Contacts of the helix formed by residues 1094 - 1106 (chain A) in PDB entry 3MP6
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 THR1094 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1088A ALA* 4.6 1.1 - - - -
1093A GLN* 1.3 76.6 - - - +
1095A VAL* 1.3 59.4 + - - +
1096A ASP* 3.6 8.1 + - - +
1097A GLU* 2.9 47.7 + - - +
1098A ALA* 2.9 28.2 + - - +
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Residues in contact with VAL1095 (chain A).
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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927A LYS* 3.8 13.5 - - + +
930A LEU* 4.1 10.1 - - + -
931A THR* 3.8 33.7 - - + +
934A VAL* 3.8 32.8 - - + -
1088A ALA* 4.3 8.0 - - + +
1093A GLN 4.0 0.2 + - - -
1094A THR* 1.3 72.9 - - - +
1096A ASP* 1.3 65.8 + - - +
1098A ALA 3.8 0.2 - - - -
1099A LEU* 2.9 51.7 + - + +
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Residues in contact with ASP1096 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922A ASP* 4.2 2.8 - - - +
927A LYS* 3.4 40.3 + - - +
1094A THR* 3.3 8.1 + - - +
1095A VAL* 1.3 79.3 - - - +
1097A GLU* 1.3 58.3 + - + +
1100A ALA* 3.0 31.9 + - - +
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Residues in contact with GLU1097 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092A ARG 4.8 1.0 - - - +
1093A GLN* 3.5 26.4 + - + +
1094A THR* 2.9 47.4 + - - +
1096A ASP* 1.3 79.2 - - + +
1098A ALA* 1.3 62.3 + - - +
1100A ALA* 3.5 4.4 + - - +
1101A ALA* 3.2 23.4 + - - +
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Residues in contact with ALA1098 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930A LEU* 5.1 0.2 - - + -
1084A ALA* 3.5 41.1 - - + +
1088A ALA* 4.2 10.3 - - + +
1093A GLN* 3.9 23.0 - - + +
1094A THR 2.9 17.9 + - - +
1095A VAL 3.9 2.7 - - - +
1097A GLU* 1.3 78.2 - - - +
1099A LEU* 1.3 57.7 + - + +
1101A ALA* 3.4 3.8 + - - +
1102A ALA 3.1 21.7 + - - -
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Residues in contact with LEU1099 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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899A ILE* 5.6 8.1 - - + -
921A VAL* 3.3 27.4 - - + +
922A ASP* 3.3 18.5 - - - +
926A ALA* 3.9 7.0 - - + +
927A LYS* 3.8 36.1 - - + +
930A LEU* 3.8 22.9 - - + -
1081A VAL* 6.0 3.8 - - + -
1084A ALA* 4.0 14.8 - - + -
1085A VAL* 6.2 0.4 - - + -
1095A VAL* 2.9 28.3 + - + +
1098A ALA* 1.3 72.3 - - - +
1100A ALA* 1.3 60.3 + - - +
1102A ALA* 3.7 6.4 - - + +
1103A GLN* 2.9 28.8 + - - +
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Residues in contact with ALA1100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922A ASP* 3.5 17.8 + - - +
1096A ASP 3.0 20.7 + - - +
1097A GLU* 3.8 6.1 - - - +
1098A ALA 3.4 0.2 - - - -
1099A LEU* 1.3 75.4 - - - +
1101A ALA* 1.3 62.4 + - - +
1103A GLN* 3.3 4.0 + - - +
1104A THR* 3.2 25.2 + - - -
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Residues in contact with ALA1101 (chain A).
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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1083A THR* 6.6 0.4 - - + -
1093A GLN* 5.2 8.7 - - - +
1097A GLU 3.2 11.4 + - - +
1098A ALA* 3.7 9.6 - - - +
1100A ALA* 1.3 77.4 - - - +
1102A ALA* 1.3 58.6 + - - +
1104A THR* 3.2 8.8 + - - -
1105A ASN* 2.9 41.8 + - - +
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Residues in contact with ALA1102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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921A VAL* 3.8 13.9 - - + -
1080A ALA* 3.8 33.4 - - + +
1081A VAL* 4.6 4.0 - - + +
1084A ALA* 3.9 9.4 - - + -
1098A ALA 3.1 17.1 + - - +
1099A LEU* 3.7 8.3 - - + +
1100A ALA 3.3 0.2 - - - -
1101A ALA* 1.3 76.6 - - - +
1103A GLN* 1.3 56.1 + - - +
1106A ALA* 2.8 36.4 + - - +
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Residues in contact with GLN1103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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917A LYS 5.5 2.4 + - - -
919A VAL* 2.8 49.2 + - - +
921A VAL* 3.4 22.4 + - - +
922A ASP* 3.6 19.7 + - + +
1099A LEU 2.9 17.6 + - - +
1100A ALA* 3.5 7.4 - - - +
1101A ALA 3.3 0.2 - - - -
1102A ALA* 1.3 76.9 - - - +
1104A THR* 1.3 63.3 - - - +
1106A ALA* 3.9 5.5 + - - +
1107A ALA* 4.2 11.3 + - - +
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Residues in contact with THR1104 (chain A).
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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1100A ALA 3.2 10.7 + - - -
1101A ALA* 3.2 11.9 + - - -
1103A GLN* 1.3 82.7 - - - +
1105A ASN* 1.3 73.2 + - - +
1106A ALA 3.7 0.2 + - - -
1107A ALA* 3.7 10.6 + - - +
1108A ALA* 3.9 10.4 + - + +
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Residues in contact with ASN1105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076A ALA* 4.0 12.5 - - - +
1080A ALA* 4.1 13.7 - - + -
1101A ALA* 2.9 27.8 + - - +
1102A ALA* 4.9 0.2 - - - -
1104A THR* 1.3 88.7 - - - +
1106A ALA* 1.3 64.1 + - - +
1107A ALA 3.0 3.6 + - - -
1108A ALA* 3.2 22.8 + - - +
1126A LEU* 3.9 35.1 - - + +
1127A VAL 4.6 10.0 + - - +
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Residues in contact with ALA1106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907A PHE* 3.8 4.8 - - + -
919A VAL* 4.0 25.6 - - + -
921A VAL* 5.1 2.0 - - + -
1073A GLN* 3.0 24.1 + - - +
1076A ALA* 3.7 9.6 - - - +
1077A PHE* 3.7 25.1 + - + -
1080A ALA* 3.7 12.0 - - + +
1081A VAL* 5.6 0.2 - - + -
1102A ALA 2.8 18.8 + - - +
1103A GLN 4.3 0.4 - - - +
1104A THR 3.5 0.2 - - - -
1105A ASN* 1.3 77.1 - - - +
1107A ALA* 1.3 56.4 + - - +
1108A ALA 3.4 0.2 - - - -
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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