Contacts of the helix formed by residues 123 - 142 (chain B) in PDB entry 4MQP
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 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ASP* 4.2 22.4 - - - -
126A VAL* 4.1 10.0 - - - +
317A PRO* 5.4 2.0 - - - -
319A PHE* 6.4 1.1 - - - -
121B SER* 3.6 1.8 + - - -
122B ASP* 1.3 82.9 - - - +
124B GLY* 1.3 65.0 + - - +
125B SER* 3.8 2.6 + - - -
126B VAL* 3.3 26.0 + - - +
127B SER 3.0 18.2 + - - -
291B SER* 5.5 0.7 - - - -
292B LEU 4.9 1.8 - - - +
293B ALA* 3.3 14.5 - - - +
501B 2B1 4.0 10.6 + - - -
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Residues in contact with GLY 124 (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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123B SER* 1.3 73.9 - - - +
125B SER* 1.3 62.0 + - - +
127B SER* 2.9 19.6 + - - -
128B VAL* 3.1 8.3 + - - +
256B ILE* 3.3 28.1 - - - +
282B GLY* 5.7 1.5 - - - -
292B LEU 5.4 0.4 + - - -
293B ALA* 3.9 5.8 - - - +
501B 2B1 3.4 24.4 + - - -
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Residues in contact with SER 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A VAL* 5.4 2.2 - - - -
315A HIS* 5.7 0.8 + - - -
123B SER* 3.3 2.6 - - - -
124B GLY* 1.3 72.2 - - - +
126B VAL* 1.3 64.3 + - - +
128B VAL* 3.2 4.7 + - - +
129B GLU* 3.1 24.6 + - - +
158B HIS 4.3 9.9 - - - -
159B GLY* 3.3 6.9 - - - -
160B ASP* 3.1 24.5 + - - +
161B THR* 3.5 31.7 + - - -
164B ALA* 4.7 0.6 - - - +
501B 2B1 2.8 28.1 + - - -
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Residues in contact with VAL 126 (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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123A SER* 4.2 8.7 - - - +
125A SER* 5.3 2.7 - - - -
126A VAL* 3.6 23.6 - - + -
161A THR* 4.0 15.5 - - + -
121B SER* 3.5 24.9 - - - +
122B ASP 4.8 1.6 - - - +
123B SER* 3.3 23.4 + - - +
124B GLY 3.2 0.4 - - - -
125B SER* 1.3 79.1 - - - +
127B SER* 1.3 57.4 + - - +
129B GLU* 3.1 8.7 + - - +
130B VAL* 2.9 27.1 + - + +
161B THR* 5.2 0.4 - - + -
315B HIS* 3.9 22.9 - - + +
317B PRO* 4.8 5.6 - - + -
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Residues in contact with SER 127 (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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121B SER* 3.6 15.2 + - - -
123B SER 3.0 11.0 + - - -
124B GLY* 2.9 15.3 + - - -
126B VAL* 1.3 76.6 - - - +
128B VAL* 1.3 56.7 + - - +
130B VAL* 3.5 1.7 + - - -
131B ALA 2.9 17.7 + - - -
256B ILE* 3.4 16.1 - - - +
280B CYS* 3.5 13.4 - - - +
293B ALA* 3.8 8.2 - - - +
294B ALA 3.8 13.5 + - - -
295B THR* 2.9 31.0 + - - -
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Residues in contact with VAL 128 (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 GLY 3.1 15.6 + - - +
125B SER 3.5 8.1 - - - +
126B VAL 3.1 0.2 - - - -
127B SER* 1.3 75.6 - - - +
129B GLU* 1.3 60.2 + - - +
131B ALA* 3.2 4.9 + - + +
132B ALA* 3.0 26.0 + - - +
158B HIS* 3.5 35.2 - - + +
163B LEU* 4.4 4.5 - - + -
164B ALA* 4.2 15.3 - - + -
167B ILE* 4.4 11.7 - - + -
218B VAL* 5.6 4.0 - - + -
254B ASP* 3.5 24.7 - - + +
256B ILE* 3.9 8.5 - - + -
280B CYS* 4.0 9.6 - - - -
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Residues in contact with GLU 129 (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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129A GLU* 4.5 0.7 - - - +
161A THR* 3.5 22.0 - - + -
162A PHE* 3.0 43.0 + - + +
125B SER 3.1 15.8 + - - +
126B VAL 3.1 5.6 + - - +
128B VAL* 1.3 75.7 - - - +
130B VAL* 1.3 55.6 + - - +
132B ALA* 3.3 3.5 + - - +
133B LYS* 2.9 29.2 + - - +
161B THR* 2.6 28.3 + - - +
162B PHE 4.8 0.4 - - - -
163B LEU* 3.1 39.2 + - - +
164B ALA 3.2 6.6 + - - +
315B HIS* 4.9 5.2 - - + -
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Residues in contact with VAL 130 (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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119B PHE* 3.9 26.2 - - + -
121B SER* 4.8 1.6 - - - -
126B VAL* 2.9 23.2 + - + +
127B SER* 3.6 9.4 - - - +
129B GLU* 1.3 72.2 - - - +
131B ALA* 1.3 59.7 + - - +
133B LYS* 3.2 7.4 + - + +
134B MET* 2.9 51.9 + - + +
295B THR* 3.7 13.0 - - - +
313B LEU* 4.6 6.3 - - + -
315B HIS* 3.4 38.4 - - + +
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Residues in contact with ALA 131 (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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127B SER 2.9 15.3 + - - +
128B VAL* 3.2 10.1 + - + +
130B VAL* 1.3 75.9 - - - +
132B ALA* 1.3 56.8 + - - +
134B MET* 3.4 3.7 + - - +
135B ALA* 3.0 28.1 + - - +
252B ILE* 3.8 15.4 - - + +
278B ILE* 3.6 26.9 - - + +
280B CYS* 3.6 16.4 - - - -
295B THR* 3.7 8.9 - - + +
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Residues in contact with ALA 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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162A PHE* 4.2 5.6 - - + -
128B VAL 3.0 8.2 + - - +
129B GLU 3.6 8.1 - - - +
131B ALA* 1.3 75.8 - - - +
133B LYS* 1.3 58.1 + - - +
135B ALA* 3.3 5.9 + - - +
136B LEU* 2.9 39.6 + - + +
150B LEU* 4.5 14.6 - - + -
163B LEU* 3.6 34.8 - - + -
252B ILE* 4.6 5.1 - - - +
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Residues in contact with LYS 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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160A ASP* 2.9 17.8 + - - +
162A PHE* 4.0 18.1 - - + -
165A MET* 3.5 28.1 - - - +
178A TRP* 3.6 21.6 - - + -
129B GLU 2.9 15.0 + - - +
130B VAL* 3.2 7.4 + - - +
132B ALA* 1.3 73.8 - - - +
134B MET* 1.3 56.9 + - - +
136B LEU* 3.8 0.2 - - - -
137B GLN* 2.8 41.7 + - - +
313B LEU* 3.9 10.5 - - + -
314B MET 2.7 35.4 + - - +
315B HIS* 2.9 28.5 + - + +
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Residues in contact with MET 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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22A TRP* 4.1 13.9 - - + -
117B THR* 5.5 0.2 - - - +
118B VAL 5.8 0.2 - - - -
119B PHE* 3.8 28.9 - - + +
130B VAL* 2.9 21.5 + - + +
131B ALA 3.5 7.6 - - - +
133B LYS* 1.3 75.6 - - - +
135B ALA* 1.3 58.4 + - - +
138B TYR* 2.9 32.2 + - - +
278B ILE* 4.0 12.6 - - + -
295B THR* 3.8 29.8 - - + +
297B CYS* 3.9 24.9 - - - -
301B VAL* 4.6 1.8 - - + -
305B ILE* 3.5 23.2 - - + +
313B LEU* 4.0 23.8 - - + -
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Residues in contact with ALA 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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131B ALA 3.0 14.5 + - - +
132B ALA* 3.3 9.2 + - - +
134B MET* 1.3 77.6 - - - +
136B LEU* 1.3 62.5 + - + +
138B TYR* 3.4 2.4 + - - +
139B TRP* 3.2 30.8 + - - -
150B LEU* 5.2 0.9 - - + -
215B ALA* 4.2 7.4 - - + -
216B ALA* 4.0 21.8 - - + -
250B LEU* 3.7 23.6 - - + -
252B ILE* 4.2 3.1 - - + -
278B ILE* 3.9 5.5 - - + +
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Residues in contact with LEU 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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162A PHE* 4.7 11.0 - - + -
178A TRP* 3.7 28.5 - - + -
181A VAL* 4.4 17.9 - - + -
132B ALA* 2.9 24.8 + - + +
133B LYS* 3.9 1.3 - - - +
135B ALA* 1.3 75.8 - - + +
137B GLN* 1.3 64.0 + - - +
139B TRP* 3.4 3.5 + - - +
140B ARG* 3.0 33.9 + - - +
147B LYS 4.6 2.6 - - - +
148B ARG* 3.8 40.2 - - + +
150B LEU* 4.8 9.2 - - + -
215B ALA* 3.8 17.9 - - + -
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Residues in contact with GLN 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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177A LEU* 5.5 2.0 - - + -
178A TRP* 3.4 32.0 - - + -
133B LYS* 2.8 18.5 + - - +
134B MET* 4.8 0.2 - - - -
136B LEU* 1.3 71.7 - - - +
138B TYR* 1.3 60.2 + - - +
140B ARG* 3.7 8.5 - - + +
141B GLY* 2.8 26.3 + - - -
305B ILE* 3.6 29.4 + - + +
310B ALA* 3.5 19.5 - - + +
312B ALA 2.7 25.8 + - - -
313B LEU* 3.2 15.1 - - - +
314B MET* 3.2 25.4 + - - +
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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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134B MET 2.9 20.9 + - - +
135B ALA 3.5 4.3 - - - +
136B LEU 3.2 0.2 - - - -
137B GLN* 1.3 76.8 - - - +
139B TRP* 1.3 107.6 + + - +
141B GLY* 3.1 4.3 + - - -
142B ARG* 3.1 51.5 + - + +
250B LEU* 3.7 23.0 - - + +
300B ASP* 3.2 28.1 + - - -
301B VAL* 3.7 26.5 - - + -
304B THR* 3.5 30.1 - - + +
305B ILE* 3.8 10.0 - - + +
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Residues in contact with TRP 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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135B ALA 3.2 22.1 + - - -
136B LEU 3.4 3.8 + - - +
137B GLN 3.3 0.4 - - - -
138B TYR* 1.3 95.2 - + - +
140B ARG* 1.3 65.1 + - - +
142B ARG* 3.0 41.0 + - + +
144B LEU* 2.8 58.6 + - + +
145B PRO* 5.3 0.2 - - + -
147B LYS* 3.4 33.0 - - + +
215B ALA* 2.9 39.1 + - + +
248B GLU* 3.3 43.5 - - + -
249B VAL 4.5 0.2 - - - -
250B LEU* 3.8 18.7 - - + +
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Residues in contact with ARG 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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177A LEU* 3.2 30.5 + - + +
178A TRP* 4.5 12.5 - - - -
180A ASP* 3.5 15.6 + - - -
181A VAL* 3.3 26.9 - - - +
136B LEU* 3.0 35.1 + - - +
137B GLN* 3.7 10.8 - - + +
139B TRP* 1.3 76.3 - - - +
141B GLY* 1.3 56.5 + - - +
143B GLY* 3.0 19.2 + - - -
144B LEU 4.4 3.1 + - - +
145B PRO* 2.9 49.1 + - + +
147B LYS 5.3 1.0 + - - -
148B ARG* 3.6 13.3 - - - +
309B ALA* 5.6 2.5 + - - +
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Residues in contact with GLY 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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137B GLN 2.8 18.9 + - - -
138B TYR 3.1 6.2 + - - -
140B ARG* 1.3 74.3 - - - +
142B ARG* 1.3 56.6 + - - +
143B GLY 3.2 1.0 + - - -
304B THR* 3.9 21.7 - - - +
305B ILE* 5.5 0.2 - - - -
307B ALA 5.3 1.0 - - - +
308B GLY* 4.1 20.4 - - - -
309B ALA 5.1 1.3 - - - -
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Residues in contact with ARG 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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138B TYR* 3.1 40.2 + - + +
139B TRP* 3.0 44.7 + - + +
141B GLY* 1.3 75.0 - - - +
143B GLY* 1.3 60.9 + - - +
144B LEU* 3.5 17.3 + - + +
248B GLU* 3.9 18.8 + - - -
304B THR* 3.7 19.3 - - + -
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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