Contacts of the helix formed by residues 135 - 155 (chain A) in PDB entry 5PNT
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 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A ARG* 4.2 26.1 - - - +
61A SER* 5.7 0.5 - - - -
62A CYS* 5.5 0.9 - - - +
65A ARG* 3.7 25.1 + - - +
134A ASN* 1.3 79.2 - - - +
136A SER* 1.3 60.5 + - - +
138A PHE* 3.1 10.1 + - - +
139A GLU* 3.0 21.5 + - - +
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Residues in contact with SER 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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134A ASN* 3.2 12.6 + - - -
135A ASP* 1.3 76.9 - - - +
137A ASP* 1.3 60.1 + - - +
139A GLU* 3.4 9.3 + - - +
140A THR* 3.0 30.7 + - - -
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Residues in contact with ASP 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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130A PRO* 3.9 22.2 - - + -
133A GLY* 3.3 10.1 - - - -
134A ASN* 2.7 41.9 + - - +
136A SER* 1.3 80.9 - - - +
138A PHE* 1.3 55.8 + - - +
140A THR* 3.3 8.2 + - - -
141A VAL* 3.1 30.3 + - - +
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Residues in contact with PHE 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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17A CYS* 4.1 19.1 - - + -
21A ILE* 4.6 10.7 - - + +
56A ASP* 3.8 12.3 - - + -
58A ARG* 3.5 44.4 - - + +
59A GLY* 3.6 31.2 - - - -
62A CYS* 3.9 18.7 - - + -
130A PRO* 3.4 42.4 - - + -
134A ASN 3.3 22.0 - - - -
135A ASP* 3.1 11.0 + - - +
137A ASP* 1.3 76.4 - - - +
139A GLU* 1.3 64.6 + - - +
141A VAL* 3.2 8.3 + - + +
142A TYR* 3.0 22.7 + - - +
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Residues in contact with GLU 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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62A CYS* 3.8 10.3 - - - -
65A ARG* 5.2 5.5 + - - -
66A HIS* 2.8 34.8 + - - -
135A ASP 3.0 13.4 + - - +
136A SER* 3.6 11.4 - - - +
137A ASP 3.3 0.2 - - - -
138A PHE* 1.3 75.6 - - - +
140A THR* 1.3 58.7 + - - +
142A TYR* 3.4 2.1 + - - +
143A GLN* 2.9 64.7 + - + +
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Residues in contact with THR 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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124A GLN* 4.3 13.2 - - - +
136A SER 3.0 15.1 + - - -
137A ASP* 3.6 11.5 - - - -
138A PHE 3.2 0.4 - - - -
139A GLU* 1.3 74.7 - - - +
141A VAL* 1.3 65.3 + - + +
143A GLN* 3.3 7.3 + - + +
144A GLN* 2.9 45.5 + - + +
147A ARG* 5.6 1.1 - - - +
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Residues in contact with VAL 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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17A CYS 4.9 0.7 - - - +
18A ARG* 4.0 24.0 - - + +
21A ILE* 4.6 12.1 - - + -
127A ILE* 4.0 17.9 - - + -
128A GLU 3.8 22.2 - - - +
130A PRO* 3.9 18.2 - - + -
137A ASP 3.1 15.6 + - - +
138A PHE* 3.2 8.0 + - - +
140A THR* 1.3 75.2 - - - +
142A TYR* 1.3 58.4 + - - +
144A GLN* 3.3 12.0 + - - +
145A CYS* 2.9 44.5 + - - -
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Residues in contact with TYR 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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21A ILE* 4.2 12.5 - - + +
25A VAL* 3.9 21.3 - - + -
62A CYS* 4.1 10.5 - - - -
63A MET* 3.8 19.5 - - - -
66A HIS* 3.4 58.8 + + + +
68A ILE* 4.1 17.2 - - + +
138A PHE 3.0 13.2 + - - +
139A GLU* 3.5 7.9 - - - +
141A VAL* 1.3 77.1 - - - +
143A GLN* 1.3 77.7 + - - +
145A CYS* 3.1 3.8 + - - +
146A VAL* 2.9 47.3 + - + +
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Residues in contact with GLN 143 (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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66A HIS* 4.3 2.4 + - - -
139A GLU* 2.9 48.0 + - + +
140A THR* 3.3 6.9 + - + +
142A TYR* 1.3 94.0 - - - +
144A GLN* 1.3 61.6 + - - +
146A VAL* 3.4 7.2 + - - +
147A ARG* 3.2 40.5 + - - +
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Residues in contact with GLN 144 (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 ASP* 6.0 0.9 - - - -
124A GLN* 3.3 47.9 - - + +
126A ILE 3.1 20.0 + - - +
127A ILE* 3.7 37.0 - - + +
128A GLU 4.5 3.0 - - - +
140A THR* 2.9 34.9 + - + +
141A VAL* 3.5 8.7 - - - +
143A GLN* 1.3 76.7 - - - +
145A CYS* 1.3 57.5 + - - +
147A ARG* 3.3 14.3 + - - +
148A CYS* 2.9 36.5 + - - -
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Residues in contact with CYS 145 (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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18A ARG 4.7 1.3 - - - -
21A ILE* 4.4 2.5 - - + -
22A ALA* 3.9 39.7 - - + -
25A VAL* 4.2 9.4 - - + -
91A MET* 5.1 1.6 - - - -
116A LEU* 4.3 9.6 - - - -
127A ILE* 4.4 8.5 - - - -
141A VAL* 2.9 40.3 + - - +
142A TYR* 3.5 6.5 - - - +
144A GLN* 1.3 74.3 - - - +
146A VAL* 1.3 59.1 + - - +
148A CYS* 4.6 4.5 - - - -
149A CYS* 2.9 38.3 + - - -
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Residues in contact with VAL 146 (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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25A VAL* 3.9 21.8 - - + -
29A LEU* 5.8 1.3 - - + -
142A TYR* 2.9 51.0 + - + +
143A GLN* 3.9 7.9 - - - +
144A GLN 3.3 0.2 - - - -
145A CYS* 1.3 75.3 - - - +
147A ARG* 1.3 63.1 + - - +
149A CYS* 4.3 0.3 - - - +
150A ARG* 3.2 51.1 + - + +
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Residues in contact with ARG 147 (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 ASP* 2.8 45.9 + - - +
121A PRO* 4.1 11.1 - - + +
122A GLN* 3.0 41.4 + - - +
124A GLN* 2.7 29.3 + - - +
140A THR* 5.6 1.4 - - - +
143A GLN* 3.2 21.7 + - - +
144A GLN* 3.5 27.0 - - - +
146A VAL* 1.3 80.1 - - + +
148A CYS* 1.3 61.9 + - - +
150A ARG* 3.6 26.0 + - - +
151A ALA* 3.3 23.4 + - - +
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Residues in contact with CYS 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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116A LEU* 3.5 44.2 - - + +
117A GLY* 3.7 10.5 - - - -
119A TYR* 3.8 11.2 - - + +
120A ASP* 3.5 29.6 - - - -
124A GLN 5.4 0.9 - - - -
127A ILE* 4.7 3.8 - - - -
144A GLN* 2.9 24.1 + - - +
145A CYS 4.2 1.1 - - - +
147A ARG* 1.3 74.4 - - - +
149A CYS* 1.3 60.7 + - - +
151A ALA* 3.4 1.2 + - - -
152A PHE* 2.8 30.9 + - - +
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Residues in contact with CYS 149 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A PHE* 4.3 16.4 - - - -
22A ALA 3.9 22.2 - - - -
25A VAL* 4.1 8.1 - - + -
26A PHE* 4.1 19.9 - - + -
29A LEU* 3.8 19.7 - - + +
116A LEU* 4.7 6.7 - - - -
145A CYS* 2.9 32.1 + - - +
146A VAL 4.3 0.4 - - - +
148A CYS* 1.3 73.9 - - - +
150A ARG* 1.3 66.8 + - - +
152A PHE* 3.8 6.6 - - - +
153A LEU* 3.0 24.3 + - - +
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Residues in contact with ARG 150 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LEU* 3.8 29.8 - - + -
121A PRO* 5.7 4.8 - - - +
146A VAL* 3.2 40.6 + - + +
147A ARG* 3.9 29.6 + - - +
149A CYS* 1.3 78.0 - - - +
151A ALA* 1.3 64.2 + - - +
153A LEU* 3.3 4.4 + - - +
154A GLU* 3.3 30.7 + - - +
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Residues in contact with ALA 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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119A TYR* 3.2 31.0 - - + +
121A PRO* 4.2 11.9 - - + -
147A ARG 3.3 12.9 + - - +
148A CYS 3.8 0.7 - - - +
149A CYS 3.3 0.2 - - - -
150A ARG* 1.3 78.6 - - - +
152A PHE* 1.3 65.0 - - - +
154A GLU* 3.3 24.7 + - - +
155A LYS* 3.5 22.6 + - - +
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Residues in contact with PHE 152 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A VAL* 4.3 5.4 - - + -
10A PHE* 5.6 0.2 - + - -
26A PHE* 3.6 27.4 - + - -
39A TRP* 3.9 21.8 - + - -
87A TYR* 3.6 47.3 - + + -
89A LEU* 3.9 24.7 - - + -
116A LEU* 5.1 1.8 - - + -
119A TYR* 3.4 48.6 - + + -
148A CYS 2.8 22.3 + - - +
149A CYS* 3.8 5.6 - - - +
151A ALA* 1.3 72.7 - - - +
153A LEU* 1.3 57.4 + - - +
155A LYS* 3.2 3.9 + - - -
156A ALA* 2.9 34.4 + - + +
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Residues in contact with LEU 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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26A PHE* 3.8 16.4 - - + -
29A LEU* 3.8 29.2 - - + -
30A VAL* 3.8 28.5 - - + -
33A GLN* 4.2 25.4 - - + +
35A ILE* 4.2 12.6 - - + -
39A TRP* 4.1 17.0 - - + +
149A CYS 3.0 16.6 + - - +
150A ARG 3.5 5.2 - - - +
152A PHE* 1.3 79.5 - - - +
154A GLU* 1.3 61.3 + - + +
155A LYS 3.2 1.0 + - - -
156A ALA* 3.4 14.1 + - - +
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Residues in contact with GLU 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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150A ARG* 3.3 22.1 + - - +
151A ALA* 3.5 14.2 - - - +
152A PHE 3.2 0.8 - - - -
153A LEU* 1.3 77.8 - - + +
155A LYS* 1.3 63.0 + - + +
156A ALA 3.7 0.2 - - - -
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Residues in contact with LYS 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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87A TYR* 4.6 4.2 + - - -
118A SER 5.5 2.2 + - - -
119A TYR* 4.0 38.1 + - + +
151A ALA* 3.5 16.6 + - - +
152A PHE* 3.2 6.9 + - - +
153A LEU 3.2 0.2 - - - -
154A GLU* 1.3 83.7 - - + +
156A ALA* 1.3 61.2 + - - +
157A HIS* 4.1 0.9 + - - +
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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