Contacts of the helix formed by residues 1107 - 1127 (chain C) in PDB entry 4DDI
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1103C ALA 4.1 9.4 + - - +
1104C LEU* 3.6 7.2 - - + +
1106C ASP* 1.3 76.1 - - + +
1108C SER* 1.3 63.2 + - - +
1109C LYS* 3.4 31.8 + - - -
1110C GLU* 3.1 32.9 + - + +
1111C LEU* 3.1 24.6 + - - +
1256C LYS* 5.4 14.3 + - + +
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Residues in contact with SER1108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1106C ASP 3.2 7.4 + - - -
1107C ASP* 1.3 70.6 + - - +
1109C LYS* 1.3 61.9 + - - +
1110C GLU 3.2 1.6 - - - -
1111C LEU* 3.2 14.9 + - - +
1112C GLN* 3.0 36.7 + - - +
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Residues in contact with LYS1109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107C ASP* 3.4 24.8 + - - +
1108C SER* 1.3 77.5 - - - +
1110C GLU* 1.3 68.1 + - - +
1112C GLN* 3.6 5.7 + - - +
1113C ARG* 3.0 29.7 + - + +
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Residues in contact with GLU1110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104C LEU* 3.8 19.3 - - + -
1107C ASP* 3.1 31.6 + - + +
1108C SER 3.2 0.2 - - - -
1109C LYS* 1.3 86.1 - - - +
1111C LEU* 1.3 61.2 + - - +
1113C ARG* 3.0 40.4 + - - +
1114C PHE* 2.9 32.4 + - + +
1228C SER 4.7 1.7 - - - +
1229C VAL* 4.5 9.2 - - + +
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Residues in contact with LEU1111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101C LEU* 6.4 0.2 - - + -
1104C LEU* 3.8 31.8 - - + +
1107C ASP 3.1 18.3 + - - +
1108C SER* 3.2 15.0 + - - +
1110C GLU* 1.3 77.6 - - - +
1112C GLN* 1.3 60.2 + - + +
1114C PHE* 3.5 1.6 - - + +
1115C LYS* 2.9 30.9 + - + +
1146C ILE* 4.3 16.4 - - + -
1149C VAL* 3.7 26.2 - - + +
1150C GLU* 3.6 39.0 - - + +
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Residues in contact with GLN1112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108C SER* 3.0 24.1 + - - +
1109C LYS* 3.9 5.2 - - - +
1111C LEU* 1.3 77.9 - - + +
1113C ARG* 1.3 65.5 + - - +
1115C LYS* 3.1 26.2 + - - +
1116C ALA* 3.0 24.3 + - - +
1150C GLU* 5.6 3.6 - - - -
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Residues in contact with ARG1113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109C LYS* 3.0 20.7 + - + +
1110C GLU* 3.0 38.8 + - - +
1112C GLN* 1.3 76.4 - - - +
1114C PHE* 1.3 73.0 + - - +
1116C ALA* 3.8 5.5 + - - +
1117C VAL* 3.2 48.3 + - + +
1227C LEU 3.5 16.4 + - - -
1228C SER* 2.9 29.6 + - - -
1229C VAL* 3.7 8.3 - - - +
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Residues in contact with PHE1114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100C HIS* 4.9 16.8 - + + -
1101C LEU* 4.5 8.3 - - + -
1104C LEU* 3.5 27.8 - - + -
1110C GLU* 2.9 19.7 + - + +
1111C LEU 3.5 5.2 - - - +
1113C ARG* 1.3 95.2 - - - +
1115C LYS* 1.3 67.2 + - - +
1117C VAL* 3.1 9.0 + - + +
1118C SER* 3.0 37.6 + - - -
1142C PHE* 3.8 15.0 - + - -
1146C ILE* 3.8 22.9 - - + -
1227C LEU* 3.5 39.0 - - + -
1229C VAL* 4.7 5.4 - - + -
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Residues in contact with LYS1115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1111C LEU* 2.9 19.5 + - + +
1112C GLN* 3.4 23.0 + - - +
1114C PHE* 1.3 78.2 - - - +
1116C ALA* 1.3 63.0 + - - +
1118C SER* 3.2 10.7 + - - -
1119C ALA* 3.0 23.3 + - + +
1143C MET* 4.0 10.4 - - + +
1146C ILE* 4.5 19.5 - - + -
1150C GLU* 2.6 35.7 + - + +
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Residues in contact with ALA1116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112C GLN 3.0 15.2 + - - +
1113C ARG* 3.9 7.9 - - - +
1114C PHE 3.2 0.2 - - - -
1115C LYS* 1.3 77.0 - - - +
1117C VAL* 1.3 58.3 + - + +
1119C ALA* 3.3 7.8 + - - +
1120C LYS* 3.0 27.9 + - - +
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Residues in contact with VAL1117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113C ARG* 3.2 38.1 - - + +
1114C PHE* 3.1 8.8 + - + +
1116C ALA* 1.3 76.8 - - + +
1118C SER* 1.3 58.3 + - - +
1120C LYS* 3.3 8.6 + - + +
1121C SER* 2.9 30.0 + - - -
1226C ALA 4.3 17.3 - - - +
1227C LEU* 4.7 16.4 - - + +
1228C SER* 4.8 1.8 - - - +
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Residues in contact with SER1118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1114C PHE* 3.0 25.4 + - - -
1115C LYS 3.3 9.2 - - - -
1117C VAL* 1.3 76.1 - - - +
1119C ALA* 1.3 61.9 + - - +
1121C SER* 2.5 28.1 + - - -
1139C HIS* 3.2 9.4 - - - -
1142C PHE* 3.8 15.0 - - - -
1143C MET* 3.6 22.9 - - - -
1146C ILE* 3.4 18.1 - - - +
1227C LEU* 5.6 1.0 - - - +
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Residues in contact with ALA1119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115C LYS* 3.0 13.4 + - + +
1116C ALA* 3.3 9.8 + - - +
1118C SER* 1.3 76.3 - - - +
1120C LYS* 1.3 61.9 + - - +
1122C LYS* 3.7 14.9 + - - +
1123C GLU* 4.3 10.9 - - - +
1139C HIS* 4.2 5.1 + - - +
1143C MET* 3.5 17.6 - - + +
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Residues in contact with LYS1120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116C ALA 3.0 14.5 + - - +
1117C VAL* 3.5 12.3 - - + +
1118C SER 3.2 0.2 - - - -
1119C ALA* 1.3 76.5 - - - +
1121C SER* 1.3 63.6 + - - +
1122C LYS 3.2 0.9 + - - -
1123C GLU* 3.5 23.4 + - + +
1124C ASP* 2.3 66.6 + - - +
1127C SER* 5.6 0.4 + - - -
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Residues in contact with SER1121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117C VAL* 2.9 15.7 + - - -
1118C SER* 2.5 24.0 + - - -
1120C LYS* 1.3 77.6 - - - +
1122C LYS* 1.3 61.6 + - - +
1124C ASP* 3.3 9.4 - - - +
1125C LEU* 2.9 28.9 + - - +
1142C PHE* 5.6 0.3 - - - -
1174C TYR* 2.7 24.0 + - - -
1178C LEU* 3.7 25.2 - - - +
1185C ARG* 6.0 2.2 - - - +
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Residues in contact with LYS1122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118C SER 3.6 1.0 + - - -
1119C ALA 3.9 6.3 - - - +
1120C LYS 3.2 0.8 + - - -
1121C SER* 1.3 79.5 + - - +
1123C GLU* 1.3 76.3 + - - +
1125C LEU* 2.9 22.2 + - - +
1126C VAL* 2.9 22.2 + - + +
1132C GLU* 3.9 20.3 + - - +
1135C ILE* 4.2 12.4 - - + +
1136C GLU* 4.4 21.9 + - + +
1139C HIS* 3.4 48.4 + - + +
1140C ASN* 5.9 0.2 - - - +
1174C TYR* 3.6 8.1 - - - +
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Residues in contact with GLU1123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119C ALA 4.3 9.7 - - - +
1120C LYS* 3.6 27.4 + - - +
1122C LYS* 1.3 92.7 + - - +
1124C ASP* 1.3 55.9 + - - +
1126C VAL* 3.6 13.0 - - + +
1127C SER* 2.7 39.7 + - - -
1132C GLU* 5.6 2.2 - - - +
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Residues in contact with ASP1124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120C LYS* 2.3 60.9 + - - +
1121C SER* 3.3 12.3 - - - +
1122C LYS 3.1 0.2 - - - -
1123C GLU* 1.3 79.2 - - - +
1125C LEU* 1.3 55.8 + - + +
1127C SER* 3.0 16.8 + - - -
1128C GLN* 3.2 17.2 + - - +
1185C ARG* 3.7 33.7 + - - +
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Residues in contact with LEU1125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121C SER 2.9 18.0 + - - +
1122C LYS 2.9 6.3 + - - +
1124C ASP* 1.3 76.5 - - + +
1126C VAL* 1.3 61.2 + - - +
1128C GLN* 2.9 25.5 + - - +
1129C GLY 3.1 0.5 + - - -
1130C PHE* 3.1 41.2 + - + -
1135C ILE* 4.2 12.6 - - + -
1174C TYR* 3.6 32.3 - - + +
1177C LEU* 4.0 14.8 - - + +
1178C LEU* 3.8 15.7 - - + -
1181C GLY* 3.6 31.2 - - - -
1185C ARG* 4.9 5.2 - - - +
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Residues in contact with VAL1126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1122C LYS* 2.9 18.1 + - + +
1123C GLU* 3.9 11.9 - - + +
1125C LEU* 1.3 75.7 - - - +
1127C SER* 1.3 58.6 + - - +
1128C GLN 3.0 0.2 - - - -
1129C GLY* 3.0 18.9 + - - -
1130C PHE 3.4 18.0 - - - +
1132C GLU* 3.8 42.6 - - + +
1135C ILE* 3.7 18.6 - - + -
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Residues in contact with SER1127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120C LYS* 5.6 0.2 + - - -
1123C GLU 2.7 23.6 + - - -
1124C ASP* 3.0 14.7 + - - -
1126C VAL* 1.3 76.4 - - - +
1128C GLN* 1.3 57.2 + - - +
1129C GLY 3.2 2.2 + - - -
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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