Contacts of the helix formed by residues 151 - 167 (chain O) in PDB entry 5L4K
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 VAL 151 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74O LEU* 5.7 5.4 - - + -
110O ALA* 4.8 9.9 - - + -
112O ILE* 4.0 38.9 - - + +
113O LEU* 3.7 31.2 - - + -
142O LEU* 4.2 1.8 - - + -
145O LEU* 4.2 13.5 - - + -
148O VAL* 4.7 1.6 - - + -
149O THR 2.6 10.0 + - - +
150O SER* 1.3 81.4 - - - +
152O HIS* 1.3 83.2 + - + +
153O SER 3.2 2.0 - - - -
154O ARG* 3.2 8.8 + - - +
155O PHE* 3.0 23.9 + - - +
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Residues in contact with HIS 152 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142O LEU* 3.6 40.6 - - + +
145O LEU* 4.5 3.8 - - - +
146O PRO 4.1 4.3 + - - -
147O GLY* 4.4 9.2 - - - -
148O VAL* 3.5 40.1 + - + +
149O THR 3.2 19.0 + - - +
151O VAL* 1.3 85.2 - - + +
153O SER* 1.3 64.1 + - - +
155O PHE* 4.7 4.3 - - - -
156O TYR* 2.9 54.3 + - + +
182O CYS* 4.7 9.6 - - + -
150U PRO* 6.3 1.3 - - + +
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Residues in contact with SER 153 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149O THR* 4.1 14.4 - - - +
150O SER 4.9 4.6 + - - -
151O VAL 3.2 1.0 - - - +
152O HIS* 1.3 77.7 - - - +
154O ARG* 1.3 70.6 + - - +
156O TYR* 4.7 0.2 - - - -
157O ASP* 2.9 19.6 + - - +
179O PHE* 3.2 35.7 - - - -
182O CYS* 3.5 20.0 - - - -
183O VAL* 4.5 9.7 - - - +
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Residues in contact with ARG 154 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78O GLU* 3.8 24.5 + - - +
81O LEU* 3.9 25.8 - - - +
112O ILE* 6.3 0.7 - - + -
113O LEU* 3.9 21.3 - - + +
116O THR* 4.7 15.0 - - - +
150O SER 3.9 20.0 + - - +
151O VAL* 3.2 10.5 + - - +
153O SER* 1.3 80.4 - - - +
155O PHE* 1.3 66.0 + - - +
157O ASP* 2.9 9.6 + - - +
158O LEU* 2.9 21.6 + - - +
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Residues in contact with PHE 155 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112O ILE* 4.1 8.1 - - + -
116O THR* 3.7 23.7 - - + +
135O ILE* 3.8 21.8 - - + -
138O VAL* 3.5 27.6 - - + -
139O GLU* 3.5 40.4 - - - -
142O LEU* 3.9 25.6 - - + -
151O VAL 3.0 17.0 + - - +
152O HIS* 4.1 1.3 - - - +
154O ARG* 1.3 75.2 - - - +
156O TYR* 1.3 81.6 + + - +
158O LEU* 3.1 7.4 + - + +
159O SER* 3.0 38.3 + - - -
175O ASP* 5.6 0.4 - - - -
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Residues in contact with TYR 156 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139O GLU* 5.2 0.9 - - - -
142O LEU* 4.5 11.2 - - + +
152O HIS* 2.9 49.9 + - + +
153O SER 3.8 2.7 - - - +
155O PHE* 1.3 95.0 - + - +
157O ASP* 1.3 58.7 + - - +
159O SER* 3.2 1.9 + - - -
160O SER* 2.9 19.3 + - - -
175O ASP* 2.6 42.7 - - - +
178O ARG* 3.4 51.3 + - + -
179O PHE* 3.7 32.0 - - + +
182O CYS* 5.2 3.4 - - + -
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Residues in contact with ASP 157 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153O SER 2.9 14.3 + - - +
154O ARG* 2.9 11.2 + - - +
156O TYR* 1.3 73.5 - - - +
158O LEU* 1.3 68.4 + - - +
160O SER* 2.6 22.9 + - - -
161O LYS* 3.0 37.4 + - - +
179O PHE* 4.0 18.0 - - + -
196O ARG* 3.1 30.2 + - - -
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Residues in contact with LEU 158 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115O LYS 4.7 1.1 - - - +
116O THR* 3.8 40.2 - - + +
119O GLY* 4.2 26.2 - - - +
120O ALA* 4.3 8.5 - - + +
123O LEU* 4.3 17.7 - - + -
131O THR* 4.7 8.1 - - + -
134O THR* 5.4 2.5 - - + -
135O ILE* 4.2 22.9 - - + -
138O VAL* 6.0 1.1 - - + -
154O ARG 2.9 11.3 + - - +
155O PHE* 3.3 13.0 - - + +
157O ASP* 1.3 79.0 + - - +
159O SER* 1.3 63.5 + - - +
161O LYS* 3.1 5.8 + - - +
162O TYR* 2.9 18.9 + - - +
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Residues in contact with SER 159 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135O ILE* 3.6 15.5 - - - +
155O PHE* 3.0 36.4 + - - -
156O TYR* 3.2 1.9 + - - -
158O LEU* 1.3 76.3 - - - +
160O SER* 1.3 58.2 + - - +
162O TYR* 3.0 8.0 + - - +
163O TYR* 2.9 45.7 + - - -
175O ASP* 3.3 25.2 + - - -
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Residues in contact with SER 160 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156O TYR 2.9 12.4 + - - -
157O ASP* 2.6 28.8 + - - -
159O SER* 1.3 75.3 - - - +
161O LYS* 1.3 56.5 + - - +
163O TYR* 3.6 5.6 + - - -
164O GLN* 2.9 23.6 + - - +
172O TYR* 3.2 35.3 - - - -
175O ASP* 3.7 2.6 + - - -
176O ALA* 4.0 21.5 - - - +
196O ARG* 3.8 14.1 + - - -
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Residues in contact with LYS 161 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123O LEU* 4.1 15.9 - - + -
157O ASP* 3.0 40.4 + - - +
158O LEU* 3.6 9.9 - - + +
160O SER* 1.3 77.5 + - - +
162O TYR* 1.3 64.5 + - - +
164O GLN* 3.0 9.5 + - + +
165O THR* 2.9 25.3 + - - -
196O ARG* 4.9 7.6 - - - +
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Residues in contact with TYR 162 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123O LEU* 4.1 18.1 - - + +
128O LEU* 3.6 33.9 + - + +
129O GLN* 5.5 1.0 + - - -
131O THR* 4.3 11.4 - - + -
132O LYS* 3.5 36.8 - - + +
135O ILE* 3.7 28.0 - - + -
158O LEU* 2.9 10.8 + - + +
159O SER 3.0 6.3 + - - +
161O LYS* 1.3 76.3 - - - +
163O TYR* 1.3 88.1 + + - +
165O THR* 3.2 16.2 + - - -
166O ILE* 3.3 39.6 + - + +
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Residues in contact with TYR 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135O ILE* 5.1 9.0 - - + +
159O SER* 2.9 33.0 + - - +
160O SER* 3.9 4.0 - - - +
162O TYR* 1.3 98.7 - + - +
164O GLN* 1.3 61.3 + - - +
166O ILE* 3.4 4.4 + - - +
167O GLY 3.3 3.6 + - - -
168O ASN* 3.3 47.9 + - + +
169O HIS* 5.4 0.5 + - - -
171O SER* 3.5 45.3 - - - -
172O TYR* 3.8 12.3 - - + +
175O ASP* 4.0 17.7 - - + -
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Residues in contact with GLN 164 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160O SER 2.9 18.5 + - - +
161O LYS* 3.0 10.9 + - + +
163O TYR* 1.3 74.8 - - - +
165O THR* 1.3 65.3 + - - +
167O GLY* 3.5 8.4 + - - -
169O HIS* 4.2 21.8 + - - -
172O TYR* 3.4 35.9 + - + -
199O THR* 4.9 9.3 - - - +
203O ALA* 5.3 4.1 - - - +
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Residues in contact with THR 165 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123O LEU* 4.0 16.3 - - + +
128O LEU* 4.2 32.3 - - + -
161O LYS 2.9 14.0 + - - -
162O TYR* 3.2 9.6 + - - -
164O GLN* 1.3 79.5 - - - +
166O ILE* 1.3 63.4 + - - +
167O GLY 3.1 1.0 + - - -
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Residues in contact with ILE 166 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128O LEU* 3.9 27.8 - - + -
162O TYR* 3.3 45.7 + - + +
163O TYR* 3.4 3.8 + - - +
165O THR* 1.3 76.5 - - + +
167O GLY* 1.3 57.6 + - - +
168O ASN* 3.8 26.2 - - + +
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Residues in contact with GLY 167 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163O TYR 3.3 5.4 + - - -
164O GLN* 3.5 6.7 + - - -
165O THR 3.1 6.9 + - - -
166O ILE* 1.3 76.8 - - - +
168O ASN* 1.3 58.5 + - - +
169O HIS* 2.8 40.0 + - - -
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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