Contacts of the helix formed by residues 111 - 118 (chain D) in PDB entry 1C04
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 PHE 111 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D GLY 4.8 0.2 - - - -
38D VAL* 5.1 2.5 - - + -
61D VAL* 2.3 64.8 - - + -
87D ILE* 4.2 9.9 - - + -
91D LYS* 3.7 52.5 - - + -
106D LEU* 3.2 29.2 + - + +
107D ARG 4.6 0.2 + - - -
109D LYS* 3.5 29.4 - - + -
110D ASP* 1.3 73.3 - - - +
112D MET* 1.3 63.4 + - - +
113D LYS 3.4 2.5 - - - -
114D ILE* 3.4 20.6 + - + +
115D ILE* 3.2 26.5 + - - +
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Residues in contact with MET 112 (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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107D ARG* 3.5 59.0 - - - +
110D ASP* 3.1 27.4 + - - +
111D PHE* 1.3 76.4 - - - +
113D LYS* 1.3 60.6 + - - +
115D ILE* 3.4 12.5 + - + +
116D SER* 3.0 28.2 + - - -
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Residues in contact with LYS 113 (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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91D LYS 5.5 0.7 - - - +
92D SER* 4.7 12.6 - - - +
93D PRO* 3.6 31.0 - - + -
111D PHE 3.4 0.6 - - - -
112D MET* 1.3 78.0 - - - +
114D ILE* 1.3 59.3 + - - +
116D SER* 2.8 26.2 + - - +
117D LEU* 2.9 39.6 + - + +
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Residues in contact with ILE 114 (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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11D ALA 5.0 0.2 - - - +
63D VAL* 4.9 0.2 - - + -
85D VAL* 2.4 69.5 - - + -
91D LYS 4.6 2.9 - - - +
93D PRO* 4.0 20.2 - - + -
98D ILE* 4.2 20.9 - - + +
102D VAL* 4.7 6.3 - - + -
106D LEU* 4.4 18.2 - - + -
111D PHE* 3.4 25.9 + - + +
112D MET 3.3 0.4 - - - -
113D LYS* 1.3 76.1 - - - +
115D ILE* 1.3 57.6 + - - +
117D LEU* 3.2 6.9 + - - +
118D ALA* 2.9 29.1 + - - +
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Residues in contact with ILE 115 (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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102D VAL* 4.3 8.1 - - + -
103D ALA 4.1 11.0 - - - +
104D ARG* 4.6 0.7 - - + +
106D LEU* 3.8 22.2 - - + -
107D ARG* 4.0 33.0 - - + +
111D PHE 3.2 14.9 + - - +
112D MET* 3.6 19.5 - - + +
113D LYS 3.3 0.2 - - - -
114D ILE* 1.3 77.0 - - - +
116D SER* 1.3 63.0 + - - +
117D LEU 3.6 0.2 + - - -
118D ALA* 3.6 16.1 + - - +
121D VAL* 3.9 31.8 - - + +
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Residues in contact with SER 116 (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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112D MET 3.0 13.9 + - - -
113D LYS* 2.8 34.3 + - - +
115D ILE* 1.3 81.5 - - - +
117D LEU* 1.3 62.3 + - - +
118D ALA 3.6 3.8 + - - +
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Residues in contact with LEU 117 (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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93D PRO* 3.8 28.0 - - + -
95D GLY 4.7 2.0 - - - +
96D THR* 3.9 29.6 - - - +
97D ARG* 5.3 5.9 - - - +
98D ILE* 3.6 32.0 + - + +
113D LYS* 2.9 37.7 + - + +
114D ILE 3.2 0.4 + - - +
116D SER* 1.3 80.3 + - - +
118D ALA* 1.3 64.9 + - - +
119D PRO* 3.5 5.4 - - - +
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Residues in contact with ALA 118 (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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98D ILE* 4.1 4.9 - - + +
102D VAL* 3.4 38.1 - - + -
114D ILE 2.9 14.3 + - - +
115D ILE 3.8 9.9 - - - +
116D SER 3.4 6.7 - - - +
117D LEU* 1.3 77.4 - - - +
119D PRO* 1.3 74.1 - - + +
120D GLU* 3.3 8.9 + - - +
121D VAL* 4.2 3.9 - - + +
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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