Contacts of the helix formed by residues 154 - 167 (chain B) in PDB entry 3L73
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 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B VAL 4.6 0.9 + - - -
151B ALA 3.2 11.5 + - - -
152B PHE 3.1 2.9 - - - -
153B GLN* 1.3 80.5 - - - +
155B PRO* 1.3 67.1 - - - +
156B GLN* 4.3 19.1 - - - -
157B VAL* 2.7 34.6 + - - +
58I ARG* 5.9 5.4 - - - -
76I VAL* 4.7 11.9 - - - +
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Residues in contact with PRO 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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152B PHE 5.1 2.2 - - - +
153B GLN 3.8 7.6 - - - +
154B SER* 1.3 82.7 - - - +
156B GLN* 1.3 57.2 + - + +
158B GLY* 2.6 26.5 + - - +
159B VAL* 3.3 13.2 + - - +
250B HIS* 4.0 29.8 - - + +
252B LEU 6.1 0.2 - - - +
254B HIS* 3.9 31.2 - - + +
427B SER* 5.0 9.3 + - - +
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Residues in contact with GLN 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER* 4.3 15.1 - - - -
155B PRO* 1.3 79.9 - - + +
157B VAL* 1.3 60.8 + - - +
158B GLY 3.5 0.2 + - - -
159B VAL* 3.5 8.5 - - - +
160B LEU* 3.3 24.3 - - + +
254B HIS* 4.0 4.6 + - + -
325B TYR* 3.5 15.2 - - - +
58I ARG* 4.2 34.9 + - - +
59I SER 6.0 0.2 - - - -
60I ALA* 4.9 16.3 - - + +
64I LEU* 3.8 11.5 - - - +
76I VAL* 5.1 3.9 + - - +
77I ARG 2.8 39.6 + - - -
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ALA* 3.1 23.1 - - + +
152B PHE* 3.5 20.2 - - + -
154B SER* 2.7 29.4 + - - +
156B GLN* 1.3 79.6 - - - +
158B GLY* 1.3 64.0 + - - +
160B LEU 3.8 0.8 + - - -
161B GLU* 3.3 21.7 + - + +
177B TYR* 3.8 25.1 - - + -
64I LEU* 3.5 34.9 - - + +
76I VAL* 4.4 11.0 - - + -
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Residues in contact with GLY 158 (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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152B PHE* 4.4 19.5 - - - -
154B SER 3.8 0.2 + - - -
155B PRO* 2.6 18.4 + - - -
157B VAL* 1.3 76.9 - - - +
159B VAL* 1.3 62.9 + - - -
161B GLU* 3.3 4.5 + - - +
162B ASN* 2.9 31.8 + - - -
427B SER* 5.3 1.3 - - - -
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Residues in contact with VAL 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B PRO 3.3 3.9 + - - +
156B GLN 3.5 5.4 - - - +
158B GLY* 1.3 75.1 - - - +
160B LEU* 1.3 63.5 + - + +
162B ASN* 3.3 7.9 + - - +
163B LEU* 2.8 30.9 + - - +
254B HIS* 3.9 18.6 - - + +
256B ALA* 5.1 3.6 - - + -
325B TYR* 3.2 40.6 - - + +
425B ALA* 3.6 14.5 - - + +
426B ALA* 4.4 5.2 - - - +
427B SER* 3.0 38.8 - - - +
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Residues in contact with LEU 160 (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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102B ARG* 3.4 2.9 + - - +
156B GLN* 3.3 18.5 + - - +
157B VAL 4.1 0.7 - - - +
158B GLY 3.2 1.0 - - - -
159B VAL* 1.3 85.2 - - + +
161B GLU* 1.3 61.5 + - - +
163B LEU* 3.3 11.5 + - + +
164B HIS* 3.0 33.9 + - + +
256B ALA* 5.3 1.1 - - + -
312B PHE* 4.3 16.8 - - + -
325B TYR* 4.1 11.4 - - + -
60I ALA* 3.8 26.5 - - + -
62I ARG 4.1 16.8 - - - +
63I ASP 4.6 0.4 - - - +
64I LEU* 3.5 51.4 - - + +
77I ARG 5.1 0.4 - - - +
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Residues in contact with GLU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ARG* 2.9 30.4 + - - +
152B PHE* 4.1 21.3 - - + -
157B VAL* 3.3 16.8 + - + +
158B GLY* 3.3 8.4 + - - +
160B LEU* 1.3 79.7 - - - +
162B ASN* 1.3 65.4 + - - +
163B LEU 3.2 1.2 + - - -
164B HIS* 3.5 4.9 + - - +
165B ALA* 3.4 17.5 + - - +
173B ALA 5.2 0.7 - - - +
175B PRO* 3.6 16.3 - - + +
176B LEU* 3.0 33.5 + - - +
177B TYR* 3.3 22.1 + - - +
64I LEU* 4.5 5.7 - - + +
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Residues in contact with ASN 162 (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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152B PHE* 6.1 1.6 - - - -
158B GLY* 2.9 28.3 + - - +
159B VAL* 3.6 6.1 - - - +
161B GLU* 1.3 79.9 - - - +
163B LEU* 1.3 65.6 + - - +
165B ALA* 3.4 8.1 + - - +
166B ALA* 3.2 4.3 + - - +
244B ILE* 3.1 50.6 - - + +
246B GLU* 3.8 22.9 + - - +
425B ALA* 4.2 7.1 - - + +
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Residues in contact with LEU 163 (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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159B VAL 2.8 16.6 + - - +
160B LEU* 3.5 12.8 - - + +
161B GLU 3.1 0.2 - - - -
162B ASN* 1.3 73.3 - - - +
164B HIS* 1.3 53.6 + - - +
165B ALA 2.6 4.0 + - - -
166B ALA* 2.5 28.2 + - + +
167B ALA* 2.7 17.0 + - + +
256B ALA* 3.5 33.0 - - + +
258B VAL* 4.2 17.0 - - + -
312B PHE* 3.7 32.5 - - + -
321B LEU* 4.3 8.3 - - + -
423B SER* 4.0 14.8 - - - +
424B MET 4.3 1.3 - - - -
425B ALA* 3.4 24.2 - - + +
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Residues in contact with HIS 164 (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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102B ARG* 3.1 51.0 + - - +
160B LEU* 3.0 25.6 + - + -
161B GLU 3.9 2.0 - - - +
163B LEU* 1.3 81.2 - - + +
165B ALA* 1.3 57.3 + - - +
167B ALA* 4.0 3.1 - - - -
168B TYR* 3.5 18.9 + + - +
172B LEU* 3.3 13.2 - - + +
173B ALA* 2.9 25.7 - - - +
312B PHE* 5.0 13.0 - + - -
314B VAL* 5.2 2.0 - - + -
316B TYR* 2.6 42.2 + + - -
321B LEU* 4.3 16.9 - - + +
63I ASP* 5.7 0.2 - - - -
64I LEU* 5.4 7.6 - - + -
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Residues in contact with ALA 165 (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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161B GLU 3.4 12.5 + - - +
162B ASN* 3.4 14.4 - - - +
163B LEU 2.6 5.7 + - - -
164B HIS* 1.3 77.2 - - - +
166B ALA* 1.3 56.7 + - - +
168B TYR 3.2 16.1 - - - +
173B ALA* 4.0 16.3 - - - +
240B TRP* 3.3 13.2 - - - -
244B ILE* 3.7 12.1 - - + -
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Residues in contact with ALA 166 (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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162B ASN 3.2 4.9 + - - +
163B LEU* 2.5 15.5 + - + +
165B ALA* 1.3 71.3 - - - +
167B ALA* 1.3 58.5 + - - +
168B TYR 3.2 2.2 + - - -
240B TRP* 3.6 11.7 - - - -
241B GLY 3.0 7.1 + - - -
242B GLY 2.6 54.3 + - - +
244B ILE* 3.7 23.3 - - + +
423B SER* 3.9 4.0 - - - -
424B MET 4.4 5.2 - - - +
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Residues in contact with ALA 167 (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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163B LEU 2.7 13.9 + - - +
166B ALA* 1.3 79.5 - - - +
168B TYR* 1.3 85.3 + - + +
239B TYR* 3.7 14.6 - - + -
240B TRP 3.3 14.4 + - - -
241B GLY 4.3 0.9 - - - +
258B VAL* 4.9 1.3 - - + -
321B LEU* 3.8 22.0 - - + -
423B SER* 3.5 21.7 + - - +
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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