Contacts of the helix formed by residues 135 - 155 (chain B) in PDB entry 4FZY
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 ARG 135 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B GLU* 3.1 6.5 - - - +
18B GLU* 2.9 33.7 + - - +
36B LEU* 3.5 23.0 - - - +
51B HIS 3.9 15.6 + - - -
52B ARG 5.6 0.8 + - - -
53B ILE* 4.0 13.9 - - - +
57B MET* 4.0 19.6 - - - +
130B GLY 5.5 1.0 + - - -
131B LEU* 4.2 29.5 - - + +
132B HIS* 3.2 43.9 + - + +
133B HIS 3.1 2.0 - - - -
134B HIS* 1.3 84.3 - - - +
136B ALA* 1.3 67.5 + - - +
137B LEU 2.9 5.1 + - - +
138B TYR* 3.3 4.4 + - + +
139B ASP* 3.1 20.3 + - - +
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ASP* 3.5 17.0 - - - +
8B GLU* 3.0 14.5 + - + -
18B GLU* 3.1 29.2 + - + +
19B ILE* 3.6 8.3 - - - -
20B ALA* 3.1 31.9 - - + +
135B ARG* 1.3 72.0 - - - +
137B LEU* 1.3 58.3 + - - +
140B CYS* 3.2 28.1 + - - -
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLU* 5.0 0.8 + - - +
20B ALA* 3.4 9.6 - - + -
21B SER 4.0 1.6 - - - +
22B VAL* 3.8 16.4 - - + -
32B PRO* 4.0 14.1 - - + -
33B MET 3.9 17.5 - - - +
34B SER* 4.0 18.8 - - - +
128B PRO* 4.0 14.4 - - + -
131B LEU* 3.4 26.4 - - + +
135B ARG* 3.1 1.8 - - - +
136B ALA* 1.3 77.2 - - - +
138B TYR* 1.3 70.2 + - - +
140B CYS* 2.8 19.6 + - + +
141B TYR* 3.1 31.3 + - + -
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Residues in contact with TYR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B MET* 4.5 5.8 - - + +
118B TYR* 5.9 1.2 - - - -
127B THR* 3.2 41.2 + - + +
128B PRO* 4.3 10.7 - - + +
131B LEU* 3.2 30.5 - - + +
132B HIS* 3.4 19.3 - - - +
133B HIS* 3.3 35.4 - - + +
135B ARG* 3.3 5.8 + - + +
137B LEU* 1.3 77.7 - - - +
139B ASP* 1.3 68.2 + - - +
141B TYR* 3.0 16.5 + - - +
142B ILE* 3.2 34.1 + - + +
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Residues in contact with ASP 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ASP* 3.3 22.7 - - - +
114B ASN* 3.6 16.4 + - - +
115B MET* 4.6 4.6 - - - +
133B HIS* 3.9 4.2 + - - +
134B HIS* 3.1 39.7 + - - -
135B ARG 3.1 5.4 + - - +
138B TYR* 1.3 88.2 - - - +
140B CYS* 1.3 54.8 + - - +
142B ILE* 3.2 9.1 + - - +
143B THR* 2.8 33.3 + - - +
201B NA 2.3 25.4 - - - -
12D A 3.9 0.9 + - - -
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Residues in contact with CYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 3.7 16.6 - - + +
6B ASP* 3.7 15.9 - - - +
20B ALA* 3.3 32.3 - - - -
21B SER* 3.6 8.5 - - - -
22B VAL* 4.0 20.0 - - + -
136B ALA 3.2 22.8 + - - -
137B LEU* 2.8 15.5 + - - +
139B ASP* 1.3 76.5 - - - +
141B TYR* 1.3 54.3 + - - +
143B THR 3.2 1.4 + - - -
144B ALA* 2.8 32.1 + - - +
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Residues in contact with TYR 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B VAL* 3.9 8.1 - - + -
29B ILE* 3.6 36.7 - - + +
32B PRO* 3.3 27.7 - - + +
125B VAL* 3.5 9.7 - - + +
126B GLN* 3.4 26.8 + - - +
127B THR* 4.0 15.5 - - + -
128B PRO* 3.5 29.6 - - + +
137B LEU* 3.1 39.7 + - + -
138B TYR 3.0 8.7 + - - +
140B CYS* 1.3 77.1 - - - +
142B ILE* 1.3 61.9 + - - +
144B ALA* 4.0 3.8 - - - +
145B ALA* 3.1 24.8 + - - +
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Residues in contact with ILE 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ASN* 3.9 24.2 - - - +
115B MET* 4.1 14.4 - - + -
118B TYR* 3.8 55.1 - - + +
125B VAL* 4.3 7.2 - - + -
127B THR* 4.4 3.6 - - + -
138B TYR* 3.2 44.2 + - + +
139B ASP* 3.2 8.9 + - - +
140B CYS 3.1 0.2 - - - -
141B TYR* 1.3 76.9 - - - +
143B THR* 1.3 63.5 + - - +
144B ALA 3.2 0.3 + - - -
145B ALA* 3.3 6.9 + - - +
146B LEU* 3.1 21.5 + - + +
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Residues in contact with THR 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 4.0 22.7 - - + -
5B ILE 6.0 0.2 - - - -
6B ASP* 6.0 2.5 - - - +
78B VAL* 4.6 1.1 - - + -
79B ALA* 4.4 2.0 - - - -
80B HIS* 3.9 17.9 - - + +
99B THR* 3.6 30.6 - - + +
114B ASN* 2.6 32.5 + - - +
139B ASP* 2.8 17.0 + - - +
142B ILE* 1.3 72.5 - - - +
144B ALA* 1.3 57.4 + - - +
146B LEU* 3.4 6.2 + - + +
147B LEU* 3.0 25.1 + - - +
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 3.7 17.7 - - + +
22B VAL* 3.7 21.8 - - + -
24B VAL* 3.9 6.2 - - + +
29B ILE* 3.9 17.9 - - + -
140B CYS 2.8 17.0 + - - +
141B TYR* 4.0 2.5 - - - +
143B THR* 1.3 74.2 - - - +
145B ALA* 1.3 66.2 + - - +
146B LEU 3.1 1.1 - - - -
147B LEU* 3.1 3.6 + - - +
148B ILE* 2.9 29.9 + - - +
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Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ILE* 4.3 1.2 - - - +
118B TYR* 4.3 11.4 - - + -
123B LEU* 3.9 13.6 - - + +
124B ASN 5.3 0.4 - - - -
125B VAL* 3.4 37.0 - - + -
141B TYR 3.1 12.3 + - - +
142B ILE 3.5 5.4 - - - +
144B ALA* 1.3 76.3 - - - +
146B LEU* 1.3 61.9 + - - +
148B ILE* 3.5 10.9 + - - +
149B ASP* 3.1 21.7 + - - +
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B HIS* 4.0 30.1 - - + +
99B THR* 4.1 15.0 - - - +
103B ALA* 5.2 0.2 - - + -
107B TRP* 4.2 24.2 - - + -
114B ASN* 4.6 10.3 - - - +
117B LEU* 4.0 30.3 - - + -
118B TYR* 6.0 2.0 - - + +
121B ARG* 4.7 3.1 - - + -
123B LEU* 3.9 19.2 - - + +
142B ILE* 3.1 13.3 + - + +
143B THR* 3.5 8.1 - - - +
144B ALA 3.1 0.8 - - - -
145B ALA* 1.3 74.1 - - - +
147B LEU* 1.3 59.4 + - - +
149B ASP* 3.1 5.4 + - + +
150B ILE* 2.9 38.6 + - + +
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LEU* 4.1 20.0 - - + -
4B ILE* 3.6 26.7 - - + -
24B VAL* 4.2 6.3 - - + -
78B VAL* 3.9 20.2 - - + -
97B ILE* 4.9 0.9 - - + -
99B THR* 4.1 19.9 - - + +
102B LEU* 4.7 5.6 - - + -
143B THR 3.0 14.0 + - - +
144B ALA* 3.4 8.7 - - - +
146B LEU* 1.3 75.8 - - - +
148B ILE* 1.3 51.8 + - - +
150B ILE* 2.8 11.2 + - + +
151B MET* 2.7 43.0 + - + +
161B MET* 3.7 31.2 - - + -
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Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL* 3.8 27.1 - - + -
27B GLY* 4.1 31.2 - - - +
28B LYS* 4.5 0.4 - - - +
29B ILE* 3.9 30.3 - - + +
144B ALA 2.9 21.3 + - - +
145B ALA* 3.7 7.2 - - - +
147B LEU* 1.3 76.3 - - - +
149B ASP* 1.3 57.9 + - - +
151B MET* 3.3 8.7 + - - +
152B ASN* 2.9 47.5 + - - +
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Residues in contact with ASP 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B TRP* 3.7 5.5 - - + -
121B ARG* 2.7 49.3 + - - +
123B LEU* 4.0 23.0 - - + +
145B ALA 3.1 12.8 + - - +
146B LEU* 3.1 10.5 + - + +
148B ILE* 1.3 75.7 - - - +
150B ILE* 1.3 56.6 + - - +
152B ASN* 3.4 6.4 + - - +
153B THR* 2.7 45.4 + - - -
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Residues in contact with ILE 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B THR* 3.8 34.5 - - + +
102B LEU* 4.0 28.9 - - + -
103B ALA* 4.2 5.6 - - - +
106B LEU* 3.8 19.2 - - + +
107B TRP* 3.8 20.9 - - + -
146B LEU* 2.9 30.8 + - + +
147B LEU* 2.8 10.1 + - - +
149B ASP* 1.3 77.0 - - - +
151B MET* 1.3 57.2 + - - +
153B THR* 3.4 1.4 + - - -
154B SER* 3.0 33.0 + - - +
156B TRP* 4.3 11.4 - - + -
161B MET* 4.7 6.3 - - - -
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Residues in contact with MET 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LEU* 3.7 33.2 - - + -
24B VAL* 4.6 11.2 - - + -
147B LEU* 2.7 33.9 + - + +
148B ILE* 3.8 7.0 - - - +
150B ILE* 1.3 73.2 - - - +
152B ASN* 1.3 60.9 + - - +
153B THR 3.1 1.8 - - - -
154B SER* 4.3 4.0 - - - -
155B GLY* 2.8 30.2 + - - +
156B TRP 3.9 19.1 - - - +
157B THR* 5.3 1.6 - - - -
158B ALA 5.3 2.7 - - - +
161B MET* 4.0 21.8 - - + -
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Residues in contact with ASN 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B GLY* 5.8 3.4 - - - -
148B ILE* 2.9 36.7 + - - +
149B ASP* 3.9 8.2 - - - +
151B MET* 1.3 78.4 - - - +
153B THR* 1.3 59.5 + - - +
155B GLY 4.6 1.1 - - - -
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Residues in contact with THR 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 4.2 23.8 - - + -
107B TRP* 4.0 19.0 - - + +
121B ARG* 4.2 6.6 + - - +
149B ASP* 2.7 31.5 + - - -
150B ILE 3.8 3.4 - - - -
151B MET 3.1 0.2 - - - -
152B ASN* 1.3 81.3 - - - +
154B SER* 1.3 59.4 + - - +
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Residues in contact with SER 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 4.2 11.7 - - - -
150B ILE 3.0 17.1 + - - -
153B THR* 1.3 77.9 - - - +
155B GLY* 1.3 60.4 + - - +
156B TRP* 2.8 65.9 + - - +
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Residues in contact with GLY 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B MET 2.8 18.3 + - - -
152B ASN 4.6 0.8 - - - -
153B THR 3.7 0.6 - - - -
154B SER* 1.3 75.2 - - - +
156B TRP* 1.3 65.3 + - - +
157B THR* 3.3 8.3 + - - +
160B GLN* 4.0 3.9 - - - +
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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