Contacts of the helix formed by residues 115 - 133 (chain A) in PDB entry 5EN4
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 LEU 115 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 3.0 34.4 + - + +
114A ASN* 1.3 80.4 - - - +
116A LEU* 1.3 79.5 + - + +
117A GLY 3.3 1.1 - - - -
118A THR* 3.2 6.5 + - - -
119A TYR* 3.0 20.5 + - + +
157A THR* 4.8 6.3 - - - +
160A ALA* 3.8 33.0 - - + +
161A VAL* 4.1 11.4 - - + +
164A MET* 3.9 29.4 - - + -
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 2.9 20.0 + - + +
112A GLU* 3.4 45.1 - - - +
115A LEU* 1.3 85.7 - - + +
117A GLY* 1.3 57.5 + - - +
119A TYR* 3.2 22.8 + - + +
120A THR* 2.8 37.7 + - - +
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Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL* 3.5 38.0 - - - +
64A THR* 5.1 0.2 - - - -
69A VAL* 5.5 0.2 - - - +
88A ASN* 4.5 0.9 - - - +
112A GLU 2.9 15.8 + - - -
113A LEU 3.7 8.4 + - - -
115A LEU 3.3 0.6 - - - -
116A LEU* 1.3 75.8 - - - +
118A THR* 1.3 61.2 + - - +
120A THR* 4.1 2.6 - - - -
121A LEU* 3.3 25.1 + - - +
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Residues in contact with THR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASN* 3.4 29.2 + - + +
90A ALA 4.9 5.4 + - - -
113A LEU 4.3 3.4 + - - -
114A ASN 3.7 14.5 + - - -
115A LEU* 3.2 9.5 + - - -
117A GLY* 1.3 78.4 - - - +
119A TYR* 1.3 59.1 + - - +
122A THR* 2.7 34.7 + - - +
138A ASN* 3.5 30.1 - - + +
161A VAL* 5.0 6.8 - - + +
164A MET* 3.8 19.5 - - + -
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Residues in contact with TYR 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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115A LEU* 3.0 13.4 + - + +
116A LEU* 3.5 26.9 - - + +
118A THR* 1.3 77.4 - - - +
120A THR* 1.3 70.1 + - - +
122A THR* 3.3 4.7 + - - -
123A LYS* 2.9 74.6 + - + +
164A MET* 4.2 26.7 - - - +
168A LEU* 6.3 2.2 - - + -
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Residues in contact with THR 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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63A VAL 5.0 4.0 - - - +
66A GLU* 4.4 20.9 - - + -
69A VAL* 4.3 14.1 - - + -
116A LEU* 2.8 24.5 + - - +
117A GLY* 4.1 4.9 - - - -
118A THR 3.4 0.2 - - - -
119A TYR* 1.3 88.1 - - - +
121A LEU* 1.3 65.0 + - - +
123A LYS* 3.3 6.9 + - - +
124A LEU* 3.0 42.5 + - + +
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Residues in contact with LEU 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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13A VAL* 4.4 6.7 - - + -
15A THR* 3.3 34.5 - - + -
63A VAL* 5.4 2.7 - - + -
69A VAL* 3.7 22.1 - - + +
72A LEU* 4.1 16.4 - - + -
73A VAL* 3.7 27.4 - - + -
86A VAL* 3.7 21.8 - - + -
88A ASN* 3.6 13.0 - - - +
117A GLY 3.3 14.7 + - - +
120A THR* 1.3 80.1 - - - +
122A THR* 1.3 63.6 + - - +
124A LEU* 3.3 1.4 + - - -
125A ALA* 2.9 27.2 + - + +
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Residues in contact with THR 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A VAL* 5.3 3.1 - - - -
88A ASN* 3.1 21.1 + - - +
118A THR* 2.7 24.7 + - - +
119A TYR* 3.7 5.6 - - - -
121A LEU* 1.3 79.6 - - - +
123A LYS* 1.3 64.3 + - - +
125A ALA* 3.1 5.8 + - - +
126A LEU* 3.0 39.7 + - + +
129A LEU* 5.1 0.3 - - - +
136A VAL* 4.1 25.5 - - + +
138A ASN* 5.5 0.2 - - - -
168A LEU* 4.1 27.9 - - + +
179A VAL* 6.1 0.4 - - + -
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Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A TYR* 2.9 57.7 + - + +
120A THR* 3.7 8.3 - - - +
122A THR* 1.3 78.4 - - - +
124A LEU* 1.3 71.0 + - + +
126A LEU* 3.5 21.0 + - + +
127A PRO* 3.7 8.8 - - - +
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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
----------------------------------------------------------
66A GLU* 4.7 3.4 - - + +
69A VAL* 3.8 24.0 - - + -
70A LYS* 3.7 35.2 - - + +
73A VAL* 4.1 16.3 - - + +
120A THR* 3.0 27.5 + - + +
121A LEU* 3.9 3.1 - - - +
123A LYS* 1.3 86.0 - - + +
125A ALA* 1.3 60.7 + - - +
127A PRO* 3.5 10.5 - - - +
128A TYR* 4.0 14.0 - - - -
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL* 4.6 4.0 - - + +
83A LEU* 3.8 24.7 - - + -
86A VAL* 3.8 17.7 - - + -
121A LEU* 2.9 22.7 + - + +
122A THR* 3.8 4.3 - - - +
124A LEU* 1.3 77.4 - - - +
126A LEU* 1.3 64.2 + - - +
127A PRO* 3.3 1.6 - - - -
128A TYR* 3.0 19.7 + - - +
129A LEU* 3.0 16.6 + - + +
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Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A THR* 3.0 34.3 + - + +
123A LYS* 3.8 14.4 - - + +
124A LEU 3.4 0.2 - - - -
125A ALA* 1.3 76.5 - - - +
127A PRO* 1.3 68.9 - - + +
129A LEU* 4.3 16.4 - - + -
130A ARG* 2.8 46.4 + - + +
136A VAL* 4.9 2.7 - - + -
168A LEU* 4.7 10.8 - - + -
172A GLU* 3.6 43.1 - - + +
177A VAL* 4.4 10.3 - - + -
179A VAL* 5.8 0.9 - - + -
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Residues in contact with PRO 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LYS 3.7 7.4 - - - +
124A LEU 3.5 12.6 - - - +
125A ALA 3.4 3.8 - - - -
126A LEU* 1.3 95.1 - - + +
128A TYR* 1.3 71.8 + - + +
130A ARG* 3.6 15.5 + - - +
131A LYS* 3.3 25.6 + - - +
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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
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73A VAL* 3.7 30.5 - - + +
74A SER* 5.9 2.3 - - - -
77A ILE* 3.7 36.0 - - + +
83A LEU* 3.7 26.3 + - + +
124A LEU 4.0 10.3 - - - -
125A ALA* 3.0 11.7 + - - +
127A PRO* 1.3 85.5 - - + +
129A LEU* 1.3 66.6 + - - +
131A LYS* 3.2 12.2 + - + +
132A SER* 3.2 21.0 + - - -
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Residues in contact with LEU 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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83A LEU* 3.7 16.2 - - + +
84A ASP* 3.5 34.5 - - - +
85A CYS* 3.8 5.2 - - - +
86A VAL* 4.3 5.4 - - + -
122A THR* 5.1 0.9 - - + +
125A ALA* 3.0 34.3 + - + +
126A LEU* 3.2 13.9 + - + +
128A TYR* 1.3 73.8 - - - +
130A ARG* 1.3 60.7 + - - +
132A SER* 3.7 2.5 - - - -
133A GLN* 2.9 26.0 + - - -
134A GLY* 2.9 9.9 + - - -
135A ASN 4.0 8.7 - - - +
136A VAL* 3.6 31.2 - - + -
177A VAL* 3.5 15.2 - - + +
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Residues in contact with ARG 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 LEU* 2.8 37.5 + - + +
127A PRO* 3.9 13.3 - - - +
128A TYR 3.2 0.2 - - - -
129A LEU* 1.3 78.3 - - - +
131A LYS* 1.3 63.5 + - + +
132A SER 3.5 0.2 + - - -
133A GLN* 3.5 13.2 + - - +
172A GLU* 2.7 44.2 + - - +
175A TYR* 3.5 54.4 + - + +
177A VAL* 3.7 9.9 - - + -
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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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127A PRO 3.3 15.5 + - - +
128A TYR* 3.2 13.5 + - + +
130A ARG* 1.3 79.7 - - + +
132A SER* 1.3 57.6 + - - +
133A GLN* 5.0 2.1 - - - +
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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
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10A LYS* 5.1 5.2 + - - -
82A ARG* 4.0 16.1 + - - +
83A LEU 2.8 26.2 + - - -
84A ASP* 3.5 22.7 + - - +
128A TYR 3.2 5.9 + - - -
129A LEU* 3.3 9.7 + - - -
131A LYS* 1.3 75.7 - - - +
133A GLN* 1.3 68.9 + - - +
134A GLY* 3.3 9.5 + - - -
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Residues in contact with GLN 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 LEU 2.9 7.0 + - - -
130A ARG 3.5 7.8 + - - +
131A LYS 3.4 3.9 - - - +
132A SER* 1.3 80.4 - - - +
134A GLY* 1.3 64.9 + - - +
175A TYR 3.4 24.4 + - - +
176A GLY* 4.2 19.7 - - - +
177A VAL* 4.5 4.3 - - - -
178A ARG* 5.8 2.6 + - - -
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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