Contacts of the helix formed by residues 131 - 147 (chain B) in PDB entry 4R1Z
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 SER 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ALA* 5.8 0.2 - - - +
129B ASP* 3.2 6.6 + - - -
130B TYR* 1.3 82.8 - - - +
132B SER* 1.3 63.7 + - - +
133B THR* 3.2 13.9 + - - -
134B TRP* 2.8 37.0 + - - +
135B LYS* 3.1 21.9 + - - +
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Residues in contact with SER 132 (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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152A SER* 3.2 20.3 + - - -
131B SER* 1.3 72.7 - - - +
133B THR* 1.3 60.7 + - - +
135B LYS* 3.8 12.8 - - - +
136B PHE* 2.8 29.3 + - - +
295B ASP 5.2 2.6 + - - -
296B VAL* 4.0 16.5 - - - +
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Residues in contact with THR 133 (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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131B SER* 3.1 11.5 + - - -
132B SER* 1.3 78.5 + - - +
134B TRP* 1.3 69.6 + - - +
136B PHE* 3.4 1.2 + - - +
137B HIS* 3.1 35.7 + - - +
295B ASP 4.5 2.4 + - - -
296B VAL* 3.7 12.9 - - - +
297B GLY* 3.3 41.5 + - - +
302B HIS* 3.8 17.7 - - + +
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Residues in contact with TRP 134 (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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124B ASP 5.5 2.0 - - - -
125B ILE* 3.6 35.1 - - + +
128B ALA* 4.2 11.7 - - + -
129B ASP 3.4 22.9 - - - +
130B TYR* 3.3 34.8 - + - -
131B SER* 2.8 21.8 + - - +
133B THR* 1.3 75.7 - - - +
135B LYS* 1.3 95.2 + - + +
137B HIS* 3.3 5.8 + - - +
138B ARG* 3.1 43.3 + - - +
450B VAL* 3.6 28.9 - - + -
451B ARG* 3.4 29.0 - - - +
600B HEM 3.0 20.5 + - - -
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Residues in contact with LYS 135 (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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152A SER* 3.7 29.4 - - - +
157A LYS* 6.1 4.7 - - - +
130B TYR* 3.4 29.5 + - + -
131B SER 3.1 9.7 + - - +
132B SER* 3.6 17.6 - - - +
134B TRP* 1.3 98.2 - - + +
136B PHE* 1.3 58.3 + - - +
138B ARG* 3.0 10.3 + - + +
139B LYS* 2.9 28.9 + - + +
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Residues in contact with PHE 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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150A GLU* 3.2 33.2 - - + -
151A GLY* 4.6 2.9 - - - -
152A SER* 3.6 21.3 + - - +
132B SER 2.8 21.7 + - - +
133B THR 3.8 3.8 - - - +
135B LYS* 1.3 71.2 - - - +
137B HIS* 1.3 68.5 + + - +
139B LYS* 3.1 9.3 + - + +
140B MET* 2.9 64.6 + - + +
279B LEU* 5.4 0.2 - - + -
282B ALA* 4.0 11.0 - - + -
296B VAL* 3.8 27.1 - - + -
298B LEU* 4.0 31.4 - - + -
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Residues in contact with HIS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASP 5.8 1.8 + - - +
125B ILE* 3.9 12.1 - - + -
133B THR* 3.1 28.4 + - + +
134B TRP* 3.7 6.7 - - - +
136B PHE* 1.3 84.8 - + - +
138B ARG* 1.3 64.7 + - - +
140B MET* 3.5 7.1 + - - +
141B VAL* 3.3 28.4 + - - +
279B LEU* 4.1 17.2 - - + +
297B GLY 3.2 27.6 - - - -
298B LEU* 4.3 11.6 - - + +
302B HIS* 3.5 27.3 - + + +
303B VAL* 4.5 0.8 + - - -
306B THR* 3.1 33.3 - - - +
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Residues in contact with ARG 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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125B ILE* 3.8 24.8 - - + +
134B TRP* 3.1 41.2 + - - +
135B LYS* 3.0 15.0 + - + +
137B HIS* 1.3 77.1 - - - +
139B LYS* 1.3 59.4 + - - +
141B VAL* 3.3 5.2 + - - +
142B HIS* 3.1 23.6 + - - +
450B VAL 4.2 6.9 + - - -
451B ARG 4.1 4.0 - - - -
452B VAL* 2.7 46.4 + - - +
453B CYS 4.1 3.6 + - - -
454B LEU* 3.3 34.2 - - + +
600B HEM 2.8 34.1 + - - +
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Residues in contact with LYS 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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146A CYS 4.5 9.5 - - - +
147A MET* 3.9 13.7 - - + +
148A PHE 4.2 2.7 - - - -
149A GLY* 3.1 26.1 - - - +
150A GLU* 3.8 18.2 + - - +
152A SER* 3.7 11.4 + - - +
153A VAL 3.0 43.4 + - - +
154A SER* 3.9 10.2 + - - +
135B LYS* 2.9 13.6 + - + +
136B PHE* 3.1 11.6 + - + +
138B ARG* 1.3 75.4 - - - +
140B MET* 1.3 65.7 + - + +
142B HIS* 3.3 11.7 + - - +
143B GLY* 2.9 27.4 + - - -
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Residues in contact with MET 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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147A MET* 3.3 33.7 - - + +
150A GLU* 4.5 11.9 - - - +
136B PHE* 2.9 61.4 + - + +
137B HIS* 3.7 6.7 - - - +
138B ARG 3.3 0.2 - - - -
139B LYS* 1.3 83.2 - - + +
141B VAL* 1.3 57.7 + - + +
144B ALA* 2.9 29.8 + - - +
275B LEU* 4.0 2.1 - - - +
278B ALA* 4.7 8.0 - - + +
279B LEU* 4.0 24.9 - - + -
282B ALA* 3.8 18.2 - - + -
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ILE* 4.1 0.4 - - + -
137B HIS 3.3 15.2 + - - +
138B ARG 3.6 5.8 - - - +
139B LYS 3.3 0.4 - - - -
140B MET* 1.3 74.6 - - + +
142B HIS* 1.3 58.8 + - - +
144B ALA* 3.3 1.0 + - - +
145B LEU* 2.8 40.4 + - + +
195B LEU* 5.6 4.5 - - + +
275B LEU* 3.8 17.6 - - + +
306B THR* 3.9 22.4 - - + -
310B ILE* 3.7 38.4 - - + -
454B LEU* 3.8 20.9 - - + +
600B HEM 5.9 0.9 - - + -
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Residues in contact with HIS 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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146A CYS* 4.3 28.8 + - - -
461A MET* 6.5 0.7 - - + -
138B ARG 3.1 14.9 + - - +
139B LYS* 3.6 9.7 + - - +
141B VAL* 1.3 82.7 - - - +
143B GLY* 1.3 58.4 + - - +
145B LEU* 3.6 15.1 - - + +
146B CYS* 3.2 27.9 + - - -
454B LEU* 5.0 10.3 - - + +
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Residues in contact with GLY 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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146A CYS* 4.2 11.2 - - - -
147A MET* 3.4 31.9 - - - -
139B LYS 2.9 10.5 + - - -
142B HIS* 1.3 75.0 + - - +
144B ALA* 1.3 57.0 + - - +
145B LEU 2.9 4.5 - - - -
146B CYS* 2.8 19.2 + - - +
147B MET* 3.0 17.3 + - - +
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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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147A MET* 3.1 5.0 - - - +
140B MET 2.9 21.7 + - - +
141B VAL 3.9 0.4 - - - +
143B GLY* 1.3 70.5 - - - -
145B LEU* 1.3 57.2 + - - +
147B MET* 4.2 0.4 - - - -
148B PHE* 3.2 29.5 + - - +
195B LEU* 4.4 5.3 - - + +
272B GLN* 3.5 23.5 + - - +
275B LEU* 3.5 36.7 + - + -
278B ALA* 3.9 8.7 - - + -
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Residues in contact with LEU 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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141B VAL* 2.8 21.9 + - + +
142B HIS* 3.6 16.8 - - + +
144B ALA* 1.3 78.2 - - - +
146B CYS* 1.3 67.0 + - - +
148B PHE* 3.9 2.8 + - - +
155B ILE* 3.5 33.5 - - + +
195B LEU* 3.9 25.5 - - + +
454B LEU 5.5 5.6 - - - +
455B GLY* 6.3 0.2 - - - -
457B ALA* 4.2 25.1 - - + -
458B LEU* 4.1 35.2 - - + +
461B MET* 5.2 9.0 - - + -
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Residues in contact with CYS 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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139A LYS* 4.5 11.6 - - - +
142A HIS* 3.7 27.9 + - - +
143A GLY* 4.2 6.7 + - - -
146A CYS* 2.1 51.4 - - + -
142B HIS* 3.2 24.2 - - - -
143B GLY 2.8 11.2 + - - +
145B LEU* 1.3 79.4 - - - +
147B MET* 1.3 57.8 + - - +
148B PHE 3.3 5.9 + - - +
154B SER* 5.6 0.3 - - - -
155B ILE* 4.6 5.5 - - - +
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Residues in contact with MET 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LYS* 4.7 9.0 - - + +
140A MET* 6.1 4.3 - - + -
143A GLY* 3.2 42.0 - - - +
147A MET* 3.4 35.0 - - + +
272A GLN* 4.9 14.1 - - - +
281A ARG* 6.0 3.1 - - - -
143B GLY* 3.0 17.0 + - - +
144B ALA 4.1 1.6 - - - -
146B CYS* 1.3 74.5 - - - +
148B PHE* 1.3 54.9 + - - +
149B GLY* 3.0 23.3 - - - +
150B GLU* 4.4 16.6 - - + +
272B GLN* 3.7 31.6 + - - +
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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
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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