Contacts of the helix formed by residues 1068 - 1074 (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 ASN1068 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1064B GLU 2.8 27.9 + - - -
1065B ILE 2.8 7.5 + - - +
1066B ARG 3.6 5.9 + - - -
1067B GLY* 1.3 82.1 - - - +
1069B VAL* 1.3 61.2 + - - +
1070B LEU 3.4 2.2 - - - -
1071B VAL* 3.2 15.3 + - + +
1072B LEU* 2.7 49.5 + - + +
1100B GLU* 4.1 0.2 - - - -
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Residues in contact with VAL1069 (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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1065B ILE* 3.3 15.4 + - + +
1068B ASN* 1.3 77.3 - - - +
1070B LEU* 1.3 54.3 + - - +
1072B LEU* 4.7 3.1 - - - -
1073B SER* 2.6 53.0 + - - +
1082B VAL* 3.9 14.5 - - + +
1086B VAL* 6.0 0.2 - - + -
1097B LEU* 3.6 28.0 - - + +
1100B GLU* 3.2 28.9 + - + +
1101B VAL* 3.7 20.9 - - + -
1115B MET* 4.3 4.3 - - + -
1128B MET* 4.4 11.7 - - + -
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Residues in contact with LEU1070 (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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1068B ASN 3.4 0.6 - - - -
1069B VAL* 1.3 79.6 - - - +
1071B VAL* 1.3 68.5 - - + +
1073B SER* 3.5 5.0 - - - -
1074B GLN* 3.0 43.0 + - - +
1100B GLU* 4.5 2.0 + - - -
1101B VAL* 4.2 6.7 - - + +
1104B MET* 4.4 20.2 - - - -
1106B ASP* 3.7 34.8 - - + +
1111B ALA* 3.4 33.9 - - + +
1114B THR* 4.2 10.3 - - - -
1115B MET* 3.4 20.2 - - + -
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Residues in contact with VAL1071 (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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1067B GLY 5.7 0.9 - - - +
1068B ASN* 3.2 17.5 + - + +
1070B LEU* 1.3 82.6 - - + +
1072B LEU* 1.3 69.4 + - + +
1074B GLN* 3.2 24.1 + - - +
1075B HIS* 3.6 8.5 + - - +
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Residues in contact with LEU1072 (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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1037B VAL* 4.4 9.6 - - + -
1038B GLN* 4.1 23.8 - - + +
1064B GLU 4.8 0.9 - - - +
1065B ILE* 4.1 34.5 - - + -
1068B ASN* 2.7 43.4 + - + +
1071B VAL* 1.3 78.3 - - + +
1073B SER* 1.3 57.0 + - - +
1075B HIS* 2.8 30.6 + - + +
1078B ALA* 3.6 21.5 - - + -
1079B SER 3.4 10.0 + - - -
1082B VAL* 3.6 17.0 - - + -
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Residues in contact with SER1073 (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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1069B VAL* 2.6 34.4 + - - +
1070B LEU 3.5 5.6 - - - -
1071B VAL 3.3 0.2 - - - -
1072B LEU* 1.3 73.3 - - - +
1074B GLN* 1.3 58.8 + - - +
1075B HIS 3.1 0.2 - - - -
1079B SER* 3.3 16.1 - - - +
1082B VAL* 3.7 3.0 - - - +
1115B MET* 3.1 33.5 - - - +
1120B TYR 3.4 0.5 - - - -
1121B ALA* 3.0 30.9 + - - -
1124B VAL* 3.6 18.7 - - - +
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Residues in contact with GLN1074 (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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1070B LEU* 3.0 40.4 + - + +
1071B VAL* 3.2 14.2 + - - +
1072B LEU 3.1 1.2 - - - -
1073B SER* 1.3 77.6 - - - +
1075B HIS* 1.3 57.9 + - - +
1076B LYS 3.8 0.3 + - - -
1106B ASP* 5.6 0.8 + - - -
1114B THR* 3.7 24.3 - - + +
1118B ASP* 3.5 31.0 - - + +
1120B TYR* 3.4 18.9 - - - -
1121B ALA* 4.4 7.0 - - + -
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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