Contacts of the helix formed by residues 1005 - 1017 (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 TYR1005 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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965B VAL 3.4 14.6 - - - +
966B LYS 4.5 2.7 - - - -
967B ASP* 3.6 13.7 - - - -
968B GLN* 3.3 44.8 - - + +
971B ASN* 3.4 29.5 - - - +
972B HIS* 5.8 0.2 - - - -
1003B HIS* 2.9 23.0 + + - +
1004B PRO* 1.3 93.0 - - + +
1006B GLY* 1.3 57.7 + - - +
1007B CYS 3.2 1.3 - - - -
1008B ARG* 2.8 35.6 + - - +
1009B VAL* 3.3 7.7 + - - +
17D U 5.4 13.0 - - - -
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Residues in contact with GLY1006 (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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965B VAL* 3.8 25.0 + - - +
1000B LEU* 3.1 19.7 - - - -
1003B HIS* 3.4 10.9 + - - -
1005B TYR* 1.3 80.2 - - - +
1007B CYS* 1.3 54.0 + - - +
1009B VAL* 2.7 22.6 + - - +
1010B ILE* 2.8 16.2 + - - +
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Residues in contact with CYS1007 (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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1000B LEU 2.7 10.1 + - - -
1001B SER* 3.4 22.0 - - - +
1003B HIS 3.2 23.2 + - - +
1004B PRO 3.8 13.2 - - - -
1006B GLY* 1.3 73.7 - - - +
1008B ARG* 1.3 62.0 + - - +
1010B ILE* 3.9 2.5 - - - -
1011B GLN* 3.1 30.1 + - - +
1041B TYR* 3.7 18.2 - - + +
1045B VAL* 3.6 17.8 - - + +
16D A 3.8 26.0 - - - -
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Residues in contact with ARG1008 (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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971B ASN* 5.7 0.4 - - - -
975B GLN* 3.7 17.0 - - - +
1004B PRO 3.6 17.3 - - - +
1005B TYR* 2.8 15.0 + - - +
1007B CYS* 1.3 83.2 - - - +
1009B VAL* 1.3 66.0 + - - +
1011B GLN* 3.3 6.1 + - - +
1012B ARG* 3.1 39.9 + - - +
16D A 3.4 51.3 + - + +
17D U 2.5 95.1 + - - +
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Residues in contact with VAL1009 (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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965B VAL* 4.1 15.0 - - + -
971B ASN* 4.0 11.0 - - + +
974B VAL* 3.9 13.5 - - + -
975B GLN* 3.8 24.9 - - + +
978B ILE* 3.6 16.8 - - + -
993B PHE* 3.3 34.3 - - + -
1005B TYR 3.3 10.3 + - - +
1006B GLY* 2.7 11.0 + - - +
1008B ARG* 1.3 76.2 - - - +
1010B ILE* 1.3 63.5 + - - +
1012B ARG* 3.2 5.6 + - - +
1013B ILE* 3.0 27.7 + - - +
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Residues in contact with ILE1010 (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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993B PHE* 4.6 15.0 - - + -
997B VAL* 3.4 13.2 - - + +
1000B LEU* 3.4 18.4 - - + +
1001B SER* 2.9 49.4 - - - +
1006B GLY 2.8 12.5 + - - +
1007B CYS* 4.1 4.9 - - - +
1009B VAL* 1.3 77.7 - - - +
1011B GLN* 1.3 60.5 + - - +
1013B ILE* 3.4 8.8 + - - +
1014B LEU* 3.0 33.2 + - + +
1025B ILE* 4.1 23.1 - - + -
1029B LEU* 4.7 3.4 - - + -
1045B VAL* 4.0 20.9 - - + -
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Residues in contact with GLN1011 (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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1007B CYS 3.1 18.2 + - - +
1008B ARG* 3.3 9.9 + - - +
1009B VAL 3.2 0.8 - - - -
1010B ILE* 1.3 76.7 - - - +
1012B ARG* 1.3 79.3 + - - +
1014B LEU* 3.3 7.5 + - - +
1015B GLU* 3.0 30.1 + - - +
1044B TYR* 3.6 22.1 - - - +
1045B VAL* 4.0 13.5 - - + +
1048B HIS* 2.9 36.8 + - + +
16D A 3.1 38.7 + - - +
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Residues in contact with ARG1012 (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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975B GLN* 3.4 41.7 + - + +
978B ILE* 3.3 29.4 - - + +
979B GLU* 4.8 9.4 - - - -
1008B ARG* 3.1 35.5 + - - +
1009B VAL 3.7 5.8 - - - +
1011B GLN* 1.3 95.4 + - - +
1013B ILE* 1.3 57.4 + - - +
1015B GLU* 2.7 39.6 + - - -
1016B HIS* 2.8 38.5 + - + -
1048B HIS* 4.4 1.0 - - - -
17D U 5.0 6.5 + - - +
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Residues in contact with ILE1013 (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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978B ILE* 3.4 32.5 - - + -
986B LEU* 5.7 0.7 - - + -
989B ILE* 4.0 17.7 - - + -
990B ILE* 4.4 9.6 - - + -
993B PHE* 4.2 14.8 - - + -
1009B VAL 3.0 22.6 + - - +
1010B ILE* 3.5 9.9 - - + +
1012B ARG* 1.3 77.6 - - - +
1014B LEU* 1.3 57.1 + - + +
1017B CYS* 3.0 52.6 + - + +
1022B THR* 3.4 8.1 - - + +
1025B ILE* 4.3 26.2 - - + -
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Residues in contact with LEU1014 (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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1010B ILE* 3.0 28.0 + - + +
1011B GLN* 3.6 10.5 - - - +
1012B ARG 3.1 0.2 - - - -
1013B ILE* 1.3 80.1 - - + +
1015B GLU* 1.3 59.4 + - - +
1017B CYS 4.8 2.1 - - - +
1022B THR* 4.2 19.7 - - - +
1025B ILE* 4.3 17.7 - - + -
1026B LEU* 3.8 28.9 - - + -
1029B LEU* 4.5 1.8 - - + -
1045B VAL* 4.5 7.4 - - + -
1048B HIS* 3.9 28.0 - - + -
1049B VAL* 4.1 21.1 - - + -
1052B HIS* 6.1 0.3 - - - +
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Residues in contact with GLU1015 (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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1011B GLN 3.0 5.2 - - - +
1012B ARG* 2.7 41.7 + - - +
1014B LEU* 1.3 79.0 - - - +
1016B HIS* 1.3 78.1 + - + +
1017B CYS 5.1 0.7 - - - -
1048B HIS* 3.0 41.1 - - - +
1052B HIS* 4.7 9.2 + - + -
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Residues in contact with HIS1016 (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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978B ILE* 3.0 34.3 - - + +
979B GLU* 3.4 30.4 + - + +
983B PRO* 3.8 17.8 - - + +
986B LEU* 5.9 0.4 - - + -
1012B ARG* 2.8 30.5 + - + +
1015B GLU* 1.3 99.9 + - + +
1017B CYS* 1.3 64.7 + - - +
1018B LEU* 3.9 1.2 + - - +
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Residues in contact with CYS1017 (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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978B ILE* 5.1 0.9 - - - -
983B PRO* 4.5 2.0 - - - -
986B LEU* 4.8 16.8 - - - -
990B ILE* 3.7 14.1 - - - -
1013B ILE* 3.0 51.2 + - + +
1014B LEU 4.8 2.6 - - - +
1015B GLU 5.1 0.2 - - - -
1016B HIS* 1.3 80.6 + - - +
1018B LEU* 1.3 64.6 + - - +
1019B PRO* 3.9 1.7 - - - +
1021B GLN* 3.3 25.1 - - + +
1022B THR* 3.6 14.8 - - + +
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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