Contacts of the helix formed by residues 135 - 155 (chain B) in PDB entry 4PSI
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 135 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B ARG 3.3 16.4 - - - -
132B MSE 3.0 16.5 + - - +
133B GLN 3.3 2.2 + - - -
134B ASN* 1.3 81.9 - - - +
136B ASP* 1.3 65.8 + - - +
137B PHE* 3.8 6.4 + - - +
138B LEU* 3.3 24.7 + - - +
139B ARG* 3.0 13.8 + - - +
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Residues in contact with ASP 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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133B GLN 5.2 2.6 - - - +
134B ASN 5.2 0.9 - - - -
135B SER* 1.3 76.0 + - - +
137B PHE* 1.3 63.0 + - - +
139B ARG* 3.4 27.1 + - - +
140B GLU* 3.0 39.9 + - + +
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Residues in contact with PHE 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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135B SER* 3.3 5.8 - - - +
136B ASP* 1.3 79.0 - - - +
138B LEU* 1.3 61.0 + - - +
140B GLU* 4.3 6.1 - - + +
141B LEU* 3.2 33.0 + - + +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ILE* 5.7 2.7 - - + -
128B PHE* 3.9 36.3 - - + -
131B ARG* 3.7 33.0 - - + +
132B MSE 4.2 5.4 - - + +
135B SER* 3.3 21.0 + - - +
136B ASP 3.3 0.4 - - - -
137B PHE* 1.3 76.8 - - - +
139B ARG* 1.3 65.9 + - - +
141B LEU* 3.3 16.2 + - + +
142B VAL* 2.9 33.3 + - + +
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Residues in contact with ARG 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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54B PHE* 3.7 36.1 - - + -
132B MSE 3.3 36.2 + - + +
133B GLN* 4.8 9.8 + - - +
135B SER 3.0 12.0 + - - +
136B ASP* 3.4 32.0 + - - +
138B LEU* 1.3 75.1 - - - +
140B GLU* 1.3 73.7 + - - +
142B VAL* 2.9 5.7 + - - +
143B ILE* 2.9 33.1 + - - +
162B TRP* 5.0 4.4 - - - -
164B MSE 3.3 26.2 - - - +
166B LYS* 5.8 3.8 - - - +
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASP* 3.0 23.5 + - + +
137B PHE* 4.3 6.7 - - + +
139B ARG* 1.3 89.0 + - - +
141B LEU* 1.3 60.6 + - - +
143B ILE* 3.5 10.7 + - - +
144B THR* 3.2 26.7 + - - -
162B TRP* 4.1 26.2 + - + -
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Residues in contact with LEU 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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38B HIS* 5.5 6.7 - - + -
39B SER* 4.1 26.5 - - - +
97B PHE* 5.9 1.3 - - + -
99B ILE* 6.2 4.5 - - + -
137B PHE* 3.2 30.3 + - + +
138B LEU* 3.5 17.3 - - + +
139B ARG 3.1 0.4 - - - -
140B GLU* 1.3 78.1 - - - +
142B VAL* 1.3 59.0 + - + +
144B THR* 3.3 10.6 + - + -
145B ILE* 2.8 47.7 + - + +
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Residues in contact with VAL 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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69B ILE* 5.2 7.4 - - + -
99B ILE* 4.9 10.1 - - + -
101B MSE 4.1 18.2 - - + -
122B VAL* 6.4 0.4 - - + -
124B VAL* 4.7 7.0 - - + -
128B PHE* 3.9 27.8 - - + -
132B MSE 3.7 30.7 - - + -
138B LEU* 2.9 24.2 + - + +
139B ARG 2.9 5.4 + - - +
141B LEU* 1.3 74.2 - - + +
143B ILE* 1.3 56.9 + - - +
145B ILE* 3.6 7.1 - - - +
146B ALA* 2.7 35.8 + - + +
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Residues in contact with ILE 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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54B PHE* 3.3 39.0 - - + -
56B ILE* 3.9 23.3 - - + -
67B ILE* 4.9 6.1 - - + +
69B ILE* 4.0 10.3 - - + -
132B MSE 5.0 2.0 - - + -
139B ARG* 2.9 26.6 + - + +
140B GLU* 3.6 9.9 - - - +
142B VAL* 1.3 78.0 - - - +
144B THR* 1.3 57.5 + - - +
146B ALA* 3.7 4.0 - - - +
147B ARG* 2.9 32.3 + - + +
162B TRP* 3.5 44.2 - - + +
164B MSE 5.6 1.1 - - + -
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Residues in contact with THR 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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38B HIS* 3.9 20.4 - - + +
140B GLU 3.2 11.4 + - - -
141B LEU* 3.5 13.7 - - + +
143B ILE* 1.3 79.9 - - - +
145B ILE* 1.3 62.1 + - + +
147B ARG* 3.4 28.6 + - - +
148B GLU* 3.1 36.4 + - - +
162B TRP* 4.2 11.5 + - - +
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Residues in contact with ILE 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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38B HIS* 4.2 17.7 - - + -
39B SER* 3.6 41.3 - - - +
40B ALA* 3.7 4.9 - - - +
41B ALA* 3.3 35.6 + - + +
99B ILE* 4.8 8.3 - - + -
101B MSE 3.8 10.8 - - + -
141B LEU* 2.8 36.0 + - + +
142B VAL* 3.6 8.1 - - - +
143B ILE 3.2 0.2 - - - -
144B THR* 1.3 74.1 - - - +
146B ALA* 1.3 61.2 + - - +
148B GLU* 3.3 9.0 + - + +
149B GLY* 3.0 24.6 + - - -
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Residues in contact with ALA 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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67B ILE* 4.7 2.9 - - + -
69B ILE* 4.3 14.6 - - + -
101B MSE 3.6 26.7 - - + -
103B LEU* 4.4 1.7 - - - +
122B VAL* 3.8 21.1 - - + -
142B VAL* 2.7 20.8 + - + +
143B ILE 3.7 2.9 - - - +
145B ILE* 1.3 73.2 - - - +
147B ARG* 1.3 62.5 + - - +
149B GLY* 3.1 2.3 + - - -
150B LEU* 3.0 29.1 + - - +
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Residues in contact with ARG 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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38B HIS* 5.7 0.2 + - - -
58B THR* 5.1 3.4 - - - -
67B ILE* 3.9 19.7 - - + +
143B ILE* 2.9 17.4 + - + +
144B THR* 3.5 22.8 + - - +
145B ILE 3.3 0.2 - - - -
146B ALA* 1.3 78.1 - - - +
148B GLU* 1.3 79.8 + - - +
150B LEU* 3.2 6.8 + - - +
151B GLU* 3.0 55.6 + - - +
158B LEU* 3.6 30.6 + - + +
159B ASN 3.7 18.6 - - - -
160B PRO* 3.9 31.4 + - - +
162B TRP* 4.8 8.9 - - - -
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Residues in contact with GLU 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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38B HIS* 3.2 39.1 + - - +
39B SER 5.5 0.3 - - - +
144B THR* 3.1 18.2 + - - +
145B ILE* 3.9 8.6 - - - +
147B ARG* 1.3 94.3 + - - +
149B GLY* 1.3 60.8 + - - +
151B GLU* 3.7 19.6 - - - +
152B ASP* 2.9 40.3 + - - +
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Residues in contact with GLY 149 (chain B).
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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41B ALA* 4.3 12.8 - - - -
103B LEU* 3.5 20.7 - - - +
145B ILE 3.0 14.4 + - - -
146B ALA 3.1 5.5 + - - -
148B GLU* 1.3 78.9 - - - +
150B LEU* 1.3 55.0 + - - +
152B ASP* 3.6 6.4 + - - +
153B LYS* 3.1 28.9 + - - +
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Residues in contact with LEU 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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67B ILE* 3.9 31.6 - - + -
103B LEU* 4.0 21.3 - - + -
104B GLY 4.6 1.8 - - - +
120B TYR* 3.6 36.8 - - + -
122B VAL* 4.1 13.5 - - + -
146B ALA 3.0 14.8 + - - +
147B ARG 3.2 6.3 + - - +
149B GLY* 1.3 74.7 - - - +
151B GLU* 1.3 64.9 + - - +
153B LYS* 4.7 0.2 - - - -
154B TYR* 3.0 53.3 + - + +
156B LEU* 3.7 14.1 - - + +
158B LEU* 4.4 4.5 - - + -
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Residues in contact with GLU 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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147B ARG* 3.0 46.7 + - - +
148B GLU* 3.7 18.3 - - - +
149B GLY 3.4 0.2 - - - -
150B LEU* 1.3 78.1 - - - +
152B ASP* 1.3 59.8 + - - +
155B ASN* 2.9 25.3 + - - -
156B LEU* 3.1 34.3 + - - +
157B GLN* 3.9 6.6 - - - +
158B LEU* 2.9 35.6 + - + +
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Residues in contact with ASP 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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148B GLU* 2.9 24.1 + - - +
149B GLY* 3.9 6.4 - - - +
151B GLU* 1.3 83.0 - - - +
153B LYS* 1.3 62.8 + - - +
155B ASN* 3.9 10.7 + - - +
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Residues in contact with LYS 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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43B GLU* 2.7 38.1 + - - +
103B LEU* 2.8 33.1 + - + -
105B GLU* 4.7 8.3 + - - +
149B GLY 3.1 19.3 + - - +
150B LEU 3.4 0.2 + - - -
152B ASP* 1.3 79.2 - - - +
154B TYR* 1.3 96.7 + - + +
155B ASN* 3.9 6.2 + - - -
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Residues in contact with TYR 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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103B LEU 3.0 12.5 + - - -
104B GLY 2.7 32.3 + - - -
105B GLU* 3.3 16.5 - - - -
106B PRO* 3.9 19.7 - - + -
120B TYR* 3.8 21.5 - + - +
150B LEU* 3.0 30.6 + - + +
153B LYS* 1.3 110.3 + - + +
155B ASN* 1.3 79.2 + - - +
156B LEU* 3.3 20.9 - - + +
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Residues in contact with ASN 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 GLU 2.9 14.1 + - - -
152B ASP 3.9 8.6 + - - +
153B LYS 3.6 6.1 + - - -
154B TYR* 1.3 87.3 + - - +
156B LEU* 1.3 59.8 + - - +
157B GLN* 4.7 8.0 + - - +
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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