Contacts of the helix formed by residues 118 - 135 (chain A) in PDB entry 1EF1
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 118 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A TYR* 3.5 17.2 - - + +
117A CYS* 1.3 93.0 - - - +
119A PRO* 1.4 67.3 - - + +
120A GLU* 4.1 9.4 - - + +
121A THR* 3.5 21.0 + - - +
122A ALA* 2.8 30.7 + - - +
198A LEU* 3.9 15.3 - - + -
199A GLU* 5.9 0.9 - - - +
545C HIS* 3.6 38.4 - - + +
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Residues in contact with PRO 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TYR* 4.3 6.5 - - - +
117A CYS 4.5 0.2 - - - +
118A PRO* 1.4 83.3 - - + +
120A GLU* 1.3 82.3 + - - +
122A ALA* 3.2 1.2 + - - +
123A VAL* 3.0 28.2 + - - +
156A ARG* 4.9 0.4 - - - +
157A VAL* 4.0 19.7 - - + +
160A GLN* 3.9 11.2 - - - +
161A HIS* 3.7 24.2 - - + +
529C LEU* 4.2 6.7 - - + -
533C ARG* 3.9 24.9 - - - +
542C ASP* 4.6 3.8 - - - +
545C HIS* 5.8 0.7 - - + -
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PRO* 4.1 8.4 - - + +
119A PRO* 1.3 92.9 - - - +
121A THR* 1.3 62.9 + - - +
123A VAL* 3.3 2.1 + - - +
124A LEU* 3.0 22.9 + - - +
522C LEU* 4.0 17.0 - - + +
525C LEU* 3.3 31.3 - - + +
526C THR* 3.8 33.0 - - - +
529C LEU* 4.2 18.4 - - - +
545C HIS* 5.6 1.0 + - - -
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Residues in contact with THR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A CYS* 3.7 15.3 - - - -
118A PRO* 3.5 25.6 + - - +
119A PRO 3.3 0.4 - - - -
120A GLU* 1.3 77.2 - - - +
122A ALA* 1.3 55.1 + - - +
124A LEU* 3.1 2.3 + - - +
125A LEU* 2.7 43.8 + - + +
194A ILE* 3.7 29.2 - - + -
198A LEU* 4.5 12.1 - - + -
522C LEU* 3.8 22.0 - - + +
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 5.4 2.9 - - + -
117A CYS* 3.5 16.1 - - - +
118A PRO 2.8 20.0 + - - +
119A PRO 3.2 5.4 + - - +
121A THR* 1.3 75.8 - - - +
123A VAL* 1.3 57.7 + - - +
125A LEU* 3.4 5.2 + - - +
126A ALA* 2.9 28.4 + - - +
152A LEU 4.4 1.6 - - - +
153A LEU* 3.6 17.4 - - + +
154A PRO* 4.0 18.2 - - + -
157A VAL* 4.1 10.3 - - + -
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PRO 3.0 19.4 + - - +
120A GLU 3.8 3.8 - - - +
121A THR 3.2 0.2 - - - -
122A ALA* 1.3 73.1 - - - +
124A LEU* 1.3 65.8 + - - +
126A ALA* 3.3 3.1 + - - +
127A SER* 3.1 21.8 + - - -
153A LEU* 3.9 14.8 - - + -
157A VAL* 5.1 1.3 - - + -
168A TRP* 3.9 29.2 - - + -
171A ARG* 5.5 2.5 - - + +
172A ILE* 3.8 17.4 - - + +
175A TRP* 4.4 12.6 - - + -
525C LEU* 3.5 25.8 - - + -
529C LEU* 4.1 13.0 - - + -
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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
----------------------------------------------------------
120A GLU 3.0 16.5 + - - +
121A THR* 3.1 4.0 + - - +
123A VAL* 1.3 76.5 - - - +
125A LEU* 1.3 63.4 + - - +
127A SER* 2.8 27.3 + - - +
128A TYR* 3.2 41.4 + - + +
175A TRP* 4.7 4.3 - - + -
179A HIS* 4.2 3.1 - - + -
194A ILE* 3.7 26.9 - - + -
518C VAL* 4.3 5.4 - - + -
521C HIS* 4.0 28.7 - - + -
522C LEU* 3.7 28.3 - - + -
525C LEU* 3.7 12.7 - - + +
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Residues in contact with LEU 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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110A ILE* 3.5 34.3 - - + -
117A CYS* 4.0 20.2 - - - -
121A THR* 2.7 28.3 + - + +
122A ALA* 3.7 4.7 - - - +
124A LEU* 1.3 73.7 - - - +
126A ALA* 1.3 62.7 + - - +
128A TYR* 3.0 3.9 + - + -
129A ALA 2.9 18.9 + - - -
191A TYR* 3.3 58.5 - - + +
194A ILE* 3.7 22.9 - - + -
195A ALA* 4.4 7.4 - - + -
198A LEU* 4.9 1.1 - - + -
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Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ALA 2.9 14.9 + - - +
123A VAL* 3.3 10.1 + - - +
125A LEU* 1.3 74.9 - - - +
127A SER* 1.3 57.8 + - - +
129A ALA* 3.2 9.1 + - - +
130A VAL* 2.9 35.1 + - - +
152A LEU* 3.3 40.9 - - + +
153A LEU* 4.3 1.1 - - + -
172A ILE* 4.2 13.0 - - + -
191A TYR* 5.2 0.4 - - - -
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Residues in contact with SER 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A VAL 3.1 10.3 + - - -
124A LEU* 2.8 28.2 + - - +
126A ALA* 1.3 76.0 - - - +
128A TYR* 1.3 60.7 + - - +
130A VAL* 3.4 9.1 + - - +
131A GLN* 3.1 17.8 + - - +
172A ILE* 4.5 6.7 - - - +
175A TRP* 3.4 30.9 - - - +
176A HIS* 4.2 3.3 - - - +
179A HIS* 2.8 33.9 + - - -
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Residues in contact with TYR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 3.2 41.9 + - + +
125A LEU* 3.0 8.7 + - - +
127A SER* 1.3 72.8 - - - +
129A ALA* 1.3 61.1 + - - +
131A GLN* 3.1 2.4 + - - -
132A SER* 2.9 26.6 + - - -
179A HIS* 3.2 32.2 + + - -
182A MSE 3.8 26.6 - - + +
187A ALA* 3.4 26.5 - - - +
190A GLU* 3.4 33.4 - - + +
191A TYR* 4.1 14.4 - - + -
194A ILE* 3.6 13.7 - - + -
518C VAL* 3.8 11.3 - - - +
521C HIS* 3.7 22.0 + - - -
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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
----------------------------------------------------------
103A PHE* 4.1 17.6 - - + -
107A LYS* 3.9 30.3 - - + -
125A LEU 2.9 12.6 + - - +
126A ALA* 3.5 12.3 - - - +
128A TYR* 1.3 77.0 - - - +
130A VAL* 1.3 56.6 + - + +
132A SER* 3.4 3.0 + - - -
133A LYS* 3.0 28.9 + - - +
152A LEU* 6.3 1.3 - - + -
191A TYR* 4.2 4.1 - - + -
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ALA 2.9 20.4 + - - +
127A SER* 3.6 7.0 - - - +
128A TYR 3.2 0.2 - - - -
129A ALA* 1.3 73.7 - - + +
131A GLN* 1.3 60.0 + - - +
133A LYS* 3.0 1.9 + - - -
134A TYR* 2.8 49.3 + - + +
146A TYR* 4.4 0.4 - - - +
147A LEU* 3.8 15.7 - - + -
150A ASP* 4.9 2.2 - - - +
152A LEU* 3.6 28.5 - - + -
172A ILE* 4.0 12.3 - - + -
176A HIS* 3.4 36.3 - - + +
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Residues in contact with GLN 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A SER 3.1 13.0 + - - +
128A TYR 3.1 8.0 + - - +
130A VAL* 1.3 76.4 - - - +
132A SER* 1.3 57.3 + - - +
135A GLY* 2.8 36.1 + - - +
136A ASP* 3.0 31.8 + - - +
176A HIS* 3.2 38.7 - - + +
179A HIS* 3.3 30.1 + - + +
180A ARG 4.4 0.2 + - - -
182A MSE 2.9 30.3 + - + +
183A LEU 4.9 0.2 - - - +
184A ARG* 3.6 4.3 - - - +
187A ALA* 4.0 14.4 - - + -
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PHE* 4.3 10.3 - - - -
128A TYR 2.9 12.2 + - - -
129A ALA* 3.5 12.6 - - - -
131A GLN* 1.3 79.6 - - - +
133A LYS* 1.3 62.0 + - - +
184A ARG* 3.3 39.8 + - - +
187A ALA* 3.9 7.3 - - - +
188A VAL* 3.3 25.6 - - - +
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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 ALA 3.0 18.5 + - - +
130A VAL* 3.8 2.0 - - - +
132A SER* 1.3 79.3 - - - +
134A TYR* 1.3 95.9 + - + +
149A GLY 5.6 0.6 + - - -
150A ASP* 3.1 26.6 + - - +
184A ARG* 3.2 15.2 + - - -
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Residues in contact with TYR 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 2.8 37.7 + - + +
133A LYS* 1.3 100.0 + - + +
135A GLY* 1.3 60.7 + - - +
136A ASP 3.9 0.7 + - - +
142A HIS* 4.0 34.4 + + - +
146A TYR* 3.2 28.0 + + + -
147A LEU* 3.6 13.5 - - + -
150A ASP* 3.0 39.1 + - - -
176A HIS* 3.8 16.2 - - + -
184A ARG* 3.5 12.6 + - - +
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Residues in contact with GLY 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLN* 2.8 32.7 + - - +
134A TYR* 1.3 75.7 - - - +
136A ASP* 1.3 54.2 + - - -
176A HIS* 2.7 30.5 + - - -
182A MSE 5.6 0.4 - - - -
184A ARG* 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
------------------------------------------------------------
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