Contacts of the helix formed by residues 117 - 133 (chain A) in PDB entry 1D8L
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 GLY 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 4.9 1.1 - - - -
115A GLY 4.0 0.4 - - - -
116A ILE* 1.3 84.9 - - - +
118A LYS* 1.3 69.4 + - - +
119A LYS 3.3 2.5 - - - -
120A THR* 3.3 11.4 + - - -
121A ALA* 2.8 36.4 + - - +
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Residues in contact with LYS 118 (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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107A VAL* 4.3 1.9 - - - +
111A VAL* 4.3 31.4 - - + -
116A ILE* 6.5 0.2 - - - -
117A GLY* 1.3 83.1 - - - +
119A LYS* 1.3 67.2 + - + +
121A ALA* 3.7 3.3 - - - +
122A GLU* 3.2 27.6 + - - +
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Residues in contact with LYS 119 (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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117A GLY 3.3 0.4 - - - -
118A LYS* 1.3 80.6 - - + +
120A THR* 1.3 64.4 + - + +
122A GLU* 3.6 7.5 + - - +
123A ARG* 3.0 35.2 + - + +
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Residues in contact with THR 120 (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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79A ASN 5.6 1.3 - - - -
80A GLY* 5.9 6.3 - - - +
81A VAL* 5.3 7.2 - - - +
85A LEU* 5.3 1.6 - - - +
116A ILE* 3.2 43.6 + - - +
117A GLY* 3.2 9.9 + - - -
119A LYS* 1.3 77.9 - - + +
121A ALA* 1.3 56.1 + - - +
123A ARG* 3.2 20.7 + - - +
124A LEU* 2.6 38.9 + - - +
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Residues in contact with ALA 121 (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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107A VAL* 3.5 22.9 - - + -
110A LEU* 4.1 20.6 - - + -
111A VAL* 4.0 11.7 - - + -
116A ILE* 4.3 5.2 - - + -
117A GLY 2.8 17.0 + - - +
118A LYS 3.7 2.7 - - - +
119A LYS 3.3 0.2 - - - -
120A THR* 1.3 77.3 + - - +
122A GLU* 1.3 55.8 + - - +
124A LEU* 3.1 8.9 + - - +
125A ILE* 2.9 36.5 + - - +
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Residues in contact with GLU 122 (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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105A GLU 5.6 0.5 - - - +
107A VAL* 3.7 31.9 - - + +
118A LYS 3.2 17.9 - - - +
119A LYS* 3.7 8.5 - - - +
120A THR 3.3 0.2 - - - -
121A ALA* 1.3 76.1 - - - +
123A ARG* 1.3 62.7 + - + +
125A ILE* 3.5 9.0 + - - +
126A VAL* 3.2 30.6 + - + +
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Residues in contact with ARG 123 (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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78A THR* 3.8 11.1 + - - -
79A ASN* 2.8 57.6 + - - +
81A VAL* 5.4 1.2 - - - +
119A LYS* 3.0 26.4 + - + +
120A THR* 3.3 19.9 + - - +
122A GLU* 1.3 76.6 - - + +
124A LEU* 1.3 66.3 + - - +
126A VAL* 3.2 7.2 + - - +
127A GLU* 3.2 43.9 + - - +
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Residues in contact with LEU 124 (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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75A LEU* 3.6 28.7 - - + -
78A THR* 4.1 19.7 - - + +
81A VAL* 3.9 22.2 - - + -
89A ILE* 4.1 13.2 - - + -
98A PHE* 4.7 3.4 - - + -
102A VAL* 5.6 0.4 - - - -
110A LEU* 4.3 15.5 - - + -
116A ILE* 3.6 30.7 - - + -
120A THR 2.6 18.3 + - - +
121A ALA* 3.1 6.3 + - - +
123A ARG* 1.3 74.3 - - - +
125A ILE* 1.3 56.7 + - - +
127A GLU* 3.4 3.0 + - - +
128A MET* 2.9 45.1 + - + +
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Residues in contact with ILE 125 (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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102A VAL* 3.8 29.1 - - + +
105A GLU* 3.7 36.1 - - + -
106A GLU 3.7 8.5 - - - +
107A VAL* 3.4 43.7 - - + +
110A LEU* 3.8 15.7 - - + -
121A ALA 2.9 21.2 + - - +
122A GLU* 3.8 7.9 - - - +
123A ARG 3.3 0.2 - - - -
124A LEU* 1.3 75.4 - - - +
126A VAL* 1.3 64.1 + - + +
129A LYS* 3.3 23.8 + - + +
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Residues in contact with VAL 126 (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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105A GLU* 6.4 0.7 - - + -
122A GLU* 3.2 18.0 + - + +
123A ARG* 3.2 6.9 + - - +
125A ILE* 1.3 77.7 - - + +
127A GLU* 1.3 66.9 + - + +
129A LYS* 3.1 19.0 - - + +
130A ASP* 3.0 32.8 - - - +
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Residues in contact with GLU 127 (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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77A LYS 4.7 0.3 - - - +
78A THR* 3.5 18.2 - - + -
79A ASN* 4.1 9.0 - - - +
123A ARG* 3.2 40.4 + - - +
124A LEU 4.0 2.0 - - - +
126A VAL* 1.3 81.6 - - + +
128A MET* 1.3 51.7 + - - +
130A ASP* 3.0 10.2 + - - +
131A ARG* 2.7 71.7 + - + +
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Residues in contact with MET 128 (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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71A LEU* 3.9 15.3 - - + -
74A GLU* 3.6 30.1 - - + -
75A LEU* 4.1 15.3 - - + +
98A PHE* 3.9 20.9 - - + -
102A VAL* 3.8 17.3 - - + -
124A LEU* 2.9 28.7 + - + +
127A GLU* 1.3 75.7 - - - +
129A LYS* 1.3 56.6 + - - +
131A ARG* 3.1 26.2 + - + -
132A PHE* 2.8 66.8 + - + -
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Residues in contact with LYS 129 (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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102A VAL* 3.7 17.5 + - + +
103A GLU* 3.7 27.8 + - - +
105A GLU* 3.4 37.6 + - + -
125A ILE* 3.3 21.2 + - + +
126A VAL* 3.1 24.5 - - + +
127A GLU 3.3 0.6 - - - -
128A MET* 1.3 78.6 - - - +
130A ASP* 1.3 69.3 + - - +
132A PHE* 3.6 14.8 + - - +
133A LYS* 3.9 7.8 + - - +
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Residues in contact with ASP 130 (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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126A VAL* 3.0 24.5 - - - +
127A GLU* 3.0 10.1 + - - +
129A LYS* 1.3 84.8 - - - +
131A ARG* 1.3 59.8 + - + +
133A LYS* 3.0 37.6 - - - +
134A GLY 4.8 0.2 + - - -
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Residues in contact with ARG 131 (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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74A GLU* 3.1 45.9 + - + +
77A LYS* 3.5 24.4 + - - +
78A THR* 3.2 29.9 - - - +
127A GLU* 2.7 59.1 + - + +
128A MET* 3.2 28.7 - - - +
130A ASP* 1.3 74.4 - - + +
132A PHE* 1.3 64.7 + - + +
133A LYS 3.3 0.7 + - - -
134A GLY* 3.4 15.1 + - - +
135A LEU* 5.1 4.9 - - - +
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Residues in contact with PHE 132 (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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71A LEU* 4.0 8.5 - - + -
74A GLU* 6.1 1.6 - - + -
98A PHE* 4.0 18.2 - + - -
99A VAL* 3.4 49.4 - - + -
102A VAL* 4.3 13.5 - - + -
103A GLU* 3.7 21.5 - - - +
128A MET* 2.8 59.9 + - + +
129A LYS 3.8 6.5 - - - +
130A ASP 3.4 0.6 - - - -
131A ARG* 1.3 74.8 - - + +
133A LYS* 1.3 61.0 + - - +
134A GLY 3.2 1.6 + - - -
135A LEU* 3.8 15.9 + - - +
140A PHE 5.5 3.4 - - - -
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Residues in contact with LYS 133 (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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129A LYS 3.9 6.3 + - - +
130A ASP* 3.0 25.8 - - - +
132A PHE* 1.3 77.6 - - - +
134A GLY* 1.3 61.8 + - - +
135A LEU 3.6 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