Contacts of the helix formed by residues 101 - 110 (chain 5) in PDB entry 3EXG
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 SER 101 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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965 PHE* 5.0 1.3 - - - -
1005 LEU* 1.3 73.7 - - - +
1025 VAL* 1.3 66.4 + - - +
1035 ARG* 3.0 13.2 + - - +
1045 GLU* 2.9 39.0 + - - +
1055 ILE* 3.2 22.7 + - - +
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Residues in contact with VAL 102 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415 THR* 3.8 16.4 - - + -
455 MET* 3.3 39.9 - - + -
965 PHE* 3.7 25.9 - - + -
1005 LEU 4.2 0.2 + - - -
1015 SER* 1.3 73.3 - - - +
1035 ARG* 1.3 56.3 + - - +
1055 ILE* 3.7 0.2 - - - +
1065 LEU* 2.9 35.4 + - + +
3165 GLU* 5.2 9.4 - - + +
3175 ILE* 3.9 16.4 - - + -
3205 ALA* 3.7 20.2 - - + -
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Residues in contact with ARG 103 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015 SER* 3.0 12.9 - - - +
1025 VAL* 1.3 78.2 - - - +
1045 GLU* 1.3 58.4 + - + +
1065 LEU* 3.5 1.2 + - - +
1075 ALA* 3.0 30.0 + - - +
3195 ASP* 4.3 15.0 + - - +
3205 ALA* 3.9 19.5 - - + +
3225 GLN* 5.8 1.8 - - - +
3235 PHE* 3.2 65.7 - - + +
3245 ALA* 4.7 0.7 - - - +
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Residues in contact with GLU 104 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995 GLY 5.0 0.2 - - - +
1005 LEU* 3.4 20.6 - - - +
1015 SER* 2.9 38.9 + - - +
1035 ARG* 1.3 73.0 - - + +
1055 ILE* 1.3 60.4 + - - +
1075 ALA* 3.9 1.3 - - - -
1085 GLU* 3.0 22.5 + - - +
1145 GLY 3.8 17.5 - - - +
1165 CYS* 3.2 44.1 + - + +
3235 PHE* 5.1 0.4 - - - -
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Residues in contact with ILE 105 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455 MET* 3.4 38.1 - - + -
925 HIS* 4.5 15.0 - - + +
955 THR* 3.6 31.9 - - + -
965 PHE* 3.8 24.0 - - + +
1005 LEU* 4.0 9.2 - - + -
1015 SER 3.3 14.6 - - - +
1025 VAL 3.7 0.9 - - - +
1035 ARG 3.2 0.4 - - - -
1045 GLU* 1.3 75.7 - - - +
1065 LEU* 1.3 66.8 + - - +
1085 GLU* 3.1 12.1 + - - +
1095 LEU* 3.2 24.1 + - + +
1165 CYS* 5.0 0.2 - - - -
1265 MET* 4.2 18.3 - - + +
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Residues in contact with LEU 106 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455 MET* 4.1 25.8 - - + +
485 LYS* 3.7 27.1 - - + -
495 ALA* 4.4 11.4 - - + +
525 LEU* 4.7 7.4 - - + -
585 ILE* 5.6 0.2 - - + -
1025 VAL* 2.9 40.0 + - + +
1035 ARG 4.2 0.9 - - - +
1055 ILE* 1.3 73.1 - - + +
1075 ALA* 1.3 57.4 + - - +
1095 LEU* 2.9 39.0 + - + +
1105 THR* 2.9 17.2 + - - +
3175 ILE* 4.7 2.9 - - + +
3205 ALA* 4.4 1.8 - - + +
3215 ALA* 4.0 20.0 - - + +
3245 ALA* 3.7 14.8 - - + -
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Residues in contact with ALA 107 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035 ARG 3.0 20.0 + - - +
1045 GLU 3.9 0.2 - - - +
1065 LEU* 1.3 76.9 - - - +
1085 GLU* 1.3 61.6 + - - +
1105 THR* 3.3 3.8 + - - -
1115 GLY 3.1 15.6 + - - -
1125 ARG* 3.2 17.6 + - + -
1145 GLY* 3.6 8.7 - - - +
1155 GLY* 3.4 25.8 - - - +
3235 PHE* 4.1 10.8 - - + -
3245 ALA* 3.5 17.2 - - + +
3275 ASP* 6.0 0.2 - - + -
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Residues in contact with GLU 108 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3044 TYR* 3.4 12.1 - - - -
1045 GLU 3.0 20.2 + - - +
1055 ILE 3.1 4.6 + - - +
1075 ALA* 1.3 76.9 - - - +
1095 LEU* 1.3 63.1 + - - +
1115 GLY* 3.3 10.6 + - - -
1155 GLY* 3.5 4.7 - - - -
1165 CYS* 3.9 15.3 - - - -
1175 ALA* 2.5 45.7 + - + -
1185 LYS 3.2 0.7 + - - -
1195 GLY* 3.1 16.2 + - - -
1215 GLY* 2.9 14.5 + - - -
1225 GLY* 2.7 39.6 + - - +
1265 MET* 4.2 10.3 - - + -
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Residues in contact with LEU 109 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3044 TYR* 2.7 27.7 + - - -
495 ALA* 4.1 11.0 - - + -
585 ILE* 3.3 34.5 - - + +
625 CYS* 5.0 1.6 - - - -
925 HIS* 4.1 20.6 - - + +
1055 ILE* 3.2 19.7 - - + +
1065 LEU* 2.9 30.5 + - + +
1085 GLU* 1.3 78.8 - - - +
1105 THR* 1.3 58.3 + - - +
1115 GLY 3.1 4.0 + - - -
1225 GLY 4.5 0.4 - - - -
1235 SER* 3.5 39.9 - - - +
1265 MET* 4.7 5.6 - - - -
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Residues in contact with THR 110 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3044 TYR* 4.7 0.4 - - - -
525 LEU* 4.3 13.7 - - + -
575 ILE* 3.4 42.6 - - + +
585 ILE* 4.1 9.2 - - + -
1065 LEU 2.9 12.1 + - - +
1075 ALA 3.3 9.2 + - - -
1095 LEU* 1.3 74.5 - - - +
1115 GLY* 1.3 60.5 + - - +
1125 ARG* 2.9 19.1 + - - +
3245 ALA* 2.9 35.6 + - + +
3255 THR* 4.5 2.5 - - + -
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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