Contacts of the helix formed by residues 1107 - 1128 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1103B ALA 4.5 8.3 - - - +
1104B LEU* 3.6 14.2 + - - +
1106B ASP* 1.3 87.4 + - - +
1108B SER* 1.3 79.0 + - - +
1109B LYS* 3.2 24.5 + - - +
1110B GLU* 3.3 29.2 + - + +
1111B LEU* 3.6 13.9 + - - +
1256B LYS* 5.1 8.7 + - - +
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Residues in contact with SER1108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1106B ASP 3.9 7.2 + - - -
1107B ASP* 1.3 78.5 + - - +
1109B LYS* 1.3 71.2 + - - +
1111B LEU* 3.8 6.3 - - - +
1112B GLN* 3.6 20.8 + - - +
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Residues in contact with LYS1109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107B ASP* 3.4 13.0 + - - +
1108B SER* 1.3 84.5 - - - +
1110B GLU* 1.3 69.9 + - - +
1111B LEU 3.2 0.2 - - - -
1112B GLN* 3.0 10.6 + - - +
1113B ARG* 2.9 27.8 + - - +
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Residues in contact with GLU1110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1104B LEU* 3.8 23.1 - - + -
1107B ASP* 3.3 29.6 + - + +
1109B LYS* 1.3 82.5 - - - +
1111B LEU* 1.3 61.7 + - - +
1113B ARG* 2.3 45.0 + - - +
1114B PHE* 2.9 33.9 + - + +
1229B VAL* 5.0 9.0 - - + +
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Residues in contact with LEU1111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1104B LEU* 3.5 32.6 - - + +
1105B LEU 5.5 0.2 - - - -
1106B ASP 5.8 0.2 - - - +
1107B ASP 3.6 15.4 + - - +
1108B SER* 3.8 7.0 - - - +
1109B LYS 3.2 0.2 - - - -
1110B GLU* 1.3 80.3 - - - +
1112B GLN* 1.3 59.2 + - + +
1114B PHE* 3.8 1.0 - - - +
1115B LYS* 2.9 36.9 + - + +
1146B ILE* 4.1 20.5 - - + +
1149B VAL* 3.2 33.7 - - + +
1150B GLU* 3.4 35.4 - - + +
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Residues in contact with GLN1112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108B SER 3.8 12.1 - - - +
1109B LYS* 3.0 13.3 + - - +
1111B LEU* 1.3 81.9 - - + +
1113B ARG* 1.3 57.6 + - - +
1115B LYS* 3.3 8.9 + - - +
1116B ALA* 2.9 27.5 + - - +
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Residues in contact with ARG1113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109B LYS 2.9 14.0 + - - +
1110B GLU* 2.3 42.8 + - - +
1112B GLN* 1.3 75.2 - - - +
1114B PHE* 1.3 65.3 + - - +
1116B ALA* 3.1 8.5 + - + +
1117B VAL* 2.9 28.9 + - + +
1227B LEU 4.4 2.0 + - - -
1228B SER* 3.1 40.0 + - - +
1229B VAL* 4.9 1.8 - - - +
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Residues in contact with PHE1114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100B HIS* 4.9 13.2 - + + -
1101B LEU* 3.8 18.8 - - + -
1104B LEU* 3.7 26.9 - - + -
1110B GLU* 2.9 20.0 + - + +
1111B LEU 3.8 3.4 - - - +
1113B ARG* 1.3 78.3 - - - +
1115B LYS* 1.3 58.1 + - - +
1117B VAL* 3.3 8.1 - - + +
1118B SER* 2.9 33.5 + - - -
1142B PHE* 3.8 24.0 - + - -
1146B ILE* 3.8 28.7 - - + -
1227B LEU* 3.9 37.2 - - + -
1229B VAL* 4.2 20.6 - - + -
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Residues in contact with LYS1115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1111B LEU* 2.9 23.0 + - + +
1112B GLN* 3.5 7.2 - - - +
1113B ARG 3.2 0.2 - - - -
1114B PHE* 1.3 76.6 - - - +
1116B ALA* 1.3 58.4 + - - +
1118B SER* 2.8 19.5 + - - -
1119B ALA* 2.9 20.0 + - + +
1143B MET* 4.1 22.2 - - + +
1146B ILE* 4.2 19.3 - - + -
1150B GLU* 3.0 41.3 + - - +
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Residues in contact with ALA1116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112B GLN 2.9 13.8 + - - +
1113B ARG* 3.1 11.2 + - + +
1115B LYS* 1.3 76.1 - - - +
1117B VAL* 1.3 58.6 + - - +
1119B ALA* 3.1 7.3 + - - +
1120B LYS* 2.9 28.9 + - - +
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Residues in contact with VAL1117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113B ARG* 2.9 23.9 + - + +
1114B PHE* 3.3 19.5 - - + +
1116B ALA* 1.3 73.0 - - - +
1118B SER* 1.3 61.1 + - - +
1120B LYS* 3.4 6.5 + - + +
1121B SER* 2.9 29.6 + - - -
1226B ALA 4.1 19.5 - - - +
1227B LEU* 4.0 24.2 - - + +
1228B SER* 4.6 8.7 - - - +
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Residues in contact with SER1118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1114B PHE* 2.9 19.5 + - - -
1115B LYS 2.8 19.6 + - - -
1117B VAL* 1.3 78.8 - - - +
1119B ALA* 1.3 59.6 + - - +
1121B SER* 2.3 27.8 + - - -
1139B HIS* 3.2 14.4 - - - -
1142B PHE* 3.5 30.7 - - - -
1143B MET* 3.5 3.5 - - - -
1146B ILE* 3.2 19.3 - - - +
1174B TYR* 3.8 1.0 + - - -
1227B LEU* 4.9 6.1 - - - -
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Residues in contact with ALA1119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115B LYS* 2.9 20.4 + - + +
1116B ALA* 3.1 6.5 + - - +
1118B SER* 1.3 76.8 + - - +
1120B LYS* 1.3 63.0 + - - +
1121B SER 3.4 0.3 + - - -
1122B LYS* 3.6 16.6 + - - +
1123B GLU* 4.2 4.3 + - - +
1139B HIS* 3.9 11.6 + - + +
1143B MET* 4.0 13.9 - - + -
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Residues in contact with LYS1120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116B ALA 2.9 14.3 + - - +
1117B VAL* 3.9 7.4 - - + +
1119B ALA* 1.3 75.1 - - - +
1121B SER* 1.3 66.0 + - - +
1123B GLU* 3.0 29.0 + - + +
1124B ASP* 3.0 48.1 + - - +
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Residues in contact with SER1121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117B VAL* 2.9 18.7 + - - -
1118B SER* 2.3 30.4 + - - -
1120B LYS* 1.3 77.2 - - - +
1122B LYS* 1.3 55.1 + - - +
1124B ASP* 3.4 11.8 + - - +
1125B LEU* 2.9 33.5 + - - +
1174B TYR* 2.7 19.0 + - - -
1178B LEU* 3.6 23.4 - - - +
1226B ALA 6.0 1.3 - - - -
1227B LEU* 5.9 1.1 - - - -
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Residues in contact with LYS1122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119B ALA 3.6 5.3 + - - +
1120B LYS 3.2 0.6 - - - -
1121B SER* 1.3 82.0 + - - +
1123B GLU* 1.3 67.3 + - - +
1125B LEU* 3.2 7.0 + - - +
1126B VAL* 2.9 40.0 + - + +
1132B GLU* 3.7 33.2 + - - -
1135B ILE* 4.6 7.0 - - + -
1136B GLU* 3.5 36.3 + - - +
1139B HIS* 3.5 50.2 - - + +
1140B ASN* 5.4 1.0 + - - -
1174B TYR* 3.6 6.3 - - - +
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Residues in contact with GLU1123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119B ALA 4.2 3.0 + - - +
1120B LYS* 3.0 35.7 + - + +
1122B LYS* 1.3 95.0 - - - +
1124B ASP* 1.3 58.5 + - - +
1126B VAL* 3.3 8.7 + - - +
1127B SER* 2.9 32.9 + - - -
1132B GLU* 5.2 5.7 - - - +
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Residues in contact with ASP1124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120B LYS* 3.0 46.3 + - - +
1121B SER* 3.5 11.5 + - - +
1123B GLU* 1.3 76.6 - - - +
1125B LEU* 1.3 56.8 + - + +
1127B SER* 2.6 22.0 + - - -
1128B GLN* 2.9 20.8 + - - +
1185B ARG* 3.9 27.3 + - - +
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Residues in contact with LEU1125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1121B SER 2.9 23.3 + - - +
1122B LYS* 3.5 4.5 - - - +
1124B ASP* 1.3 70.8 - - + +
1126B VAL* 1.3 60.4 + - - +
1128B GLN* 2.8 21.5 + - - +
1129B GLY 3.3 2.1 + - - -
1130B PHE* 3.1 50.4 + - + -
1135B ILE* 3.9 12.8 - - + -
1174B TYR* 4.0 22.7 - - + +
1177B LEU* 3.7 28.9 - - + +
1178B LEU* 4.0 24.7 - - + +
1181B GLY* 3.9 12.6 - - - -
1185B ARG* 5.5 2.7 - - - +
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Residues in contact with VAL1126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1122B LYS* 2.9 31.3 + - + +
1123B GLU* 3.8 11.0 - - + +
1125B LEU* 1.3 72.2 - - - +
1127B SER* 1.3 61.8 + - - +
1129B GLY* 3.2 12.3 + - - -
1130B PHE 3.7 15.0 - - - +
1132B GLU* 3.8 43.1 - - + +
1135B ILE* 3.7 19.1 - - + -
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Residues in contact with SER1127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123B GLU 2.9 15.5 + - - -
1124B ASP* 2.6 27.7 + - - -
1126B VAL* 1.3 77.7 - - - +
1128B GLN* 1.3 58.2 + - - +
1129B GLY* 3.2 1.8 + - - -
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Residues in contact with GLN1128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124B ASP 2.9 9.9 + - - +
1125B LEU* 2.8 18.3 + - - +
1127B SER* 1.3 76.9 - - - +
1129B GLY* 1.3 57.4 + - - +
1130B PHE* 3.6 11.5 - - + -
1181B GLY* 2.8 36.7 + - - +
1184B GLN* 3.9 13.6 - - + +
1185B ARG* 2.9 51.5 + - - +
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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