Contacts of the helix formed by residues 1015 - 1025 (chain B) in PDB entry 4EC0
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 ALA1015 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1006B LEU* 4.1 10.1 - - + -
1008B TYR* 3.3 39.6 - - + -
1012B ARG 3.2 0.8 + - - -
1014B ARG* 1.3 78.8 - - - +
1016B GLU* 1.3 65.7 + - - +
1017B ILE 3.3 1.3 - - - -
1018B ILE* 3.0 19.5 + - - +
1019B ARG* 3.1 30.9 + - - +
1052B PRO* 4.1 9.2 - - + -
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Residues in contact with GLU1016 (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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1012B ARG* 3.0 40.7 + - + +
1013B GLY 3.7 8.5 - - - +
1014B ARG 3.4 1.2 - - - -
1015B ALA* 1.3 77.4 - - - +
1017B ILE* 1.3 63.2 + - - +
1019B ARG* 2.9 31.3 + - - +
1020B TYR* 2.9 36.3 + - + +
1033B ARG* 4.8 1.0 + - - -
1155B ILE* 3.7 16.4 - - + -
1190B TRP* 2.8 31.5 + - - -
1194B ARG* 2.9 19.9 + - - +
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Residues in contact with ILE1017 (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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1013B GLY 4.9 1.0 + - - -
1014B ARG 4.0 16.5 + - - +
1016B GLU* 1.3 77.7 - - - +
1018B ILE* 1.3 69.3 + - + +
1020B TYR* 3.2 1.6 + - - +
1021B ILE* 3.1 28.8 + - + +
1064B SER* 4.3 2.7 - - - +
1065B LEU* 4.2 14.8 - - + -
1068B ALA* 4.1 16.4 - - + -
1148B TRP* 3.8 33.4 - - + +
1151B PHE* 3.6 31.0 - - + -
1152B TYR* 3.8 32.1 - - + +
1155B ILE* 3.4 9.9 - - + +
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Residues in contact with ILE1018 (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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1006B LEU* 4.0 29.4 - - + -
1014B ARG 4.6 0.7 - - - +
1015B ALA 3.0 10.3 + - - +
1017B ILE* 1.3 80.6 - - + +
1019B ARG* 1.3 62.8 + - - +
1021B ILE* 3.1 9.8 + - - +
1022B PHE* 3.0 49.9 + - + -
1052B PRO* 4.3 10.1 - - + -
1054B LEU* 4.9 0.7 - - + -
1064B SER* 3.9 30.5 - - - +
1067B ILE* 3.8 32.5 - - + -
1068B ALA* 4.4 5.4 - - - +
1071B LEU* 3.9 10.5 - - + -
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Residues in contact with ARG1019 (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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1006B LEU* 3.7 11.6 - - + +
1008B TYR* 3.9 5.7 - - - +
1009B PHE 3.7 12.1 + - - -
1011B MET 2.9 27.7 + - - -
1012B ARG* 3.4 9.5 + - - +
1015B ALA* 3.1 30.5 + - - +
1016B GLU* 2.9 26.8 + - - +
1018B ILE* 1.3 77.0 - - - +
1020B TYR* 1.3 61.6 + - - +
1022B PHE* 3.5 5.9 + - - +
1023B ALA* 3.0 23.7 + - - +
1029B TYR* 3.6 18.7 + - - +
1031B ASP* 2.8 24.1 + - - -
1032B HIS 5.5 0.4 + - - -
1033B ARG* 3.3 25.6 - - - +
1190B TRP* 3.6 35.8 - - + +
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Residues in contact with TYR1020 (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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1016B GLU* 2.9 45.0 + - + +
1017B ILE 3.6 8.5 - - - +
1019B ARG* 1.3 76.7 - - - +
1021B ILE* 1.3 58.5 + - - +
1023B ALA* 3.3 6.3 + - - +
1024B TYR* 2.9 30.7 + - - +
1151B PHE* 3.8 32.0 - + + -
1154B GLU* 2.6 34.6 + - - -
1155B ILE* 3.5 23.2 - - + +
1158B THR* 6.0 0.3 - - - -
1181B VAL* 4.7 3.4 - - + -
1187B VAL* 3.9 31.2 - - + +
1190B TRP* 3.6 17.9 - + - -
1191B ILE* 3.9 5.0 - - + +
1194B ARG* 3.1 19.6 + - - -
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Residues in contact with ILE1021 (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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1017B ILE* 3.1 25.3 + - + +
1018B ILE* 3.1 7.4 + - - +
1020B TYR* 1.3 77.7 - - - +
1022B PHE* 1.3 60.2 + - + +
1024B TYR* 3.7 4.8 - - - +
1025B LEU* 2.9 52.1 + - + +
1068B ALA* 3.5 42.6 - - + +
1071B LEU* 3.8 23.6 - - + -
1072B THR* 3.7 18.6 - - + -
1077B LEU* 4.2 7.9 - - + -
1148B TRP* 4.4 4.7 - - + -
1151B PHE* 4.4 10.3 - - + -
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Residues in contact with PHE1022 (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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1004B TYR* 3.7 31.2 - + + -
1006B LEU* 4.8 0.4 - - + -
1018B ILE* 3.0 37.9 + - + +
1019B ARG 3.8 1.8 - - - +
1021B ILE* 1.3 76.3 - - + +
1023B ALA* 1.3 58.7 + - - +
1025B LEU 3.6 0.2 - - - -
1026B ASP* 3.0 8.5 + - - -
1027B ILE* 2.9 53.8 + - + +
1029B TYR* 3.4 55.4 - + + -
1054B LEU* 3.8 23.6 - - + -
1071B LEU* 3.7 31.6 - - + -
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Residues in contact with ALA1023 (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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1019B ARG 3.0 17.3 + - - +
1020B TYR* 3.6 5.4 - - - +
1021B ILE 3.2 0.2 - - - -
1022B PHE* 1.3 78.1 - - - +
1024B TYR* 1.3 63.0 + - - +
1026B ASP* 3.1 14.1 + - - +
1029B TYR* 5.3 1.9 - - + -
1186B ALA* 3.4 21.4 - - - +
1187B VAL* 5.3 0.9 - - - -
1190B TRP* 3.8 32.5 - - + -
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Residues in contact with TYR1024 (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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1020B TYR 2.9 16.2 + - - +
1021B ILE 3.7 3.4 - - - +
1023B ALA* 1.3 79.1 - - - +
1025B LEU* 1.3 70.0 + - + +
1026B ASP* 3.4 1.7 + - - +
1076B ASP* 2.5 40.7 + - - -
1077B LEU* 3.4 27.8 - - + -
1146B VAL* 4.3 12.1 - - + +
1151B PHE* 3.7 27.8 - + + -
1184B ILE* 4.0 26.9 - - + -
1186B ALA* 3.7 15.9 - - + +
1187B VAL* 4.7 2.2 - - + +
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Residues in contact with LEU1025 (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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1021B ILE* 2.9 34.1 + - + +
1024B TYR* 1.3 97.9 - - + +
1026B ASP* 1.3 71.6 + - - +
1027B ILE* 3.3 28.7 + - + +
1071B LEU 3.6 23.6 - - - +
1075B THR* 4.0 30.7 - - + +
1076B ASP* 4.5 2.7 - - - +
1077B LEU* 4.6 2.7 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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