Contacts of the helix formed by residues 130 - 141 (chain A) in PDB entry 1EEJ
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A PRO* 4.0 0.3 - - - +
126A GLN* 3.5 27.2 - - - +
127A GLY 2.7 23.6 + - - -
128A LEU 3.4 2.8 + - - -
129A ASP* 1.3 77.1 - - - +
131A ASP* 1.3 63.3 + - - +
132A ALA* 3.7 9.2 + - - +
133A GLU* 3.4 13.7 + - - +
134A LYS* 3.3 32.3 + - - +
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Residues in contact with ASP 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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97A THR* 5.2 4.7 - - + -
130A SER* 1.3 74.4 - - - +
132A ALA* 1.3 57.5 + - - +
134A LYS* 3.1 18.1 + - - +
135A GLU* 2.8 39.2 + - + +
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Residues in contact with ALA 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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95A ASP* 3.5 27.4 - - - +
96A ILE* 4.7 0.7 - - - -
97A THR* 3.8 20.7 - - + +
124A PRO* 4.0 12.6 - - + -
125A ARG 5.2 0.2 - - - +
126A GLN* 5.4 4.7 - - + -
130A SER* 3.2 11.1 - - - +
131A ASP* 1.3 79.0 - - - +
133A GLU* 1.3 57.9 + - - +
135A GLU* 3.5 3.2 + - - +
136A MET* 3.0 38.2 + - + +
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Residues in contact with GLU 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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124A PRO* 4.0 7.3 - - + +
127A GLY 3.9 2.7 - - - +
128A LEU* 2.9 48.6 - - + +
130A SER* 3.4 14.5 + - - +
131A ASP 3.2 0.2 - - - -
132A ALA* 1.3 78.3 - - - +
134A LYS* 1.3 62.7 + - - +
136A MET* 3.9 1.1 - - - -
137A LYS* 2.9 38.8 + - - +
167A ILE* 4.0 30.8 - - + +
168A ALA 5.8 0.4 - - - -
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Residues in contact with LYS 134 (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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128A LEU 5.3 1.4 + - - +
129A ASP* 4.5 11.5 + - - +
130A SER* 3.3 31.1 + - - +
131A ASP* 3.1 19.0 + - - +
133A GLU* 1.3 84.8 - - + +
135A GLU* 1.3 64.4 + - + +
137A LYS* 3.4 5.4 + - - +
138A ALA* 3.2 21.7 + - - +
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Residues in contact with GLU 135 (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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96A ILE* 3.8 25.4 - - + -
131A ASP* 2.8 27.6 + - + +
132A ALA 3.9 0.9 - - - +
134A LYS* 1.3 77.9 - - + +
136A MET* 1.3 59.8 + - - +
138A ALA* 3.4 7.5 + - - +
139A ILE* 3.1 27.5 + - - +
152A VAL* 4.4 11.7 - - + +
158A VAL* 3.6 26.5 - - - +
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Residues in contact with MET 136 (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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94A THR* 3.6 17.0 - - - +
95A ASP* 3.9 13.2 - - - +
96A ILE* 3.5 35.4 - - + -
122A ALA* 3.9 15.7 - - + -
123A PHE 3.8 7.9 - - - +
124A PRO* 3.6 40.2 - - + -
132A ALA 3.0 25.3 + - - +
133A GLU* 4.2 2.7 - - - +
135A GLU* 1.3 74.4 - - - +
137A LYS* 1.3 61.6 + - - +
138A ALA 3.2 0.4 - - - -
139A ILE* 4.0 6.3 - - - -
140A TRP* 2.9 53.9 + - + +
167A ILE* 4.0 3.1 - - + -
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Residues in contact with LYS 137 (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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133A GLU* 2.9 30.7 + - - +
134A LYS* 3.6 6.7 - - - +
135A GLU 3.3 0.2 - - - -
136A MET* 1.3 76.9 - - - +
138A ALA* 1.3 61.0 + - - +
140A TRP* 3.7 0.9 + - - +
141A CYS* 3.1 54.9 + - - -
161A ALA 4.6 6.7 - - - +
162A SER* 4.2 8.5 - - - +
163A CYS 3.6 17.8 + - - +
165A VAL* 3.1 30.3 + - + +
166A ASP* 5.5 0.6 - - - +
167A ILE* 3.8 15.4 - - + +
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Residues in contact with ALA 138 (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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134A LYS 3.2 10.9 + - - +
135A GLU* 3.6 10.8 - - - +
136A MET 3.2 0.4 - - - -
137A LYS* 1.3 79.0 - - - +
139A ILE* 1.3 64.3 + - - +
141A CYS* 3.4 3.6 + - - +
142A ALA* 3.2 20.6 + - - +
158A VAL* 4.4 15.3 - - + +
159A ALA 4.1 20.9 - - - +
160A PRO* 4.4 4.9 - - + -
161A ALA* 4.1 21.7 - - - +
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Residues in contact with ILE 139 (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 ILE* 3.8 20.4 - - + -
96A ILE* 3.5 30.7 - - + -
135A GLU 3.1 16.6 - - - +
136A MET* 3.2 11.6 + - + +
138A ALA* 1.3 77.8 - - - +
140A TRP* 1.3 65.8 + - + +
141A CYS 3.1 0.2 - - - -
142A ALA* 3.1 19.4 + - - +
145A LYS* 3.9 9.8 - - - +
148A ALA* 4.1 7.9 - - - +
149A PHE* 3.7 31.0 - - + +
152A VAL* 3.5 36.1 - - + -
158A VAL* 4.6 2.7 - - + -
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Residues in contact with TRP 140 (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 GLU* 2.6 32.2 + - - -
79A ILE* 3.6 31.8 - - + +
94A THR* 4.5 2.9 - - + -
120A TYR* 3.6 19.6 + - + -
121A LEU 3.7 2.9 - - - -
122A ALA* 3.6 39.5 - - + -
136A MET* 2.9 50.1 + - + +
137A LYS 4.2 2.0 - - - +
139A ILE* 1.3 83.1 - - + +
141A CYS* 1.3 59.8 + - - +
142A ALA 3.4 0.9 - - - +
145A LYS* 4.0 22.6 - - + +
149A PHE* 4.1 20.9 - + - -
163A CYS* 4.1 0.3 - - - -
165A VAL* 3.7 35.5 - - + +
167A ILE* 4.4 2.5 - - + -
170A HIS* 3.6 17.5 - + - -
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Residues in contact with CYS 141 (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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137A LYS* 3.1 38.4 + - - +
138A ALA 3.7 5.8 - - - +
139A ILE 3.1 1.2 - - - -
140A TRP* 1.3 76.5 - - - +
142A ALA* 1.3 62.9 + - - +
143A LYS 3.9 0.7 + - - -
161A ALA* 4.3 10.7 - - - +
162A SER* 3.3 16.7 - - - +
163A CYS* 2.0 64.0 - - + +
165A VAL* 4.2 0.4 - - - -
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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