Contacts of the helix formed by residues 137 - 154 (chain B) in PDB entry 4AD7
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 ASN 137 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU 2.3 29.9 + - - +
134B TYR 3.1 3.5 + - - -
136B GLN* 1.3 81.9 - - - +
138B ALA* 1.3 63.2 + - - +
139B ARG* 3.3 2.9 - - - -
140B ALA* 3.0 18.0 + - + +
141B PHE* 3.2 21.3 - - + -
170B LEU* 4.3 8.1 - - + -
173B ARG* 3.8 26.4 - - - +
174B LEU* 3.2 26.3 - - - +
177B GLN* 2.8 30.9 + - - +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B TYR* 3.0 33.9 + - + +
135B THR* 4.1 11.0 - - - +
136B GLN 3.4 2.6 - - - -
137B ASN* 1.3 76.5 - - - +
139B ARG* 1.3 58.6 + - - +
141B PHE* 3.0 14.5 + - - +
142B ARG* 2.9 26.7 + - - +
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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
----------------------------------------------------------
136B GLN 5.1 1.5 + - - +
137B ASN 3.2 1.0 + - - -
138B ALA* 1.3 78.4 - - - +
140B ALA* 1.3 57.1 + - - +
142B ARG* 3.3 41.0 - - - +
143B ASP* 2.9 53.6 + - - +
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Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ASN 3.0 13.4 + - - +
139B ARG* 1.3 76.7 - - - +
141B PHE* 1.3 60.8 + - + +
143B ASP* 3.5 6.5 + - - +
144B LEU* 2.9 27.4 + - - +
166B PHE* 3.7 18.9 - - + -
170B LEU* 4.9 3.8 - - + -
173B ARG* 3.5 30.3 - - - +
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Residues in contact with PHE 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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122B LEU* 4.3 23.6 - - + -
126B PHE* 4.3 6.3 - + - -
133B LEU 4.8 1.1 - - - -
134B TYR* 4.0 22.0 - + - -
137B ASN* 3.2 43.1 - - + -
138B ALA* 3.0 11.1 + - - +
140B ALA* 1.3 75.5 - - + +
142B ARG* 1.3 64.7 + - - +
144B LEU* 3.1 8.0 + - - +
145B TYR* 2.9 31.0 + - + -
166B PHE* 4.1 16.2 - + - -
170B LEU* 4.0 19.7 - - + -
174B LEU* 5.7 0.4 - - + -
321B LEU* 3.7 29.2 - - + -
325B ILE* 3.6 31.0 - - + -
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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
----------------------------------------------------------
119B GLU* 3.9 19.7 - - - +
123B GLN* 6.2 2.2 - - - +
138B ALA 2.9 12.5 + - - +
139B ARG* 3.3 56.5 - - - +
141B PHE* 1.3 76.1 - - - +
143B ASP* 1.3 61.5 + - - +
145B TYR* 3.2 6.1 + - - +
146B SER* 2.9 31.1 + - - +
149B ARG* 5.6 1.1 - - - +
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Residues in contact with ASP 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ARG* 2.9 51.4 + - - +
140B ALA* 3.9 6.1 - - - +
142B ARG* 1.3 79.6 + - - +
144B LEU* 1.3 60.9 + - - +
146B SER* 3.4 12.0 + - - -
147B GLU* 2.9 36.5 + - + +
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ALA 2.9 15.4 + - - +
141B PHE* 3.3 9.2 - - - +
143B ASP* 1.3 77.8 - - - +
145B TYR* 1.3 58.5 + - + +
147B GLU* 3.2 6.2 + - - +
148B LEU* 2.9 40.9 + - + +
162B THR* 4.6 9.6 - - + -
163B LEU* 3.7 29.8 - - + -
166B PHE* 3.6 48.7 - - + -
209B LEU* 5.4 2.0 - - + -
317B VAL* 5.3 2.2 - - + -
321B LEU* 3.8 27.8 - - + -
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Residues in contact with TYR 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 3.6 37.2 - - + +
118B SER* 2.7 25.1 + - - -
119B GLU* 3.4 59.7 - - + +
122B LEU* 4.0 21.3 - - + -
141B PHE* 2.9 25.7 + - + -
142B ARG 3.5 2.2 - - - +
144B LEU* 1.3 78.7 - - + +
146B SER* 1.3 57.4 + - - +
148B LEU* 3.2 10.4 + - + +
149B ARG* 2.9 36.0 + - - +
317B VAL* 3.8 11.6 - - + +
318B HIS* 3.5 22.3 + - - +
321B LEU* 4.3 10.3 - - + -
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Residues in contact with SER 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ARG* 2.9 17.9 + - - +
143B ASP* 3.4 18.5 + - - -
144B LEU 3.2 0.2 - - - -
145B TYR* 1.3 77.1 - - - +
147B GLU* 1.3 57.5 + - - +
149B ARG* 3.1 22.3 + - - +
150B LEU* 2.9 35.6 + - - +
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Residues in contact with GLU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASP* 2.9 22.3 + - + +
144B LEU* 3.5 9.0 - - + +
146B SER* 1.3 76.4 - - - +
148B LEU* 1.3 59.1 + - + +
150B LEU* 3.4 15.1 + - - +
151B TYR* 2.9 29.9 + - - +
156B ASN* 3.7 27.1 + - - +
158B HIS* 5.5 1.7 - - - -
159B LEU* 5.5 1.3 - - + +
162B THR* 3.6 33.9 + - + -
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 4.2 15.3 - - + -
144B LEU* 2.9 27.3 + - + +
145B TYR* 3.2 15.2 + - + +
147B GLU* 1.3 78.7 - - + +
149B ARG* 1.3 57.6 + - - +
151B TYR* 3.4 4.3 + - + +
152B TYR* 2.9 28.2 + - - +
159B LEU* 3.8 28.3 - - + -
162B THR* 6.3 0.4 - - + -
163B LEU* 4.7 11.2 - - + -
209B LEU* 6.2 1.6 - - + -
213B ALA* 5.2 4.9 - - + -
217B PHE* 3.8 28.6 - - + -
317B VAL* 4.0 35.2 - - + -
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Residues in contact with ARG 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLN* 5.8 11.0 - - + +
115B LEU* 3.6 25.6 - - + +
116B ASN* 3.2 28.4 + - - +
119B GLU* 3.3 34.2 + - - -
142B ARG* 4.4 1.6 + - - +
145B TYR* 2.9 13.8 + - - +
146B SER* 3.1 35.4 + - - +
148B LEU* 1.3 73.8 - - - +
150B LEU* 1.3 60.3 + - + +
152B TYR* 3.2 10.2 + - + +
153B ARG* 2.9 38.2 + - - +
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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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146B SER* 2.9 19.4 + - - +
147B GLU* 3.7 17.7 - - - +
149B ARG* 1.3 76.3 - - + +
151B TYR* 1.3 59.0 + - - +
153B ARG* 3.1 24.0 + - - +
154B GLY 2.9 9.0 + - - -
155B ALA* 2.9 44.7 + - + -
156B ASN* 3.2 24.7 - - - +
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Residues in contact with TYR 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 GLU 2.9 18.7 + - - +
148B LEU* 3.6 6.3 - - + +
150B LEU* 1.3 76.6 - - - +
152B TYR* 1.3 61.8 + - - +
154B GLY* 3.1 9.0 + - - -
156B ASN* 3.3 27.5 - - - +
157B LEU* 3.9 21.8 - - + -
158B HIS 5.0 0.4 - - - -
159B LEU* 3.7 44.0 - - + +
214B THR* 3.8 15.0 - - - +
217B PHE* 3.6 35.4 - + + -
218B VAL* 3.2 23.9 - - + +
221B ARG* 3.3 36.4 + - - -
475B ASP 4.5 3.0 + - - -
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Residues in contact with TYR 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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108B ASP* 2.9 29.6 + - - -
111B PHE* 3.3 45.6 - + + +
112B GLN* 4.1 19.7 - - + -
115B LEU* 5.6 2.0 - - + -
148B LEU 2.9 18.3 + - - +
149B ARG* 3.4 11.7 - - + +
151B TYR* 1.3 76.9 - - - +
153B ARG* 1.3 66.9 + - + +
154B GLY 3.1 0.2 - - - -
217B PHE* 3.6 32.5 - + + -
220B ALA* 4.0 11.4 - - + -
221B ARG* 3.2 41.7 - - + +
224B VAL* 3.6 10.9 - - + +
314B ILE* 5.5 0.9 - - + -
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Residues in contact with ARG 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLN* 6.1 4.5 - - - +
149B ARG* 2.9 24.2 + - + +
150B LEU* 3.1 26.4 + - - +
152B TYR* 1.3 86.7 - - + +
154B GLY* 1.3 61.9 + - - +
155B ALA* 3.6 6.2 + - + +
221B ARG* 4.8 2.0 - - - -
225B GLN* 4.9 7.3 + - - -
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Residues in contact with GLY 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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150B LEU 2.9 3.0 + - - -
151B TYR 3.1 14.9 + - - -
152B TYR 3.1 0.6 - - - -
153B ARG* 1.3 79.8 - - - +
155B ALA* 1.3 65.2 + - - +
156B ASN 3.6 1.6 - - - -
157B LEU* 3.4 20.1 - - - +
221B ARG* 3.8 15.7 - - - -
225B GLN* 5.4 2.5 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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