Contacts of the helix formed by residues 1018 - 1030 (chain B) in PDB entry 1M8X
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 LEU1018 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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983B PRO* 3.3 45.1 - - + -
984B GLN* 4.3 8.5 - - + +
1016B HIS 5.1 0.7 - - - +
1017B CYS* 1.3 74.3 - - - +
1019B PRO* 1.3 70.2 - - + +
1020B ASP* 3.1 20.6 - - - +
1021B GLN* 2.7 38.7 + - - +
1022B THR* 2.9 11.9 + - - +
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Residues in contact with PRO1019 (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 CYS 3.9 2.2 - - - +
1018B LEU* 1.3 96.8 - - + +
1020B ASP* 1.3 56.7 + - - +
1022B THR* 3.3 10.7 + - - +
1023B LEU* 3.0 31.0 + - - +
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Residues in contact with ASP1020 (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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987B GLN* 4.1 8.3 + - - +
1018B LEU* 3.2 22.5 - - - +
1019B PRO* 1.3 79.3 - - - +
1021B GLN* 1.3 75.4 + - - +
1023B LEU* 4.0 7.2 - - - +
1024B PRO* 3.5 14.6 - - - +
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Residues in contact with GLN1021 (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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983B PRO* 2.9 29.1 + - - +
984B GLN* 4.0 3.6 + - - +
987B GLN* 3.2 42.9 + - - +
990B ILE* 3.8 21.1 - - + +
1013B ILE* 5.5 0.2 - - - -
1017B CYS* 3.3 22.1 - - + +
1018B LEU* 2.7 36.3 + - - +
1020B ASP* 1.3 92.1 - - - +
1022B THR* 1.3 59.2 + - - +
1023B LEU 3.2 1.3 - - - -
1024B PRO* 3.0 22.6 - - - +
1025B ILE* 3.7 9.4 - - - +
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Residues in contact with THR1022 (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 ILE* 3.4 27.4 - - + +
1014B LEU* 4.2 22.9 - - - +
1017B CYS* 3.6 23.1 - - + +
1018B LEU 2.9 4.6 + - - +
1019B PRO* 3.3 17.0 + - - +
1021B GLN* 1.3 75.2 - - - +
1023B LEU* 1.3 69.3 + - - +
1025B ILE* 2.9 12.7 + - - +
1026B LEU* 2.8 35.3 + - - +
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Residues in contact with LEU1023 (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 PRO 3.0 20.2 + - - +
1020B ASP* 4.0 7.4 - - - +
1022B THR* 1.3 76.8 + - - +
1024B PRO* 1.3 67.9 - - + +
1026B LEU* 3.3 5.7 + - - +
1027B GLU* 2.9 77.6 + - + +
1054B ARG* 4.1 25.4 - - - +
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Residues in contact with PRO1024 (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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990B ILE* 4.0 17.3 - - + -
994B LYS* 5.6 12.6 - - + -
1020B ASP 3.5 11.0 - - - +
1021B GLN 3.0 27.8 - - - +
1023B LEU* 1.3 91.8 - - + +
1025B ILE* 1.3 62.7 + - + +
1027B GLU* 3.5 18.4 + - - +
1028B GLU* 3.4 23.9 + - - +
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Residues in contact with ILE1025 (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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990B ILE* 4.5 15.0 - - + +
993B PHE* 4.0 28.9 - - + -
997B VAL* 3.7 31.9 - - + +
1010B ILE* 4.1 21.3 - - + -
1013B ILE* 4.3 15.9 - - + -
1014B LEU* 4.3 9.2 - - + -
1021B GLN 3.7 17.0 - - - +
1022B THR* 2.9 12.2 + - - +
1024B PRO* 1.3 78.6 - - + +
1026B LEU* 1.3 62.4 + - - +
1028B GLU* 3.1 6.8 + - - +
1029B LEU* 3.1 26.7 + - + +
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Residues in contact with LEU1026 (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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1014B LEU* 3.8 17.7 - - + -
1022B THR* 2.8 32.5 + - - +
1023B LEU* 3.9 3.6 - - - +
1025B ILE* 1.3 70.7 - - - +
1027B GLU* 1.3 54.9 + - - +
1028B GLU 2.7 15.3 + - - -
1029B LEU* 2.9 35.0 + - + +
1030B HIS* 3.0 22.7 + - + +
1049B VAL* 4.0 24.7 - - + -
1053B GLY* 6.0 1.6 - - - -
1054B ARG* 4.5 15.3 - - + +
1057B ASP* 3.4 33.9 - - + +
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Residues in contact with GLU1027 (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 LEU* 2.9 62.7 + - + +
1024B PRO* 3.5 14.3 - - + +
1025B ILE 3.3 0.2 - - - -
1026B LEU* 1.3 75.5 - - + +
1028B GLU* 1.3 56.0 + - - +
1030B HIS* 4.4 9.3 - - - +
1031B GLN* 2.9 28.3 + - - +
1054B ARG* 5.4 3.1 - - - +
1060B LYS* 5.5 5.4 - - - +
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Residues in contact with GLU1028 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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994B LYS* 4.2 6.4 - - - +
995B GLY* 3.2 24.4 + - - -
996B GLN 3.3 8.5 + - - -
997B VAL* 2.9 45.5 + - + +
998B PHE* 3.9 6.5 + - + +
1024B PRO 3.4 10.8 + - - +
1025B ILE 3.1 9.4 + - - +
1026B LEU 2.7 1.4 + - - -
1027B GLU* 1.3 78.4 - - - +
1029B LEU* 1.3 63.4 + - - +
1030B HIS 3.2 1.8 - - - -
1031B GLN* 3.3 33.0 + - - +
1032B HIS* 4.0 12.8 + - + -
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Residues in contact with LEU1029 (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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997B VAL* 3.6 12.6 - - + +
998B PHE* 6.0 0.7 - - - +
1001B SER* 3.4 25.6 - - - +
1010B ILE* 4.7 1.1 - - + -
1014B LEU* 4.5 4.7 - - + -
1025B ILE* 3.1 25.9 + - + +
1026B LEU* 2.9 34.4 + - + +
1028B GLU* 1.3 77.8 - - - +
1030B HIS* 1.3 65.8 + - + +
1032B HIS 3.3 2.3 + - - -
1033B THR* 3.2 19.7 + - - -
1036B LEU* 3.4 27.3 - - + +
1045B VAL* 3.6 25.8 - - + -
1046B ILE* 4.6 6.9 - - + +
1049B VAL* 4.5 9.2 - - + -
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Residues in contact with HIS1030 (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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1026B LEU* 3.0 27.7 + - + +
1027B GLU* 4.4 6.7 - - - +
1028B GLU 3.2 0.2 - - - -
1029B LEU* 1.3 75.2 - - + +
1031B GLN* 1.3 58.4 + - + +
1032B HIS 2.8 11.7 + - - -
1033B THR* 3.3 23.7 + - - +
1049B VAL* 5.3 2.2 - - + -
1057B ASP* 2.6 61.1 + - + -
1060B LYS* 3.4 42.0 - - + +
1061B ILE* 4.4 10.7 - - + +
1064B GLU* 5.1 4.0 - - - +
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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