Contacts of the helix formed by residues 1117 - 1134 (chain B) in PDB entry 3EFJ
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 ASP1117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199A LYS* 3.7 15.5 - - - +
1200A PHE* 5.8 0.2 - - - -
1201A VAL* 3.8 31.7 + - + +
1203A ARG* 3.1 23.1 + - - -
1260A PHE 4.7 2.4 - - - +
1116B THR* 1.3 85.1 + - - +
1118B ILE* 1.3 64.6 + - - +
1119B GLY* 2.9 26.9 + - - -
1120B GLU* 2.9 33.2 + - - +
1121B VAL* 3.1 20.6 + - - +
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Residues in contact with ILE1118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1130A ILE* 5.0 15.0 - - + -
1134A PHE* 5.6 2.9 - - + -
1198A LYS* 3.7 20.4 - - + +
1199A LYS* 3.1 25.3 + - + +
1200A PHE* 3.8 23.3 - - + -
1054B ASP* 5.5 1.5 + - - -
1057B ALA* 3.2 27.6 - - + +
1058B LEU* 3.7 29.4 - - + -
1059B ASN 5.0 1.6 - - - +
1117B ASP* 1.3 73.5 - - - +
1119B GLY* 1.3 57.4 + - - +
1121B VAL* 3.5 3.0 + - - +
1122B SER* 2.6 44.2 + - - +
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Residues in contact with GLY1119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1130A ILE* 3.9 16.9 - - - +
1200A PHE* 5.0 8.4 - - - -
1117B ASP* 2.9 9.2 + - - -
1118B ILE* 1.3 79.9 - - - +
1120B GLU* 1.3 61.1 + - - +
1122B SER* 3.5 1.9 + - - -
1123B GLN* 3.0 36.4 + - - +
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Residues in contact with GLU1120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1203A ARG* 3.7 22.6 + - - +
1260A PHE 5.6 1.0 - - - +
1114B ARG* 3.6 9.9 - - - +
1115B ILE* 4.1 18.5 - - + +
1116B THR* 2.9 34.9 + - - +
1117B ASP* 2.9 32.5 + - - +
1119B GLY* 1.3 72.7 - - - +
1121B VAL* 1.3 59.6 + - - +
1123B GLN* 3.3 6.5 + - - +
1124B PHE* 2.9 28.8 + - - +
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Residues in contact with VAL1121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1054B ASP* 4.3 11.0 - - - +
1058B LEU* 3.9 26.2 - - + -
1115B ILE* 3.5 24.9 - - + +
1116B THR* 3.6 13.2 - - - +
1117B ASP 3.1 15.9 + - - +
1118B ILE* 4.0 4.7 - - - +
1120B GLU* 1.3 73.9 - - - +
1122B SER* 1.3 53.2 + - - +
1124B PHE* 3.2 4.9 + - + +
1125B LEU* 2.8 45.7 + - + +
1147B LEU* 4.4 20.0 - - + -
1153B PRO* 5.7 1.8 - - + -
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Residues in contact with SER1122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1126A THR* 5.0 4.0 - - - -
1130A ILE* 3.5 28.1 - - - +
1058B LEU* 4.0 15.0 - - - +
1062B LEU* 4.0 24.9 - - - +
1118B ILE* 2.6 25.2 + - - +
1119B GLY 3.6 1.3 - - - -
1121B VAL* 1.3 76.9 - - - +
1123B GLN* 1.3 58.3 + - - +
1125B LEU* 3.4 8.1 + - - +
1126B THR* 2.9 30.2 + - - +
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Residues in contact with GLN1123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1123A GLN* 3.2 47.9 + - + +
1126A THR* 3.2 9.3 + - - -
1127A GLU* 3.6 25.3 + - - +
1130A ILE* 5.9 2.0 - - - +
1119B GLY 3.0 22.4 + - - +
1120B GLU* 3.7 5.8 - - - +
1122B SER* 1.3 73.8 - - - +
1124B PHE* 1.3 60.5 + - - +
1126B THR* 3.0 16.3 - - - +
1127B GLU* 2.8 32.8 + - - +
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Residues in contact with PHE1124 (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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2B MT3 3.4 43.1 - + - -
1112B LEU* 4.0 16.6 - - + -
1115B ILE* 4.3 15.5 - - + -
1120B GLU 2.9 13.5 + - - +
1121B VAL* 3.3 15.0 - - + +
1123B GLN* 1.3 75.1 - - - +
1125B LEU* 1.3 69.6 + - + +
1127B GLU* 3.5 1.2 + - - -
1128B GLY* 3.0 18.0 + - - -
1145B ILE* 3.6 31.3 - - + +
1147B LEU* 4.0 13.7 - - + -
1153B PRO* 3.6 35.0 - - + -
1154B LEU 4.4 1.6 - - - -
1155B VAL* 3.5 20.0 - - + -
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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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1058B LEU* 3.4 31.2 - - + -
1062B LEU* 4.8 7.6 - - + -
1063B VAL* 5.5 4.5 - - + -
1066B VAL* 3.7 35.1 - - + +
1121B VAL* 2.8 23.3 + - + +
1122B SER* 3.5 7.9 - - - +
1123B GLN 3.2 0.2 - - - -
1124B PHE* 1.3 76.1 - - + +
1126B THR* 1.3 62.3 + - - +
1128B GLY* 3.0 12.0 + - - -
1129B ILE* 3.0 18.1 + - - +
1145B ILE* 3.4 28.2 - - + +
1147B LEU* 4.0 28.9 - - + -
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Residues in contact with THR1126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062A LEU* 4.3 9.0 - - - +
1122A SER* 3.8 26.4 + - - +
1123A GLN* 4.6 0.8 + - - -
1126A THR* 3.5 27.3 - - + +
1062B LEU* 5.1 1.5 - - - +
1122B SER 2.9 19.6 + - - +
1123B GLN* 3.0 34.1 - - - +
1125B LEU* 1.3 74.2 - - - +
1127B GLU* 1.3 60.9 + - - +
1129B ILE* 3.2 22.5 + - - +
1130B ILE* 3.2 16.2 + - - +
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Residues in contact with GLU1127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B MT3 3.8 21.2 - - + -
1123B GLN 2.8 18.0 + - - +
1124B PHE* 3.7 5.4 - - - +
1126B THR* 1.3 76.6 + - - +
1128B GLY* 1.3 55.8 + - - +
1130B ILE* 3.4 13.7 + - + +
1131B MET* 3.0 28.2 + - - +
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Residues in contact with GLY1128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B MT3 3.7 17.7 - - - -
1069B VAL* 4.0 11.4 - - - -
1124B PHE 3.0 11.6 + - - -
1125B LEU* 3.0 6.0 + - - -
1127B GLU* 1.3 73.0 - - - +
1129B ILE* 1.3 59.3 + - - +
1132B LYS* 2.9 33.4 + - - +
1142B LEU* 3.6 14.2 - - - +
1145B ILE* 5.1 2.0 - - - -
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Residues in contact with ILE1129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059A ASN* 3.2 37.9 - - + +
1062A LEU* 4.4 17.7 - - + -
1062B LEU* 4.7 2.5 - - + -
1065B ALA* 3.8 28.7 - - + +
1066B VAL* 3.7 31.0 - - + -
1068B HIS* 4.4 3.7 - - - +
1069B VAL* 4.0 13.9 - - + -
1125B LEU 3.0 15.7 + - - +
1126B THR* 3.4 15.7 - - - +
1128B GLY* 1.3 77.6 - - - +
1130B ILE* 1.3 62.7 + - + +
1132B LYS* 4.0 1.6 - - - +
1133B ASP* 3.1 29.6 + - - +
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Residues in contact with ILE1130 (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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1059A ASN* 5.7 3.8 - - + +
1062A LEU* 5.6 3.1 - - + -
1118A ILE* 4.0 17.0 - - + -
1119A GLY* 4.2 17.9 - - - +
1122A SER* 3.7 33.4 - - - +
1126B THR* 3.2 15.3 + - - +
1127B GLU* 3.6 12.1 - - - +
1128B GLY 3.2 0.2 - - - -
1129B ILE* 1.3 77.6 - - + +
1131B MET* 1.3 66.9 + - - +
1133B ASP* 3.2 17.6 + - - +
1134B PHE* 3.6 37.5 + - + -
1200B PHE* 4.1 11.9 - - + -
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Residues in contact with MET1131 (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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2B MT3 3.5 52.5 - - + +
1127B GLU 3.0 16.1 + - - +
1130B ILE* 1.3 77.4 - - - +
1132B LYS* 1.3 63.3 + - - +
1134B PHE* 3.2 34.3 + - + +
1139B VAL* 6.1 0.4 - - + -
1140B LEU* 3.2 31.6 - - + +
1141B SER* 4.1 1.3 - - - -
1142B LEU* 3.9 27.7 + - + +
1157B LEU* 3.7 21.3 - - + -
1221B ALA* 5.9 2.7 - - - -
1222B ASP* 6.4 0.2 - - - -
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Residues in contact with LYS1132 (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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1068B HIS* 3.0 37.7 + - + +
1069B VAL* 3.8 28.8 - - + +
1128B GLY 2.9 19.7 + - - +
1129B ILE 4.0 3.4 - - - +
1130B ILE 3.2 0.2 - - - -
1131B MET* 1.3 77.1 - - - +
1133B ASP* 1.3 61.1 - - - +
1134B PHE 3.5 6.2 + - - +
1142B LEU* 3.4 31.1 - - + +
1143B LEU* 3.8 17.9 + - - +
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Residues in contact with ASP1133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059A ASN* 2.8 39.6 + - - +
1060A PRO* 5.2 1.1 - - - +
1068B HIS* 4.1 12.1 - - - -
1129B ILE 3.1 16.1 - - - +
1130B ILE* 3.2 10.2 + - - +
1132B LYS* 1.3 74.9 - - - +
1134B PHE* 1.3 70.1 + - + +
1135B SER* 3.3 8.1 + - - -
1194B TYR* 4.2 2.1 + - - -
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Residues in contact with PHE1134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118A ILE* 4.4 3.4 - - + -
1130B ILE* 3.6 25.8 + - + -
1131B MET* 3.2 31.2 + - + +
1132B LYS 3.7 7.6 - - - +
1133B ASP* 1.3 82.0 - - + +
1135B SER* 1.3 59.3 + - - +
1136B HIS 4.2 0.4 - - - -
1139B VAL* 4.6 16.6 - - + -
1140B LEU 5.8 0.9 - - - +
1141B SER* 5.0 13.0 - - - -
1194B TYR* 3.4 23.8 - + + -
1195B LEU* 4.0 16.2 - - + -
1198B LYS* 3.9 26.7 - - + -
1200B PHE* 3.6 45.5 - + + -
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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