Contacts of the helix formed by residues 109 - 125 (chain A) in PDB entry 1CEC
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 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A GLU 3.3 10.5 - - - +
108A ASP* 1.3 91.0 - - - +
110A ASN* 1.3 66.6 + - - +
112A GLN* 3.3 20.1 + - - +
113A LYS* 3.1 21.0 + - - +
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Residues in contact with ASN 110 (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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108A ASP* 2.9 25.9 + - - +
109A PRO* 1.3 80.0 - - - +
111A GLN* 1.3 66.4 + - - +
113A LYS* 3.2 10.0 + - - +
114A ARG* 3.2 29.7 + - - +
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Residues in contact with GLN 111 (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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57A ASP* 4.8 2.6 - - - +
93A PRO* 3.1 38.4 - - - +
94A GLY* 3.8 9.2 + - - +
104A THR* 4.2 12.6 + - - +
105A LEU* 3.7 12.7 - - - +
108A ASP* 3.0 33.8 + - + +
110A ASN* 1.3 75.9 - - - +
112A GLN* 1.3 57.3 + - - +
114A ARG* 2.9 38.1 + - - +
115A PHE* 3.1 25.8 + - - +
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Residues in contact with GLN 112 (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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105A LEU* 3.0 38.0 + - + +
106A PHE* 3.7 19.8 + - - +
107A GLU 4.2 2.0 + - - -
108A ASP 3.5 17.3 + - - +
109A PRO* 3.3 15.1 - - - +
110A ASN 3.1 0.2 - - - -
111A GLN* 1.3 75.8 - - - +
113A LYS* 1.3 65.8 + - - +
115A PHE* 3.1 3.9 + - - +
116A VAL* 3.1 27.4 + - - +
151A LYS* 4.0 23.4 + - - +
152A LEU* 3.7 25.1 - - + +
155A GLU* 4.7 5.9 - - - +
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Residues in contact with LYS 113 (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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109A PRO 3.1 12.1 + - - +
110A ASN* 3.2 13.4 + - - +
112A GLN* 1.3 76.9 - - - +
114A ARG* 1.3 66.0 + - + +
116A VAL* 3.4 4.0 + - + +
117A ASP* 3.0 60.0 + - - +
120A ARG* 4.7 7.6 - - - +
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Residues in contact with ARG 114 (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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51A TYR* 3.7 15.6 - - - -
55A GLU* 2.6 44.9 + - - +
57A ASP* 2.9 37.9 + - - +
60A VAL* 3.5 38.1 - - + +
93A PRO* 4.0 11.0 - - + +
110A ASN* 3.2 14.5 + - - +
111A GLN* 2.9 39.3 + - - +
112A GLN 3.3 0.2 - - - -
113A LYS* 1.3 81.6 - - + +
115A PHE* 1.3 61.2 + - - +
117A ASP* 3.9 6.5 - - - +
118A ILE* 3.0 32.2 + - - +
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Residues in contact with PHE 115 (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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89A MET* 3.5 26.2 - - - -
92A ALA* 3.9 13.9 - - + -
93A PRO* 4.2 8.5 - - + +
105A LEU* 4.2 6.1 - - + -
111A GLN 3.1 13.2 + - - +
112A GLN* 3.1 12.3 + - - +
114A ARG* 1.3 79.2 - - - +
116A VAL* 1.3 66.6 + - + +
118A ILE* 3.3 4.6 + - - +
119A TRP* 3.3 32.5 + + - -
137A LEU* 3.4 31.0 - - + -
138A LEU* 3.9 19.1 - - + -
149A TRP* 4.2 10.3 - + - -
152A LEU* 3.8 34.1 - - + -
156A CYS* 3.9 20.0 - - + -
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Residues in contact with VAL 116 (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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112A GLN 3.1 15.5 + - - +
113A LYS* 4.0 3.8 - - - +
115A PHE* 1.3 77.3 - - + +
117A ASP* 1.3 58.4 + - - +
119A TRP* 3.3 2.4 + - - +
120A ARG* 2.9 39.7 + - - +
152A LEU* 4.2 19.1 - - + -
155A GLU* 4.2 9.9 - - + +
156A CYS* 4.2 31.6 - - + +
159A ALA* 3.3 32.1 - - + -
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Residues in contact with ASP 117 (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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63A TYR* 3.5 18.0 + - - +
113A LYS* 3.0 53.0 + - - +
114A ARG* 3.9 6.6 - - - +
115A PHE 3.3 0.2 - - - -
116A VAL* 1.3 78.2 - - - +
118A ILE* 1.3 58.3 + - - +
120A ARG* 3.0 35.4 + - - +
121A PHE* 2.8 30.7 + - - +
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Residues in contact with ILE 118 (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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49A PHE* 4.8 3.4 - - + -
51A TYR* 4.4 10.3 - - + -
54A ILE* 4.5 16.6 - - + -
55A GLU* 3.7 24.7 - - + +
63A TYR* 4.0 23.8 - - + -
89A MET* 3.6 29.2 - - + -
93A PRO* 3.9 18.8 - - + -
114A ARG 3.0 22.1 + - - +
115A PHE* 3.7 4.9 - - - +
116A VAL 3.3 0.4 - - - -
117A ASP* 1.3 75.0 - - - +
119A TRP* 1.3 57.5 + - - +
121A PHE* 3.4 5.5 + - + +
122A LEU* 3.0 42.1 + - + +
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Residues in contact with TRP 119 (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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49A PHE* 4.2 14.8 - + - -
87A LEU* 3.9 16.6 - - + -
89A MET* 3.7 24.8 - - + +
115A PHE* 3.3 30.4 + + - -
116A VAL 3.3 7.8 + - - +
117A ASP 3.2 0.4 - - - -
118A ILE* 1.3 76.4 - - - +
120A ARG* 1.3 58.7 + - - +
122A LEU* 3.7 21.0 - - + +
123A ALA* 2.9 31.9 + - - +
135A PHE* 3.5 45.1 - + + -
136A GLU 3.4 25.8 - - - -
137A LEU* 3.2 24.2 + - + +
156A CYS* 3.7 23.8 - - - -
160A ILE* 3.8 21.3 - - + +
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Residues in contact with ARG 120 (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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113A LYS* 4.7 9.7 - - - +
116A VAL* 2.9 25.5 + - - +
117A ASP* 3.0 32.1 + - - +
119A TRP* 1.3 75.1 - - - +
121A PHE* 1.3 61.9 + - - +
123A ALA* 4.5 1.1 - - - -
124A LYS* 3.3 29.3 + - - +
159A ALA* 3.4 38.8 - - + +
160A ILE* 4.9 2.8 - - - +
162A GLU* 4.4 12.2 + - - -
163A ILE* 3.4 34.0 - - + +
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Residues in contact with PHE 121 (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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54A ILE* 5.7 2.5 - - + -
63A TYR* 3.2 44.0 - + + -
65A GLU* 4.6 3.8 - - - -
68A LEU* 3.6 39.5 - - + -
117A ASP 2.8 17.7 + - - +
118A ILE* 3.6 5.2 - - + +
120A ARG* 1.3 77.8 - - - +
122A LEU* 1.3 67.7 + - + +
124A LYS* 3.4 10.6 + - + +
125A ARG* 2.9 49.8 + - + +
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Residues in contact with LEU 122 (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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49A PHE* 4.0 23.1 - - + -
54A ILE* 4.5 6.5 - - + -
68A LEU* 4.0 24.0 - - + -
71A ILE* 5.0 1.1 - - + -
87A LEU* 4.1 10.5 - - + -
118A ILE* 3.0 29.7 + - + +
119A TRP* 3.2 32.5 + - + +
121A PHE* 1.3 81.1 - - + +
123A ALA* 1.3 64.6 + - - +
125A ARG* 4.2 2.2 - - - -
126A TYR* 3.0 51.9 + - + +
135A PHE* 3.6 9.3 - - + -
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Residues in contact with ALA 123 (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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119A TRP 2.9 17.5 + - - +
120A ARG* 3.8 5.8 - - - +
121A PHE 3.4 0.2 - - - -
122A LEU* 1.3 76.8 - - - +
124A LYS* 1.3 62.5 + - - +
126A TYR 3.6 1.2 + - - -
127A ILE* 3.1 25.8 + - - +
135A PHE* 3.5 21.1 - - + -
160A ILE* 4.2 19.1 - - + -
163A ILE* 4.2 20.4 - - + -
164A ASP* 4.7 9.3 - - + +
167A MET* 5.6 0.2 - - - +
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Residues in contact with LYS 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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120A ARG* 3.3 23.0 + - - +
121A PHE* 3.7 9.2 - - + +
122A LEU 3.2 0.4 - - - -
123A ALA* 1.3 75.1 - - - +
125A ARG* 1.3 66.3 + - - +
127A ILE* 2.9 28.1 + - - +
163A ILE* 3.7 37.9 - - + -
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Residues in contact with ARG 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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65A GLU* 3.0 38.2 + - - -
68A LEU* 3.9 17.9 - - - +
69A SER 5.2 0.2 - - - +
72A ASP* 2.7 36.7 + - - +
121A PHE* 2.9 47.0 + - + +
122A LEU* 3.3 7.2 + - - +
124A LYS* 1.3 77.0 - - - +
126A TYR* 1.3 83.7 + - + +
127A ILE* 5.4 0.3 - - - +
128A ASN* 5.3 1.2 + - - -
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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