Contacts of the helix formed by residues 124 - 141 (chain A) in PDB entry 2G9I
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 ASP 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLU* 5.2 1.0 + - - -
122A PRO* 4.4 0.4 - - - +
123A LEU* 1.3 80.6 - - + +
125A PRO* 1.3 68.3 - - - +
126A ASP* 3.4 13.5 + - - +
127A GLY* 3.1 23.3 + - - -
128A SER* 3.0 23.0 + - - -
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Residues in contact with PRO 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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99A PHE* 4.0 30.1 - - + +
122A PRO* 3.8 30.5 - - + +
123A LEU 3.9 3.1 - - - +
124A ASP* 1.3 87.8 - - - +
126A ASP* 1.3 56.5 + - - +
128A SER* 3.2 8.9 + - - +
129A ALA* 2.9 27.4 + - - +
148A ILE* 3.4 13.1 - - + +
165A ILE* 3.6 35.0 - - + +
166A GLY* 3.9 4.7 - - - +
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Residues in contact with ASP 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASP* 3.3 10.7 + - - +
125A PRO* 1.3 78.3 - - - +
127A GLY* 1.3 56.7 + - - +
129A ALA* 3.3 3.6 + - - +
130A GLU* 2.9 29.1 + - - +
165A ILE 4.6 0.2 + - - -
166A GLY* 3.2 8.6 - - - -
167A ILE 2.9 36.2 + - - +
228A SER* 3.5 13.1 + - - -
229A MSE 2.8 39.0 + - - +
230A GLU 4.5 0.7 + - - -
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Residues in contact with GLY 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASP* 3.1 22.5 + - - -
126A ASP* 1.3 73.4 - - - +
128A SER* 1.3 55.4 + - - +
130A GLU* 3.0 15.0 + - - +
131A LYS* 2.8 49.0 + - - +
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Residues in contact with SER 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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43A ILE* 3.7 13.8 - - - +
47A GLU* 2.5 37.0 + - - -
122A PRO* 4.4 0.3 - - - +
124A ASP 3.0 12.7 + - - -
125A PRO* 3.5 10.7 - - - +
127A GLY* 1.3 74.4 - - - +
129A ALA* 1.3 63.7 + - - +
131A LYS* 3.9 7.5 - - - +
132A LEU* 3.0 26.0 + - - +
148A ILE* 3.6 14.8 - - - -
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Residues in contact with ALA 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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125A PRO 2.9 12.9 + - - +
126A ASP 3.5 9.0 - - - +
128A SER* 1.3 75.4 - - - +
130A GLU* 1.3 57.3 + - - +
132A LEU* 3.6 1.0 + - - -
133A ARG* 2.9 28.9 + - - +
146A VAL* 3.6 31.7 - - + +
148A ILE* 3.5 9.5 - - + +
166A GLY 4.1 1.3 - - - +
167A ILE 3.8 28.9 - - - +
168A SER* 3.6 2.0 - - - +
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Residues in contact with GLU 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 ASP 2.9 13.5 + - - +
127A GLY* 3.0 15.2 + - - +
129A ALA* 1.3 74.9 - - - +
131A LYS* 1.3 79.0 + - - +
132A LEU 3.1 0.7 - - - -
133A ARG* 3.3 7.2 + - - +
134A ARG* 3.1 24.8 + - + +
168A SER* 3.4 20.6 - - - +
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Residues in contact with LYS 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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47A GLU* 5.9 1.1 - - - +
127A GLY* 2.8 28.3 + - - +
128A SER* 3.9 7.2 - - - +
130A GLU* 1.3 84.4 + - - +
132A LEU* 1.3 57.5 + - - +
134A ARG* 3.2 8.6 + - - +
135A ARG* 2.9 37.0 + - + +
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Residues in contact with LEU 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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20A LEU* 3.9 16.2 - - + +
21A ALA* 3.4 39.3 - - + +
24A ILE* 5.1 2.2 - - + -
36A LEU* 4.2 11.9 - - + -
38A VAL* 4.1 22.0 - - + -
43A ILE* 4.5 17.3 - - + -
128A SER 3.0 17.4 + - - +
129A ALA* 3.8 3.8 - - - +
131A LYS* 1.3 74.0 - - - +
133A ARG* 1.3 67.6 + - - +
134A ARG 3.0 1.2 + - - -
135A ARG* 3.1 5.5 + - + +
136A ILE* 3.0 29.5 + - + +
146A VAL* 4.0 21.1 - - + -
148A ILE* 5.6 0.2 - - + -
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Residues in contact with ARG 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 ALA 2.9 19.9 + - - +
130A GLU* 3.3 9.8 + - - +
132A LEU* 1.3 75.2 - - - +
134A ARG* 1.3 65.9 + - - +
136A ILE* 3.6 6.9 + - - +
137A LEU* 3.3 25.5 + - + +
142A LYS 4.9 1.2 - - - +
143A ARG* 5.7 10.1 - - - +
144A VAL* 3.2 29.9 + - - +
146A VAL* 3.9 13.8 - - + +
168A SER* 3.0 39.2 + - - +
169A GLY* 3.7 20.1 - - - +
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Residues in contact with ARG 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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130A GLU* 3.1 17.4 + - + +
131A LYS* 3.4 9.0 - - - +
132A LEU 3.0 0.6 - - - -
133A ARG* 1.3 83.2 - - - +
135A ARG* 1.3 67.0 - - + +
136A ILE 3.1 1.1 - - - -
137A LEU* 3.0 34.0 + - - +
138A GLU* 3.0 45.5 + - - +
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Residues in contact with ARG 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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19A ASP* 3.7 18.9 + - - +
21A ALA* 3.3 22.6 - - + +
22A GLU* 3.3 22.4 + - - -
131A LYS* 2.9 23.6 + - + +
132A LEU* 3.7 2.2 - - - +
134A ARG* 1.3 77.3 - - + +
136A ILE* 1.3 62.4 + - - +
138A GLU* 3.5 23.3 + - - +
139A LEU* 3.0 54.5 + - - +
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Residues in contact with ILE 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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21A ALA* 4.0 20.9 - - + +
24A ILE* 5.3 1.6 - - + -
25A SER* 4.7 2.0 - - - -
30A PHE* 4.0 30.7 - - + -
36A LEU* 3.8 29.4 - - + -
132A LEU* 3.0 26.2 + - + +
133A ARG 3.8 4.0 - - - +
135A ARG* 1.3 79.0 - - - +
137A LEU* 1.3 55.0 + - - +
139A LEU* 4.6 4.3 - - - +
140A THR* 2.8 51.4 + - + +
142A LYS 4.1 5.4 - - - +
144A VAL* 3.7 28.5 - - + -
146A VAL* 5.0 0.9 - - + -
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Residues in contact with LEU 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 ARG* 3.3 13.4 + - + +
134A ARG* 3.0 39.2 + - - +
136A ILE* 1.3 79.1 - - - +
138A GLU* 1.3 58.3 + - + +
141A GLY* 2.8 51.3 + - - +
142A LYS 3.5 17.5 - - - +
143A ARG* 3.8 37.7 - - + +
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Residues in contact with GLU 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 ARG* 3.0 38.6 + - - +
135A ARG* 3.8 36.4 + - - +
137A LEU* 1.3 78.8 - - + +
139A LEU* 1.3 64.7 + - + +
141A GLY 4.4 1.2 + - - -
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Residues in contact with LEU 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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21A ALA* 3.8 27.1 - - + +
22A GLU* 3.8 22.4 - - + +
25A SER* 3.8 16.6 - - - +
135A ARG* 3.0 44.7 + - - +
136A ILE* 3.9 2.0 - - - +
138A GLU* 1.3 77.9 - - + +
140A THR* 1.3 70.6 + - + +
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Residues in contact with THR 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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25A SER* 3.5 35.2 - - - +
28A VAL 5.8 0.4 - - - +
30A PHE* 4.4 7.7 - - + +
136A ILE* 2.8 24.4 + - + +
139A LEU* 1.3 82.7 - - + +
141A GLY* 1.3 61.4 + - - +
142A LYS* 3.0 42.2 + - - +
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Residues in contact with GLY 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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32A ASP* 4.1 2.9 - - - +
137A LEU* 2.8 29.9 + - - +
138A GLU 4.4 1.4 + - - -
139A LEU 3.8 0.4 - - - -
140A THR* 1.3 77.8 - - - +
142A LYS* 1.3 65.2 + - - +
143A ARG* 4.0 5.0 + - - +
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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