Contacts of the helix formed by residues 1036 - 1046 (chain D) in PDB entry 1I7M
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 PRO1036 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1101C TYR* 3.4 35.7 - - + +
1034D THR 3.4 9.2 - - - +
1035D ILE* 1.3 92.1 - - + +
1037D ARG* 1.3 65.9 + - - +
1038D SER* 3.4 18.8 - - - +
1039D GLU* 2.9 19.5 + - + +
1040D TRP* 3.2 12.5 + - - -
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Residues in contact with ARG1037 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035D ILE 3.7 1.6 + - - -
1036D PRO* 1.3 72.3 - - - +
1038D SER* 1.3 61.5 + - - +
1040D TRP* 3.5 11.3 + - - +
1041D ASP* 2.9 63.5 + - - +
1051D ILE* 3.4 35.3 + - - +
1052D ILE 5.9 0.6 - - - -
1053D SER* 5.7 0.8 - - - +
1054D VAL* 3.7 21.7 - - - +
1063D TYR* 4.3 17.5 - - - -
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Residues in contact with SER1038 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036D PRO* 3.4 15.2 - - - +
1037D ARG* 1.3 77.5 - - - +
1039D GLU* 1.3 67.7 + - - +
1041D ASP* 2.9 27.0 + - - +
1042D ILE* 3.1 12.8 + - - +
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Residues in contact with GLU1039 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097C LEU* 3.5 20.3 - - + +
1101C TYR* 2.9 44.0 + - + +
1035D ILE* 4.1 13.2 - - + -
1036D PRO* 2.9 17.7 + - + +
1038D SER* 1.3 83.5 + - - +
1040D TRP* 1.3 63.9 + - - +
1042D ILE* 2.9 36.5 - - - +
1043D LEU* 3.1 10.7 + - - +
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Residues in contact with TRP1040 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070C MSE 3.6 32.1 - - + -
1072C VAL* 4.2 25.0 - - + +
1077C PHE* 3.8 27.4 - + - -
1094C LEU* 4.1 11.4 - - + -
1097C LEU* 3.6 23.1 - - + -
1032D LEU* 4.8 2.7 + - + -
1035D ILE* 3.3 54.8 + - + +
1036D PRO 3.2 16.8 + - - -
1037D ARG* 3.6 11.4 - - - +
1038D SER 3.2 0.2 - - - -
1039D GLU* 1.3 77.6 - - - +
1041D ASP* 1.3 61.3 + - - +
1043D LEU* 3.7 17.9 + - + +
1044D LEU* 3.1 32.8 + - - +
1051D ILE* 4.0 9.4 - - + -
1063D TYR* 4.2 16.5 + + - -
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Residues in contact with ASP1041 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037D ARG* 2.9 42.2 + - - +
1038D SER* 2.9 12.6 + - - +
1040D TRP* 1.3 76.0 - - - +
1042D ILE* 1.3 54.9 + - - +
1044D LEU* 3.2 1.7 + - - -
1045D LYS* 2.7 37.5 + - - +
1050D SER* 3.7 15.7 + - - +
1051D ILE* 3.7 16.1 + - - +
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Residues in contact with ILE1042 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097C LEU* 5.9 2.0 - - + -
1038D SER 3.1 6.8 + - - +
1039D GLU* 2.9 48.2 - - - +
1041D ASP* 1.3 74.5 - - - +
1043D LEU* 1.3 66.0 + - + +
1045D LYS* 3.2 6.7 + - + +
1046D ASP* 2.9 41.6 + - - +
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Residues in contact with LEU1043 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070C MSE 5.1 1.3 - - - -
1077C PHE* 5.9 0.4 - - + -
1079C LEU* 4.5 11.4 - - + -
1090C ALA* 3.6 38.2 - - + +
1093C PRO* 4.2 10.1 - - + -
1094C LEU* 3.8 13.7 - - + +
1097C LEU* 3.6 28.9 - - + -
1039D GLU 3.1 12.5 + - - +
1040D TRP* 4.0 19.5 - - + +
1042D ILE* 1.3 83.8 - - + +
1044D LEU* 1.3 83.0 + - + +
1046D ASP* 3.6 18.3 + - - +
1047D VAL* 3.8 11.4 + - - +
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Residues in contact with LEU1044 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070C MSE 4.3 11.4 - - + -
1079C LEU* 4.4 13.7 - - + -
1081C THR* 5.8 1.1 - - + -
1040D TRP 3.1 21.2 + - - +
1041D ASP 3.8 0.2 - - - +
1043D LEU* 1.3 90.5 - - + +
1045D LYS* 1.3 61.6 + - - +
1047D VAL* 3.1 24.1 + - + +
1049D CYS* 2.7 46.5 + - - +
1050D SER* 3.7 7.2 - - - +
1051D ILE* 3.7 33.9 - - + +
1065D LEU* 3.8 26.0 - - + -
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Residues in contact with LYS1045 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041D ASP 2.7 22.1 + - - +
1042D ILE* 3.7 7.2 - - + +
1044D LEU* 1.3 68.0 - - - +
1046D ASP* 1.3 63.5 + - - +
1047D VAL 3.0 5.9 + - - -
1048D GLN* 3.0 15.1 + - - +
1049D CYS 3.3 12.7 + - - +
1050D SER* 4.4 4.9 - - - +
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Residues in contact with ASP1046 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089C LYS* 5.9 2.4 - - - +
1090C ALA* 6.2 1.1 - - + -
1093C PRO* 6.1 3.6 - - + +
1042D ILE* 2.9 39.2 + - - +
1043D LEU* 3.6 11.7 - - - +
1044D LEU 3.2 0.4 - - - -
1045D LYS* 1.3 76.4 - - - +
1047D VAL* 1.3 62.2 + - + +
1048D GLN* 3.5 3.4 + - - +
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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