Contacts of the helix formed by residues 1041 - 1053 (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 TYR1041 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001B SER 3.4 12.7 - - - +
1002B THR 3.1 20.4 - - - +
1003B HIS 3.7 11.7 - - - +
1004B PRO* 3.5 37.3 - - + +
1007B CYS* 3.7 14.1 - - - +
1039B ASP* 2.8 6.1 + - - +
1040B GLN* 1.3 115.2 + - + +
1042B GLY* 1.3 68.0 + - - +
1043B ASN 3.2 1.8 - - - -
1044B TYR* 3.1 23.2 + - - +
1045B VAL 3.6 3.1 + - - -
16D A 3.6 44.3 + - - -
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Residues in contact with GLY1042 (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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1001B SER 3.1 16.7 + - - -
1036B LEU* 2.9 25.1 - - - -
1039B ASP* 2.6 20.0 + - - -
1041B TYR* 1.3 74.5 - - - +
1043B ASN* 1.3 60.4 + - - +
1045B VAL* 3.2 5.2 + - - +
1046B ILE* 3.1 27.7 + - - +
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Residues in contact with ASN1043 (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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1036B LEU 2.9 8.7 + - - -
1037B VAL* 3.7 17.0 - - - +
1039B ASP 3.1 16.0 + - - +
1040B GLN* 2.8 31.1 + - - +
1041B TYR 3.2 0.8 - - - -
1042B GLY* 1.3 76.2 - - - +
1044B TYR* 1.3 61.9 + - - +
1046B ILE* 3.6 1.1 + - - -
1047B GLN* 2.7 61.9 + - - +
1077B PHE* 3.9 17.2 - - + +
1081B VAL* 3.7 10.4 - - + +
15D U 2.9 28.2 + - - -
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Residues in contact with TYR1044 (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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1011B GLN* 3.6 21.7 - - - +
1040B GLN 3.5 25.8 - - - -
1041B TYR* 3.1 9.8 + - - +
1042B GLY 3.1 0.4 - - - -
1043B ASN* 1.3 78.6 - - - +
1045B VAL* 1.3 58.9 + - - +
1047B GLN* 3.2 14.7 + - + +
1048B HIS* 2.8 28.8 + - - +
15D U 3.0 61.6 + + + +
16D A 3.3 69.7 + + + +
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Residues in contact with VAL1045 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1001B SER* 4.0 16.6 - - - +
1007B CYS* 3.6 43.5 - - + +
1010B ILE* 4.0 14.6 - - + -
1011B GLN* 4.2 4.7 - - + +
1014B LEU* 4.5 5.4 - - + -
1029B LEU* 3.6 37.0 - - + -
1036B LEU* 5.9 0.4 - - + -
1041B TYR 3.6 4.2 + - - +
1042B GLY 3.2 6.8 + - - +
1044B TYR* 1.3 75.5 - - - +
1046B ILE* 1.3 64.8 + - + +
1048B HIS* 3.1 21.1 - - - +
1049B VAL* 3.3 9.4 + - - +
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Residues in contact with ILE1046 (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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1029B LEU* 4.6 11.4 - - + +
1033B THR* 4.5 11.4 - - - +
1036B LEU* 3.5 47.3 - - + -
1037B VAL* 3.9 9.0 - - + -
1042B GLY 3.1 16.9 + - - +
1043B ASN 3.9 4.3 - - - +
1045B VAL* 1.3 73.0 - - + +
1047B GLN* 1.3 67.6 + - - +
1049B VAL* 3.1 17.9 + - + +
1050B LEU* 3.3 11.7 + - + +
1061B ILE* 3.6 38.5 - - + +
1081B VAL* 3.9 17.5 - - + -
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Residues in contact with GLN1047 (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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1043B ASN* 2.7 50.0 + - - +
1044B TYR* 3.5 14.7 - - + +
1046B ILE* 1.3 76.4 - - - +
1048B HIS* 1.3 64.3 + - - +
1050B LEU* 3.0 23.3 + - - +
1051B GLU* 3.1 21.8 + - - +
1080B ASN* 3.6 11.5 - - - +
1081B VAL* 3.8 18.2 - - + -
1084B LYS* 3.0 35.1 + - + +
15D U 2.8 23.9 + - - +
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Residues in contact with HIS1048 (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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1011B GLN* 2.9 33.9 + - + +
1012B ARG* 4.4 2.0 - - - -
1014B LEU* 3.9 26.9 - - + +
1015B GLU* 3.0 49.3 - - + +
1044B TYR 2.8 13.5 + - - +
1045B VAL* 3.1 14.6 - - - +
1047B GLN* 1.3 77.3 - - - +
1049B VAL* 1.3 58.9 + - - +
1051B GLU* 3.2 8.2 + - - +
1052B HIS* 2.9 48.9 + + + +
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Residues in contact with VAL1049 (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* 4.1 12.6 - - + -
1026B LEU* 4.0 23.8 - - + -
1029B LEU* 4.5 8.1 - - + -
1030B HIS* 5.3 0.9 - - + -
1045B VAL 3.4 15.5 - - - +
1046B ILE* 3.1 11.3 + - + +
1048B HIS* 1.3 76.7 - - - +
1050B LEU* 1.3 61.0 + - - +
1053B GLY* 2.7 36.9 + - - +
1054B ARG 4.6 0.2 - - - +
1057B ASP* 3.9 28.7 - - + -
1058B LYS* 3.8 8.9 - - - +
1061B ILE* 4.0 16.2 - - + -
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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 ILE 3.3 11.6 + - - +
1047B GLN* 3.0 10.1 + - - +
1049B VAL* 1.3 76.7 - - - +
1051B GLU* 1.3 53.9 + - - +
1058B LYS* 3.5 34.2 + - + +
1061B ILE* 3.8 25.8 - - + -
1062B VAL* 4.6 2.9 - - + -
1081B VAL* 3.6 28.3 - - + +
1084B LYS* 3.4 34.8 - - + +
1085B CYS* 3.8 22.4 - - - +
1088B HIS* 2.5 34.5 + - + +
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Residues in contact with GLU1051 (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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1047B GLN* 3.1 20.7 + - - +
1048B HIS* 3.9 5.0 - - - +
1050B LEU* 1.3 79.7 - - - +
1052B HIS* 1.3 83.1 + - + +
1084B LYS* 3.2 37.3 - - + +
1088B HIS* 3.1 29.1 + - + -
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Residues in contact with HIS1052 (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 6.1 0.4 - - - +
1015B GLU* 4.7 8.3 + - + -
1048B HIS* 2.9 44.1 + + + +
1050B LEU 3.6 0.2 - - - -
1051B GLU* 1.3 101.6 + - + +
1053B GLY* 1.3 70.9 + - - +
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Residues in contact with GLY1053 (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* 6.0 3.4 - - - -
1048B HIS* 5.9 0.2 - - - -
1049B VAL* 2.7 39.7 + - - +
1052B HIS* 1.3 80.0 - - - +
1054B ARG* 1.3 61.5 + - - -
1055B PRO* 4.0 5.0 - - - +
1058B LYS* 4.6 5.8 - - - +
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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