Contacts of the helix formed by residues 1044 - 1062 (chain B) in PDB entry 3I8E
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 SER1044 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B TYR* 4.3 1.3 - - - -
1023B PRO 5.7 0.5 + - - -
1024B THR* 6.3 0.2 - - - +
1043B LEU* 1.3 74.2 - - - +
1045B GLU* 1.3 78.0 + - - +
1046B SER* 3.3 2.3 + - - -
1047B TRP* 2.8 41.6 + - - +
1048B TYR 3.6 2.3 + - - -
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Residues in contact with GLU1045 (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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3B TYR* 3.6 40.9 - - + +
1044B SER* 1.3 79.1 + - - +
1046B SER* 1.3 83.0 + - - +
1048B TYR* 3.3 13.0 + - - +
1049B ASN* 2.9 25.8 + - - +
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Residues in contact with SER1046 (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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1044B SER* 2.9 3.3 + - - -
1045B GLU* 1.3 92.5 + - - +
1047B TRP* 1.3 74.5 + - - +
1049B ASN* 3.3 8.4 + - - +
1050B LEU* 3.0 32.4 + - - +
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Residues in contact with TRP1047 (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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1023B PRO* 4.1 33.0 - - + -
1043B LEU* 4.3 17.7 - - + -
1044B SER* 2.8 29.3 + - - +
1046B SER* 1.3 89.9 + - - +
1048B TYR* 1.3 64.0 + - - +
1050B LEU* 3.4 14.6 + - + +
1051B LEU* 2.9 49.5 + - + +
1132B VAL* 3.7 33.9 - - + -
1135B GLU* 4.9 15.3 - - + -
1136B LEU* 4.4 19.7 - - + -
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Residues in contact with TYR1048 (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 SER 4.5 1.3 - - - -
3B TYR* 3.6 46.0 - + + -
4B ASN 4.6 0.4 - - - -
1043B LEU* 4.4 4.5 - - + +
1044B SER 3.6 1.6 + - - -
1045B GLU 3.3 9.3 + - - +
1047B TRP* 1.3 77.8 - - - +
1049B ASN* 1.3 70.3 + - - +
1051B LEU* 3.0 2.3 + - - +
1052B LEU* 2.6 69.4 + - + +
1086B THR* 4.1 5.7 - - - +
1087B GLY* 3.0 40.8 + - - -
1088B PHE 3.9 8.3 - - - -
1089B ILE* 3.5 29.2 - - + -
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Residues in contact with ASN1049 (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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3B TYR* 5.3 4.1 + - - -
1045B GLU* 2.9 31.1 + - - +
1046B SER* 3.3 7.5 + - - +
1048B TYR* 1.3 92.8 - - - +
1050B LEU* 1.3 61.1 + - - +
1052B LEU* 4.3 7.8 - - - +
1053B ASP* 3.3 22.7 + - - +
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Residues in contact with LEU1050 (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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1046B SER* 3.0 18.7 + - - +
1047B TRP* 3.5 17.3 - - + +
1049B ASN* 1.3 77.8 - - - +
1051B LEU* 1.3 58.0 + - + +
1053B ASP* 3.3 5.3 + - - +
1054B MET* 2.7 45.2 + - + +
1129B LEU* 4.0 29.6 - - + -
1132B VAL* 5.6 10.1 - - + -
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Residues in contact with LEU1051 (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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5B TYR* 4.5 12.6 - - + -
1043B LEU* 4.2 17.0 - - + -
1047B TRP* 2.9 37.5 + - + +
1050B LEU* 1.3 79.6 - - + +
1052B LEU* 1.3 56.1 + - - +
1053B ASP 3.1 1.6 - - - -
1054B MET* 3.4 28.5 - - + -
1055B GLN* 2.7 35.5 + - - +
1089B ILE* 3.7 26.2 - - + -
1094B ILE* 3.8 25.2 - - + +
1132B VAL* 5.4 7.2 - - + -
1133B VAL* 5.8 0.2 - - + -
1136B LEU* 4.3 11.9 - - + -
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Residues in contact with LEU1052 (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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1048B TYR* 2.6 65.5 + - + +
1049B ASN* 4.3 7.4 - - - +
1051B LEU* 1.3 71.4 - - - +
1053B ASP* 1.3 66.3 + - + +
1055B GLN* 3.3 25.3 + - - +
1056B ASN* 3.4 20.4 + - - +
1089B ILE* 4.5 4.6 - - + +
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Residues in contact with ASP1053 (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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1049B ASN 3.3 18.0 + - - +
1050B LEU* 3.5 4.0 - - - +
1051B LEU 3.1 0.2 - - - -
1052B LEU* 1.3 80.4 - - + +
1054B MET* 1.3 55.3 + - - +
1055B GLN 2.6 5.2 + - - -
1056B ASN* 2.6 35.4 + - - +
1057B ARG* 3.0 48.8 + - - +
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Residues in contact with MET1054 (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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1050B LEU* 2.7 28.7 + - + +
1051B LEU* 3.3 14.1 + - + +
1053B ASP* 1.3 70.9 - - - +
1055B GLN* 1.3 56.4 + - - +
1057B ARG* 4.2 9.3 - - - +
1058B LEU* 3.1 34.4 + - + +
1094B ILE* 3.5 48.5 - - + +
1097B PHE* 4.7 8.1 - - + -
1108B VAL* 4.2 19.1 - - + -
1129B LEU* 3.7 35.2 - - + -
1133B VAL* 3.8 15.3 - - + -
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Residues in contact with GLN1055 (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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1051B LEU 2.7 14.3 + - - +
1052B LEU* 3.3 17.0 + - - +
1053B ASP 2.6 4.6 + - - -
1054B MET* 1.3 74.0 - - - +
1056B ASN* 1.3 62.1 + - - +
1058B LEU* 3.0 19.9 + - - +
1059B ASN* 3.0 23.2 + - - +
1070B HIS* 4.6 17.6 + - - +
1088B PHE 4.3 5.3 + - - +
1089B ILE* 3.3 35.8 - - - +
1090B ASP* 3.9 9.2 + - - +
1093B LEU* 3.6 22.0 - - + -
1094B ILE* 4.5 9.2 - - + -
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Residues in contact with ASN1056 (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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1052B LEU* 3.4 22.4 + - - +
1053B ASP* 2.6 20.3 + - - +
1055B GLN* 1.3 77.9 - - - +
1057B ARG* 1.3 62.7 + - - +
1059B ASN* 3.7 19.1 + - - +
1060B LYS* 3.8 24.4 + - - +
1071B SER* 5.9 5.1 - - - -
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Residues in contact with ARG1057 (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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1053B ASP* 3.0 46.3 + - - +
1054B MET* 4.2 4.9 - - - +
1056B ASN* 1.3 76.1 - - + +
1058B LEU* 1.3 62.1 + - - +
1059B ASN 3.3 1.0 + - - -
1060B LYS* 3.5 16.6 + - - +
1061B VAL* 3.6 17.9 + - - +
1107B GLU 4.9 2.7 - - - -
1108B VAL* 2.6 57.4 + - + +
1109B VAL* 3.9 4.0 - - - +
1110B ALA* 3.7 15.6 - - - +
1111B ASN* 3.2 45.3 + - - +
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Residues in contact with LEU1058 (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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1054B MET* 3.1 25.2 + - + +
1055B GLN* 3.0 9.0 + - - +
1057B ARG* 1.3 79.4 - - - +
1059B ASN* 1.3 58.0 + - - +
1061B VAL* 4.1 3.1 - - + -
1062B ILE* 3.1 47.0 + - + +
1093B LEU* 3.5 36.2 - - + +
1094B ILE* 3.9 20.4 - - + +
1097B PHE* 3.9 22.0 - - + -
1100B ILE* 3.5 32.5 - - + -
1108B VAL* 4.7 6.1 - - + -
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Residues in contact with ASN1059 (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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58B TYR* 4.5 4.3 + - - -
1055B GLN* 3.0 21.7 + - - +
1056B ASN* 4.2 14.6 - - - +
1057B ARG 3.2 0.8 - - - -
1058B LEU* 1.3 77.5 - - - +
1060B LYS* 1.3 63.6 + - - +
1061B VAL 3.1 1.8 - - - -
1062B ILE* 2.8 27.3 - - - +
1070B HIS* 3.4 47.6 + - - +
1071B SER* 4.9 4.4 - - - +
1093B LEU* 3.6 15.6 - - - +
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Residues in contact with LYS1060 (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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1056B ASN* 3.8 16.1 + - - +
1057B ARG* 3.5 11.3 + - - +
1059B ASN* 1.3 77.4 - - + +
1061B VAL* 1.3 62.9 + - + +
1062B ILE 5.0 0.3 - - - +
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Residues in contact with VAL1061 (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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1057B ARG 3.6 15.6 + - - +
1058B LEU* 4.3 5.2 - - - +
1059B ASN 3.1 0.4 - - - -
1060B LYS* 1.3 82.7 - - + +
1062B ILE* 1.3 62.3 + - - +
1063B LYS* 3.4 16.5 + - - +
1100B ILE* 3.9 23.3 - - + -
1104B LYS* 3.6 46.5 - - + +
1107B GLU* 4.1 23.8 - - + +
1108B VAL* 4.3 9.6 - - + +
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Residues in contact with ILE1062 (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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58B TYR* 4.4 18.6 - - + +
1058B LEU* 3.1 40.1 + - + +
1059B ASN* 2.8 22.1 - - - +
1060B LYS 5.1 0.4 - - - -
1061B VAL* 1.3 77.9 - - + +
1063B LYS* 1.3 87.0 + - - +
1064B SER* 3.6 4.9 + - - +
1093B LEU* 4.1 7.2 - - + -
1096B SER* 3.1 40.8 - - - +
1100B ILE* 4.2 14.1 - - + -
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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