues in contact with PHE1114 (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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1100A HIS* 4.9 13.2 - + + -
1101A LEU* 3.8 19.5 - - + -
1104A LEU* 3.7 26.2 - - + -
1110A GLU* 2.9 19.8 + - + +
1111A LEU 3.8 3.1 - - - +
1113A ARG* 1.3 79.2 - - - +
1115A LYS* 1.3 58.9 + - - +
1117A VAL* 3.3 8.4 - - + +
1118A SER* 2.9 33.4 + - - -
1142A PHE* 3.8 23.3 - + - -
1146A ILE* 3.8 29.2 - - + -
1227A LEU* 3.9 36.6 - - + -
1229A VAL* 4.2 21.3 - - + -
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Residues in contact with LYS1115 (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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1111A LEU* 2.9 23.0 + - + +
1112A GLN* 3.5 7.2 - - - +
1114A PHE* 1.3 75.4 - - - +
1116A ALA* 1.3 58.8 + - - +
1118A SER* 2.8 18.3 + - - -
1119A ALA* 2.9 20.8 + - + +
1143A MET* 4.1 22.2 - - + +
1146A ILE* 4.2 20.2 - - + -
1150A GLU* 3.0 41.3 + - - +
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Residues in contact with ALA1116 (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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1112A GLN 2.9 13.8 + - - +
1113A ARG* 3.1 11.6 + - + +
1115A LYS* 1.3 76.3 - - - +
1117A VAL* 1.3 57.0 + - - +
1119A ALA* 3.1 7.9 + - - +
1120A LYS* 2.9 29.3 + - - +
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Residues in contact with VAL1117 (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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1113A ARG* 2.9 24.1 + - + +
1114A PHE* 3.3 20.4 - - + +
1116A ALA* 1.3 73.2 - - - +
1118A SER* 1.3 59.9 + - - +
1120A LYS* 3.4 7.0 + - + +
1121A SER* 2.9 29.3 + - - -
1226A ALA 4.1 19.5 - - - +
1227A LEU* 4.0 24.5 - - + +
1228A SER* 4.6 9.4 - - - +
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Residues in contact with SER1118 (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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1114A PHE* 2.9 19.5 + - - -
1115A LYS* 2.8 19.6 + - - -
1117A VAL* 1.3 79.5 - - - +
1119A ALA* 1.3 57.7 + - - +
1121A SER* 2.3 27.5 + - - -
1139A HIS* 3.2 15.0 - - - -
1142A PHE* 3.5 30.7 - - - -
1143A MET* 3.5 3.6 - - - -
1146A ILE* 3.2 19.4 - - - +
1174A TYR* 3.8 0.9 + - - -
1227A LEU* 4.9 6.3 - - - -
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Residues in contact with ALA1119 (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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1115A LYS* 2.9 19.7 + - + +
1116A ALA* 3.1 6.9 + - - +
1118A SER* 1.3 76.0 + - - +
1120A LYS* 1.3 63.6 + - - +
1121A SER 3.4 0.3 + - - -
1122A LYS* 3.6 16.8 + - - +
1123A GLU* 4.2 4.9 + - - +
1139A HIS* 3.9 12.7 + - + +
1143A MET* 4.0 14.4 - - + -
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Residues in contact with LYS1120 (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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1116A ALA 2.9 15.8 + - - +
1117A VAL* 3.9 7.6 - - + +
1119A ALA* 1.3 74.4 - - - +
1121A SER* 1.3 64.5 + - - +
1123A GLU* 3.0 29.9 + - + +
1124A ASP* 3.0 48.1 + - - +
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Residues in contact with SER1121 (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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1117A VAL* 2.9 18.4 + - - -
1118A SER* 2.3 30.0 + - - -
1120A LYS* 1.3 76.5 - - - +
1122A LYS* 1.3 54.4 + - - +
1124A ASP* 3.4 13.1 + - - +
1125A LEU* 2.9 33.5 + - - +
1174A TYR* 2.7 19.8 + - - -
1178A LEU* 3.6 23.3 - - - +
1226A ALA 6.0 1.8 - - - -
1227A LEU* 5.9 1.8 - - - -
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Residues in contact with LYS1122 (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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1119A ALA 3.6 6.1 + - - +
1120A LYS 3.2 0.6 - - - -
1121A SER* 1.3 81.9 + - - +
1123A GLU* 1.3 67.7 + - - +
1125A LEU* 3.2 7.7 + - - +
1126A VAL* 2.9 40.9 + - + +
1132A GLU* 3.7 34.3 + - - -
1135A ILE* 4.6 6.5 - - + -
1136A GLU* 3.5 34.4 + - - +
1139A HIS* 3.5 50.0 - - + +
1140A ASN* 5.4 1.2 + - - -
1174A TYR* 3.6 6.1 - - - +
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Residues in contact with GLU1123 (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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1119A ALA 4.2 3.1 + - - +
1120A LYS* 3.0 35.2 + - + +
1122A LYS* 1.3 94.9 - - - +
1124A ASP* 1.3 58.6 + - - +
1126A VAL* 3.3 9.4 + - + +
1127A SER* 2.9 33.5 + - - -
1132A GLU* 5.2 5.4 - - - +
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Residues in contact with ASP1124 (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 LYS* 3.0 46.6 + - - +
1121A SER* 3.5 11.5 + - - +
1123A GLU* 1.3 76.3 - - - +
1125A LEU* 1.3 56.4 + - + +
1127A SER* 2.6 22.6 + - - -
1128A GLN* 2.9 21.2 + - - +
1185A ARG* 3.9 27.9 + - - +
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Residues in contact with LEU1125 (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 SER 2.9 22.8 + - - +
1122A LYS* 3.5 3.8 - - - +
1124A ASP* 1.3 70.5 - - + +
1126A VAL* 1.3 60.9 + - - +
1128A GLN* 2.8 21.7 + - - +
1129A GLY 3.3 2.1 + - - -
1130A PHE* 3.1 48.6 + - + -
1135A ILE* 3.9 13.9 - - + -
1174A TYR* 4.0 22.4 - - + +
1177A LEU* 3.7 29.6 - - + +
1178A LEU* 3.9 24.2 - - + -
1181A GLY* 3.9 13.0 - - - -
1185A ARG* 5.5 2.2 - - - +
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Residues in contact with VAL1126 (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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1122A LYS* 2.9 31.5 + - + +
1123A GLU* 3.8 10.5 - - + +
1125A LEU* 1.3 71.0 - - - +
1127A SER* 1.3 61.8 + - - +
1129A GLY* 3.2 12.1 + - - -
1130A PHE 3.7 14.8 - - - +
1132A GLU* 3.8 43.5 - - + +
1135A ILE* 3.7 17.9 - - + +
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Residues in contact with SER1127 (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 GLU 2.9 15.8 + - - -
1124A ASP* 2.6 27.7 + - - -
1126A VAL* 1.3 78.8 - - - +
1128A GLN* 1.3 58.1 + - - +
1129A GLY 3.2 1.8 + - - -
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Residues in contact with GLN1128 (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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1124A ASP 2.9 9.3 + - - +
1125A LEU* 2.8 17.9 + - - +
1127A SER* 1.3 78.1 - - - +
1129A GLY* 1.3 57.4 + - - +
1130A PHE* 3.6 11.0 - - + -
1181A GLY* 2.8 36.5 + - - +
1184A GLN* 3.9 13.0 - - + +
1185A ARG* 2.9 50.6 + - - +
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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