Contacts of the helix formed by residues 123 - 145 (chain A) in PDB entry 3CJD
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 PRO 123 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 4.6 10.5 - - + -
116A MSE 3.8 22.9 - - + -
121A PRO 4.0 4.0 - - - +
122A VAL* 1.4 82.0 - - + +
124A GLN* 1.3 54.2 + - - +
125A TRP* 3.3 23.3 - - + +
126A TYR* 2.9 22.4 + - + +
127A GLY* 2.8 31.0 + - - -
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Residues in contact with GLN 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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122A VAL 3.5 4.3 + - - +
123A PRO* 1.3 70.3 - - - +
125A TRP* 1.3 58.2 + - - +
127A GLY* 4.5 1.6 - - - +
128A HIS* 2.9 33.7 + - - +
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Residues in contact with TRP 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.2 34.5 - - + -
61A GLU* 3.4 36.1 + - - -
64A GLY* 3.7 23.1 - - - -
67A PHE* 5.5 1.3 - + - -
123A PRO* 3.9 22.4 - - + +
124A GLN* 1.3 78.9 - - - +
126A TYR* 1.3 80.4 + + + +
128A HIS* 3.9 5.2 - - - +
129A ALA* 3.2 30.2 + - + +
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Residues in contact with TYR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.5 38.4 - - + +
63A ASN* 3.2 28.4 + - + +
64A GLY 4.4 0.2 - - - -
67A PHE* 3.4 30.7 - + - -
111A LEU* 4.5 4.9 + - - +
114A VAL* 4.2 4.5 - - - +
116A MSE 3.8 23.5 - - + +
122A VAL* 4.7 0.9 - - + -
123A PRO* 2.9 26.1 + - + +
125A TRP* 1.3 105.4 - + + +
127A GLY* 1.3 63.3 + - - +
129A ALA* 3.4 4.6 + - - +
130A MSE 3.3 20.4 + - - +
203A STE 5.2 2.5 + - - -
176B ILE* 3.7 26.5 - - + -
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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
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122A VAL* 3.6 21.6 - - - +
123A PRO 2.8 17.1 + - - -
124A GLN* 4.0 2.2 - - - -
126A TYR* 1.3 72.3 - - - +
128A HIS* 1.3 55.6 + - - +
130A MSE 3.7 7.1 + - - +
131A ALA* 3.0 28.5 + - - +
176B ILE* 5.0 1.8 - - - -
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Residues in contact with HIS 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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124A GLN 2.9 19.9 + - - +
125A TRP* 3.9 6.3 - - - +
126A TYR 3.3 0.2 - - - -
127A GLY* 1.3 75.2 - - - +
129A ALA* 1.3 60.2 + - - +
131A ALA* 3.3 8.2 + - + +
132A GLN* 2.8 61.6 + - + +
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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
----------------------------------------------------------
64A GLY* 5.6 1.6 - - - +
67A PHE* 3.7 30.9 - - + +
125A TRP* 3.2 20.1 + - + +
126A TYR* 3.4 2.9 + - - +
128A HIS* 1.3 79.0 - - - +
130A MSE 1.3 57.4 + - - +
132A GLN* 3.7 15.0 - - - +
133A LEU* 3.2 33.2 + - - +
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Residues in contact with MSE 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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67A PHE* 4.0 21.5 - - + -
126A TYR 3.3 13.3 + - - +
127A GLY 4.1 3.8 - - - +
128A HIS 3.2 0.6 - - - -
129A ALA* 1.3 74.9 - - - +
131A ALA* 1.3 69.5 + - - +
133A LEU* 3.3 9.3 + - + +
134A PHE* 3.2 50.4 + - + -
158A ARG* 4.6 9.0 - - - +
203A STE 4.0 11.2 - - + -
176B ILE* 3.1 52.3 - - + +
177B SER* 3.8 17.7 - - - -
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Residues in contact with ALA 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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127A GLY 3.0 19.9 + - - +
128A HIS* 3.6 11.4 - - + +
130A MSE 1.3 81.1 - - + +
132A GLN* 1.3 55.2 + - - +
134A PHE* 3.4 9.0 + - - +
135A SER* 3.1 26.9 + - - -
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Residues in contact with GLN 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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128A HIS* 2.8 48.0 + - + +
129A ALA* 3.7 12.6 - - - +
130A MSE 3.3 0.2 - - - -
131A ALA* 1.3 71.3 - - - +
133A LEU* 1.3 62.8 + - + +
135A SER* 2.6 26.4 + - - +
136A TYR* 3.6 28.9 + - + +
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Residues in contact with LEU 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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67A PHE* 3.6 41.1 - - + +
70A LEU* 4.2 9.2 - - + +
71A GLY* 3.6 35.9 - - - +
74A VAL* 5.3 0.4 - - + -
129A ALA 3.2 16.8 + - - +
130A MSE 3.3 9.4 + - - +
132A GLN* 1.3 74.4 - - - +
134A PHE* 1.3 58.4 - - - +
136A TYR* 3.2 36.5 + - + +
137A ILE 3.9 0.7 + - - -
203A STE 3.6 50.8 - - + +
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Residues in contact with PHE 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 MSE 3.2 35.2 + - + +
131A ALA* 3.6 12.3 - - - +
132A GLN 3.3 0.2 - - - -
133A LEU* 1.3 79.5 - - - +
135A SER* 1.3 57.8 + - - +
136A TYR 3.2 0.7 - - - -
137A ILE* 3.1 10.3 + - + +
138A THR* 2.9 31.7 + - - +
154A ASP* 5.3 3.1 - - - -
157A THR* 3.5 21.0 - - + +
158A ARG* 3.8 33.4 - - + -
161A PHE* 3.7 19.7 - + + -
203A STE 3.7 24.7 - - + -
177B SER* 3.3 37.0 - - - -
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Residues in contact with SER 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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131A ALA 3.1 11.9 + - - -
132A GLN* 2.6 26.8 + - - +
134A PHE* 1.3 74.4 - - - +
136A TYR* 1.3 69.1 + - - +
137A ILE 3.2 0.2 - - - -
138A THR* 4.1 8.6 - - - -
139A THR* 2.9 30.7 + - - -
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Residues in contact with TYR 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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71A GLY* 4.4 15.7 + - - -
74A VAL* 3.9 18.2 - - + -
75A GLY 3.9 25.6 - - - +
93A MSE 3.3 27.7 - - - +
132A GLN* 3.6 35.1 + - + +
133A LEU* 3.2 39.4 + - + +
135A SER* 1.3 82.6 + - - +
137A ILE* 1.3 57.1 + - - +
139A THR* 4.3 2.9 - - - -
140A PRO* 3.1 20.6 - - - +
203A STE 4.9 0.7 - - + -
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Residues in contact with ILE 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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90A LEU* 3.9 16.6 - - + -
93A MSE 3.9 7.4 - - + -
133A LEU 4.3 0.4 - - - +
134A PHE* 3.1 13.6 + - + +
136A TYR* 1.3 75.9 - - - +
138A THR* 1.3 63.6 + - - +
139A THR 3.3 0.7 - - - -
140A PRO* 3.3 14.9 - - - +
141A LEU* 3.5 21.0 + - + +
157A THR* 3.7 23.8 - - + +
160A LEU* 5.3 0.2 - - + -
161A PHE* 3.9 19.5 - - + -
203A STE 3.8 69.8 - - + -
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Residues in contact with THR 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 PHE* 2.9 17.6 + - - +
135A SER* 3.6 8.2 + - - -
137A ILE* 1.3 75.2 - - - +
139A THR* 1.3 63.2 + - - +
141A LEU* 3.4 3.3 + - - +
142A ALA* 3.1 23.4 + - - +
153A LEU* 3.9 33.2 - - + +
154A ASP* 5.0 2.8 - - - +
157A THR* 2.7 25.2 + - - +
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Residues in contact with THR 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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83A ASP* 6.4 0.9 - - - -
135A SER* 2.9 20.8 + - - -
136A TYR* 4.3 3.7 - - - -
138A THR* 1.3 77.9 - - - +
140A PRO* 1.4 71.9 - - + +
142A ALA* 3.2 16.6 + - - +
143A LYS* 3.4 30.1 + - - +
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Residues in contact with PRO 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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86A PRO* 3.4 43.0 - - + +
89A ARG* 4.3 9.6 - - + -
90A LEU* 3.7 17.9 - - + -
93A MSE 3.9 7.2 - - + -
136A TYR 3.1 23.1 - - - +
137A ILE 3.3 13.7 - - - +
139A THR* 1.4 89.2 - - + +
141A LEU* 1.3 54.8 + - - +
143A LYS* 3.1 9.0 + - + +
144A ILE* 3.1 25.5 + - - +
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Residues in contact with LEU 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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90A LEU* 4.1 15.7 - - + -
137A ILE* 3.5 20.5 + - + +
138A THR* 3.4 8.4 + - - +
139A THR 3.3 1.0 - - - -
140A PRO* 1.3 73.9 - - - +
142A ALA* 1.3 56.5 + - - +
144A ILE* 4.3 3.8 - - + -
145A PHE* 2.7 62.6 + - + +
153A LEU* 3.8 12.8 - - + +
156A MSE 4.0 11.4 - - + +
157A THR* 3.5 43.3 - - - +
160A LEU* 3.6 24.9 - - + -
195A VAL* 4.3 2.5 - - + -
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Residues in contact with ALA 142 (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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138A THR* 3.1 14.0 + - + +
139A THR* 3.2 12.8 + - - +
141A LEU* 1.3 74.0 - - - +
143A LYS* 1.3 61.2 + - + +
145A PHE 3.4 3.0 - - - +
146A PRO* 3.4 23.7 - - - +
153A LEU* 3.8 23.9 - - + +
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Residues in contact with LYS 143 (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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83A ASP* 3.3 40.5 + - - +
86A PRO* 4.1 21.1 - - + -
139A THR* 3.4 37.0 + - - +
140A PRO* 3.1 9.6 + - + +
142A ALA* 1.3 76.6 - - + +
144A ILE* 1.3 61.8 + - - +
146A PRO* 3.6 13.1 - - - +
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Residues in contact with ILE 144 (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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86A PRO* 3.6 21.3 - - + -
87A ASN* 3.5 24.2 - - - +
90A LEU* 3.6 31.2 - - + -
140A PRO 3.1 15.7 + - - +
141A LEU* 3.7 10.5 - - + +
143A LYS* 1.3 76.9 - - - +
145A PHE* 1.3 81.7 + - + +
146A PRO* 3.2 8.8 - - - +
195A VAL* 3.8 6.1 - - + +
196A GLY* 3.7 28.5 - - - +
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Residues in contact with PHE 145 (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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141A LEU* 2.7 36.9 + - + +
142A ALA* 3.4 11.3 - - - +
144A ILE* 1.3 85.0 - - + +
146A PRO* 1.4 65.1 - - - +
147A GLU 3.3 2.2 - - - -
148A SER* 3.3 37.7 + - - +
153A LEU* 4.2 5.2 - - + +
156A MSE 4.1 19.1 - - + -
195A VAL* 3.8 13.9 - - + -
196A GLY* 3.9 27.8 - - - -
197A ARG* 5.1 4.0 - - - -
194B GLN* 3.6 28.3 - - - -
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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