Contacts of the helix formed by residues 147 - 163 (chain A) in PDB entry 5EJC
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 ASP 147 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A MSE 4.8 1.7 - - - +
145A VAL* 3.5 3.2 - - + +
146A GLU* 1.3 75.5 - - - +
148A SER* 1.3 58.7 + - - +
149A VAL* 3.7 13.9 + - - +
150A ASP* 3.0 45.2 + - + +
151A CYS* 2.8 36.8 + - - +
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Residues in contact with SER 148 (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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85A TYR* 3.6 22.8 - - - -
104A GLN* 4.3 7.6 + - - -
108A TYR* 3.2 23.5 + - - -
146A GLU 3.3 6.7 + - - -
147A ASP* 1.3 74.4 + - - +
149A VAL* 1.3 64.2 + - - +
151A CYS* 4.4 0.2 - - - -
152A TYR* 3.1 23.7 + - - +
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Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A MSE 4.1 19.3 - - + -
81A ARG 4.2 13.2 - - - +
82A LYS* 4.4 26.5 - - + +
85A TYR* 4.0 31.6 - - + -
147A ASP* 3.2 13.3 + - - +
148A SER* 1.3 77.7 - - - +
150A ASP* 1.3 65.9 + - - +
152A TYR* 3.5 1.2 + - - +
153A TRP* 3.0 41.8 + - + -
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Residues in contact with ASP 150 (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 ALA* 5.0 6.0 - - + +
61A LYS* 3.2 29.3 + - + +
78A MSE 3.1 27.0 - - - +
145A VAL* 3.6 19.2 - - + +
147A ASP* 3.0 25.5 + - + +
149A VAL* 1.3 74.3 - - - +
151A CYS* 1.3 58.6 + - - +
153A TRP* 3.3 4.2 + - - +
154A ILE* 2.8 44.7 + - + +
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Residues in contact with CYS 151 (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 TYR* 3.8 24.2 - - - +
138A ALA 4.5 1.1 - - - -
141A MSE 3.7 15.1 - - - +
142A GLU* 3.6 38.1 - - - -
145A VAL* 3.4 18.5 - - - +
146A GLU 5.3 0.4 - - - +
147A ASP 2.8 22.6 + - - +
148A SER 3.8 4.3 - - - +
150A ASP* 1.3 73.3 - - - +
152A TYR* 1.3 54.2 + - - +
154A ILE* 3.9 2.6 - - - +
155A THR* 2.5 39.7 + - - -
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Residues in contact with TYR 152 (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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85A TYR* 4.0 16.2 - + + -
108A TYR* 3.6 45.0 - + + -
111A MSE 3.5 42.1 - - + -
112A TYR* 3.6 4.0 + - + -
115A GLU* 3.0 39.7 + - - +
134A PHE* 4.9 2.5 - + - -
148A SER 3.1 15.7 + - - +
149A VAL 3.8 2.5 - - - +
150A ASP 3.3 0.2 - - - -
151A CYS* 1.3 79.8 - - - +
153A TRP* 1.3 77.0 + + - +
155A THR* 3.2 4.9 + - - -
156A ARG* 2.8 57.9 + - + +
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Residues in contact with TRP 153 (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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61A LYS* 6.2 0.2 - - + -
66A ILE* 3.5 26.2 - - + -
78A MSE 6.0 1.1 - - + -
81A ARG* 3.2 65.9 + - + +
84A GLN* 2.8 38.4 - - + -
85A TYR* 4.7 3.6 - - + +
115A GLU* 4.8 4.3 - - - -
149A VAL* 3.0 37.1 + - + +
150A ASP* 4.0 3.8 - - - +
152A TYR* 1.3 98.3 - + - +
154A ILE* 1.3 61.0 + - - +
156A ARG* 3.5 31.3 - - - +
157A ARG* 3.1 49.8 + - + +
946E SER* 4.4 2.7 - - - -
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Residues in contact with ILE 154 (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 ALA* 4.5 10.8 - - - +
60A TRP* 3.9 18.8 - - + -
61A LYS* 4.0 20.0 - - + -
64A LEU* 3.9 17.9 - - + +
66A ILE* 3.8 18.8 - - + -
141A MSE 3.6 26.2 - - + -
145A VAL* 3.8 24.0 - - + -
150A ASP* 2.8 31.9 + - + +
151A CYS 4.0 2.2 - - - +
153A TRP* 1.3 70.6 - - - +
155A THR* 1.3 60.0 + - - +
157A ARG 3.3 0.7 + - - -
158A PHE* 2.8 36.1 + - + +
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Residues in contact with THR 155 (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 TYR* 5.2 2.0 - - - -
134A PHE* 3.9 24.9 - - + -
137A ILE* 4.2 11.9 - - + -
138A ALA* 3.8 29.6 - - + +
141A MSE 3.4 21.7 - - - +
151A CYS* 2.5 27.4 + - - -
152A TYR* 3.5 6.5 - - - -
154A ILE* 1.3 76.0 - - - +
156A ARG* 1.3 64.9 + - - +
158A PHE* 3.6 4.8 - - - +
159A VAL* 2.9 30.9 + - + +
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Residues in contact with ARG 156 (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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84A GLN* 5.2 0.4 + - - -
112A TYR* 3.8 33.3 - - + +
115A GLU* 3.1 37.1 + - - +
116A SER* 5.5 3.6 - - - +
134A PHE* 4.8 3.5 - - + -
152A TYR* 2.8 50.3 + - + +
153A TRP* 3.5 37.3 - - + +
155A THR* 1.3 72.8 - - - +
157A ARG* 1.3 77.7 + - + +
159A VAL* 3.3 1.9 + - - +
160A ASN* 2.8 39.6 + - - +
946E SER* 5.1 4.2 + - - -
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Residues in contact with ARG 157 (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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64A LEU* 3.1 46.2 + - + +
65A GLY* 3.5 22.3 + - - -
66A ILE* 3.8 14.1 - - + -
81A ARG* 4.5 10.3 - - - +
153A TRP* 3.1 41.7 + - + +
154A ILE 4.2 1.1 - - - +
156A ARG* 1.3 97.4 - - + +
158A PHE* 1.3 60.4 + - - +
160A ASN* 3.8 12.9 + - - +
161A GLN* 3.0 28.6 + - - +
942E GLN* 5.8 2.0 + - - -
946E SER* 4.8 4.9 + - - -
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Residues in contact with PHE 158 (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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60A TRP* 6.3 1.1 - + - -
64A LEU* 4.3 7.8 - - + +
137A ILE* 3.9 33.0 - - + -
141A MSE 5.4 3.1 - - - -
154A ILE* 2.8 27.1 + - + +
155A THR* 3.6 3.8 - - - +
157A ARG* 1.3 77.4 - - - +
159A VAL* 1.3 64.5 + - + +
161A GLN* 3.4 20.4 - - - +
162A LEU* 3.5 14.2 - - + +
210A CYS* 4.4 11.4 - - - -
224A TRP* 3.7 46.9 - + + -
227A VAL* 3.5 35.9 - - + -
228A VAL* 4.0 23.3 - - + -
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Residues in contact with VAL 159 (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 TYR* 4.2 9.9 - - + +
133A VAL* 6.0 3.1 - - + -
134A PHE* 4.0 34.8 - - + -
137A ILE* 4.1 36.1 - - + -
155A THR* 2.9 22.8 + - + +
156A ARG 3.8 2.5 - - - +
158A PHE* 1.3 71.7 - - - +
160A ASN* 1.3 66.9 + - - +
161A GLN 3.1 2.0 - - - -
162A LEU* 3.1 21.8 + - + +
163A ASN* 3.2 26.1 + - - +
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Residues in contact with ASN 160 (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 TYR* 5.1 10.5 + - + -
156A ARG* 2.8 27.4 + - - +
157A ARG* 3.8 15.5 + - - +
159A VAL* 1.3 77.0 - - - +
161A GLN* 1.3 56.1 + - - +
163A ASN* 3.3 8.7 + - - +
164A THR* 2.7 53.0 + - - +
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Residues in contact with GLN 161 (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 LEU 5.6 2.4 + - - -
64A LEU* 3.9 22.9 - - + +
157A ARG 3.0 16.4 + - - +
158A PHE* 3.4 13.8 - - - +
159A VAL 3.1 0.2 - - - -
160A ASN* 1.3 78.9 + - - +
162A LEU* 1.3 59.5 + - + +
164A THR* 3.7 5.4 - - - -
165A LYS* 3.0 61.5 + - + +
166A TYR* 3.1 21.2 + - + -
227A VAL* 3.7 14.1 - - - +
228A VAL* 3.5 23.1 + - - -
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Residues in contact with LEU 162 (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 VAL* 5.6 1.3 - - + -
137A ILE* 4.3 14.4 - - + -
158A PHE* 3.5 19.5 - - + +
159A VAL* 3.1 15.0 + - + +
161A GLN* 1.3 77.9 - - + +
163A ASN* 1.3 64.4 + - - +
164A THR 3.4 0.2 - - - -
166A TYR* 3.3 50.0 - - + +
167A ARG* 3.5 2.3 + - - -
170A LEU* 3.8 23.5 - - + +
208A LYS* 3.7 23.6 - - - +
210A CYS* 3.9 24.5 - - - -
227A VAL* 4.5 10.3 - - + -
232A CYS* 6.1 0.4 - - + -
235A LEU* 5.9 0.7 - - + -
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Residues in contact with ASN 163 (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 TYR* 3.8 18.8 + - - -
159A VAL* 3.2 24.9 + - - +
160A ASN* 3.3 8.3 + - - +
161A GLN 3.3 0.6 - - - -
162A LEU* 1.3 83.5 - - - +
164A THR* 1.3 66.3 + - + +
167A ARG* 3.9 26.0 + - - +
170A LEU* 5.8 0.3 - - - +
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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