Contacts of the helix formed by residues 124 - 142 (chain A) in PDB entry 6CDF
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 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A PRO 5.3 0.8 + - - -
122A ALA 3.3 0.6 - - - -
123A ALA* 1.3 75.6 - - - +
125A VAL* 1.3 62.5 + - - +
126A GLU 3.3 2.5 - - - -
127A GLU* 3.6 9.0 - - - -
128A THR* 2.6 40.0 + - - -
318A TRP* 3.1 32.0 + - - +
323A ALA* 3.6 2.1 - - - +
327A MET* 3.0 29.9 - - - +
401A NAI 4.8 7.0 - - - -
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PRO 3.7 20.2 - - - +
122A ALA* 3.5 21.9 + - + +
123A ALA 3.6 1.8 - - - -
124A SER* 1.3 77.9 - - - +
126A GLU* 1.3 66.0 + - + +
128A THR* 3.5 2.3 + - - -
129A ALA* 3.1 25.5 + - - +
184A ARG* 3.5 49.6 - - + +
185A VAL* 4.0 12.6 - - + +
188A ALA* 4.4 7.9 - - + -
401A NAI 5.2 0.7 - - - +
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Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL* 1.3 83.3 - - + +
127A GLU* 1.3 65.6 + - - +
128A THR 3.2 0.2 - - - -
129A ALA* 4.3 6.5 - - - +
130A ASP* 2.9 40.6 + - - +
188A ALA* 5.2 2.6 - - + +
192A ARG* 3.0 31.1 + - - +
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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
----------------------------------------------------------
123A ALA 3.5 14.5 - - - +
124A SER* 3.6 7.1 - - - +
125A VAL 3.5 0.2 - - - -
126A GLU* 1.3 80.1 + - - +
128A THR* 1.3 56.3 + - - +
130A ASP* 3.7 6.8 - - - +
131A SER* 3.0 31.9 + - - -
317A ALA 3.2 6.2 - - - +
318A TRP 3.7 20.0 - - - +
319A TYR 4.4 2.9 - - - +
320A SER* 2.8 39.6 + - - +
322A GLN* 5.1 2.8 - - - +
323A ALA* 3.7 13.0 + - - +
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Residues in contact with THR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A SER 2.6 23.6 + - - -
125A VAL 3.8 3.4 - - - -
127A GLU* 1.3 73.4 - - - +
129A ALA* 1.3 61.6 + - - +
131A SER* 3.4 2.3 + - - -
132A THR* 2.8 31.8 + - - -
185A VAL* 4.1 15.3 - - + -
264A THR* 4.0 17.9 + - - +
317A ALA* 3.5 16.2 - - + -
318A TRP* 3.8 5.9 - - - -
401A NAI 3.1 45.1 - - + +
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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
----------------------------------------------------------
125A VAL 3.1 12.5 + - - +
126A GLU* 3.9 3.8 - - - +
127A GLU 3.4 0.2 - - - -
128A THR* 1.3 76.5 - - - +
130A ASP* 1.3 58.3 + - - +
132A THR* 3.3 1.2 + - - -
133A LEU* 2.9 34.0 + - - +
185A VAL* 4.1 4.0 - - + +
188A ALA* 3.5 33.2 - - + -
189A VAL* 3.7 23.3 - - + +
192A ARG* 4.1 9.6 - - - +
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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 GLU* 2.9 28.2 + - - +
127A GLU* 3.7 6.4 + - - +
129A ALA* 1.3 74.1 - - - +
131A SER* 1.3 60.5 + - - +
133A LEU* 3.4 6.7 + - - +
134A CYS* 2.9 28.3 + - - +
192A ARG* 2.8 33.0 + - - -
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Residues in contact with SER 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU 3.0 18.8 + - - -
128A THR 3.7 0.9 - - - -
129A ALA 3.3 0.2 - - - -
130A ASP* 1.3 75.9 - - - +
132A THR* 1.3 62.3 + - - +
134A CYS* 3.2 8.6 + - - +
135A HIS* 3.0 33.3 + - - -
264A THR* 4.9 1.6 - - - -
316A ALA 4.5 1.6 + - - -
317A ALA* 3.2 38.8 + - - -
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Residues in contact with THR 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 THR* 2.8 23.3 + - - +
129A ALA 3.5 5.2 - - - -
130A ASP 3.2 0.4 - - - -
131A SER* 1.3 77.0 - - - +
133A LEU* 1.3 57.8 + - - +
135A HIS* 3.1 5.4 + - - +
136A ILE* 2.8 45.1 + - + +
189A VAL* 4.0 7.9 - - + -
234A THR* 3.4 25.1 - - - +
236A HIS* 3.5 18.2 - - + +
262A VAL* 4.0 8.3 - - + -
264A THR* 2.9 26.4 + - - +
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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
----------------------------------------------------------
129A ALA 2.9 20.9 + - - +
130A ASP* 3.4 7.2 + - - +
132A THR* 1.3 76.3 - - - +
134A CYS* 1.3 57.8 - - - +
136A ILE* 3.7 17.6 - - + +
137A LEU* 2.8 44.6 + - + +
189A VAL* 4.0 26.7 - - + +
192A ARG* 3.9 32.5 - - + -
193A ALA* 4.5 9.4 - - + +
196A PHE* 3.8 33.9 - - + -
198A PHE* 5.3 2.0 - - + -
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Residues in contact with CYS 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 ASP 2.9 15.3 + - - +
131A SER* 3.4 13.5 - - - +
132A THR 3.2 0.2 - - - -
133A LEU* 1.3 77.1 - - - +
135A HIS* 1.3 58.9 + - + +
137A LEU* 3.7 6.4 - - - +
138A ASN* 2.8 52.8 + - - -
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Residues in contact with HIS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 3.0 21.4 + - - +
132A THR 3.6 6.7 - - - +
134A CYS* 1.3 76.6 - - + +
136A ILE* 1.3 65.1 + - - +
138A ASN* 3.1 11.8 + - + +
139A LEU* 3.0 28.6 + - - +
262A VAL* 4.1 8.5 - - + +
264A THR* 4.1 14.2 - - + +
288A ALA* 3.5 29.9 - - + +
289A LEU 4.6 3.1 + - - -
290A ASP* 4.2 16.8 - - + -
311A ILE* 4.1 17.0 - - + +
312A CYS 5.0 0.2 - - - -
313A THR* 3.2 43.6 + - + +
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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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132A THR* 2.8 40.3 + - + +
133A LEU* 3.7 21.5 - - + +
135A HIS* 1.3 72.7 - - - +
137A LEU* 1.3 66.2 + - + +
139A LEU* 3.0 6.1 + - - +
140A TYR* 3.0 33.4 + - + -
177A LEU* 4.1 29.4 - - + -
189A VAL* 4.6 2.0 - - + -
198A PHE* 3.7 32.5 - - + -
232A CYS* 4.5 7.2 - - - -
234A THR* 4.7 2.7 - - - -
262A VAL* 4.0 22.7 - - + -
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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 LEU* 2.8 31.4 + - + +
134A CYS* 4.0 5.8 - - - +
136A ILE* 1.3 78.4 - - + +
138A ASN* 1.3 55.9 + - - +
140A TYR* 4.4 2.0 - - - +
141A ARG* 2.7 49.0 + - + +
143A ALA* 6.1 0.2 - - - -
172A ILE* 3.5 29.8 - - + -
196A PHE* 3.8 39.7 - - + -
198A PHE* 5.4 1.1 - - + -
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Residues in contact with ASN 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 CYS* 2.8 45.2 + - - +
135A HIS* 3.1 17.4 + - + +
137A LEU* 1.3 76.3 - - - +
139A LEU* 1.3 58.7 + - - +
142A ARG* 2.9 28.3 + - - +
143A ALA* 3.7 11.0 - - - +
144A THR* 3.0 36.9 + - - +
145A TRP* 4.5 1.2 - - - -
311A ILE* 4.1 20.8 - - + +
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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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135A HIS 3.0 13.8 + - - +
136A ILE* 3.0 7.2 + - - +
138A ASN* 1.3 76.2 - - - +
140A TYR* 1.3 65.1 + - - +
141A ARG 3.6 0.2 + - - -
142A ARG* 3.7 15.8 + - - +
145A TRP* 3.5 32.8 - - + -
168A GLY 5.1 1.6 - - - +
232A CYS* 5.3 0.2 - - - -
260A PHE* 3.5 51.9 - - + -
261A LEU 3.9 17.9 - - - +
262A VAL* 3.9 15.9 - - + -
286A GLY* 4.2 4.0 - - - +
287A ALA 4.0 16.6 - - - +
288A ALA* 4.0 7.4 - - + +
311A ILE* 3.7 14.6 - - + -
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Residues in contact with TYR 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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136A ILE* 3.0 32.5 + - + +
137A LEU 4.2 1.1 - - - +
139A LEU* 1.3 77.8 - - - +
141A ARG* 1.3 61.6 + - + +
169A ALA* 3.2 9.4 - - - +
170A ALA* 3.1 47.8 + - + +
172A ILE* 3.8 31.4 - - + -
175A GLU* 2.8 48.7 + - + +
198A PHE* 3.5 26.4 - + - -
231A ASP* 3.7 6.1 - - - +
232A CYS* 3.7 21.9 - - + +
260A PHE* 3.6 32.3 - + - -
403A FMT 4.0 2.5 + - - -
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Residues in contact with ARG 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 LEU* 2.7 36.8 + - + +
140A TYR* 1.3 81.0 + - + +
142A ARG* 1.3 69.9 + - - +
143A ALA* 3.1 10.3 + - + +
146A LEU* 3.7 11.8 - - - +
169A ALA* 3.6 30.3 - - - +
170A ALA 3.5 24.6 + - - +
171A ARG* 5.4 0.6 - - - +
172A ILE* 4.9 6.8 - - + +
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Residues in contact with ARG 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 ASN 2.9 18.4 + - - -
139A LEU 3.7 14.2 + - - +
141A ARG* 1.3 79.4 - - - +
143A ALA* 1.3 53.8 + - - +
144A THR 3.3 2.7 - - - -
145A TRP* 3.3 50.3 + - + +
146A LEU* 2.7 44.2 + - + +
165A VAL 4.6 7.3 + - - -
166A ALA 3.6 11.5 - - - +
167A SER 3.1 28.2 + - - -
168A GLY* 4.1 8.7 - - - -
169A ALA* 3.4 20.6 - - + +
260A PHE* 5.9 1.4 - - - -
285A ARG* 5.1 11.9 + - - +
309A ASN* 4.2 14.5 + - - -
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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
------------------------------------------------------------
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