Contacts of the helix formed by residues 127 - 144 (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 ASP 127 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122O LYS* 3.0 9.8 + - + +
125O ILE* 3.9 7.6 - - + +
126O GLY* 1.3 74.5 - - - +
128O LEU* 1.3 62.8 + - - +
129O GLN* 3.3 19.0 + - - +
130O VAL* 3.0 31.8 + - + +
131O THR* 2.9 21.7 + - - -
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Residues in contact with LEU 128 (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* 3.8 28.9 - - + +
126O GLY* 3.2 22.9 + - - +
127O ASP* 1.3 74.4 + - - +
129O GLN* 1.3 68.5 + - - +
130O VAL 3.7 0.2 - - - -
131O THR* 4.4 4.0 - - - -
132O LYS* 2.9 30.2 + - - +
162O TYR* 3.6 19.3 + - + +
165O THR* 4.2 19.5 - - + -
166O ILE* 3.9 22.4 - - + -
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Residues in contact with GLN 129 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127O ASP* 3.3 10.6 + - - +
128O LEU* 1.3 83.5 - - - +
130O VAL* 1.3 67.1 + - - +
131O THR 3.1 0.7 - - - -
132O LYS* 3.2 35.7 + - - +
133O GLU* 3.0 27.6 + - - +
162O TYR* 5.5 1.2 + - - -
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Residues in contact with VAL 130 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122O LYS* 3.5 45.8 - - + +
127O ASP* 3.0 35.7 + - + +
129O GLN* 1.3 79.6 - - - +
131O THR* 1.3 60.3 + - - +
133O GLU* 3.4 6.3 + - - +
134O THR* 2.8 30.3 + - - +
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Residues in contact with THR 131 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119O GLY* 3.7 22.4 - - - +
122O LYS* 3.3 24.4 + - - +
123O LEU* 3.6 13.1 + - + -
127O ASP 2.9 20.1 + - - -
128O LEU* 3.8 7.1 + - - -
129O GLN 3.1 0.6 - - - -
130O VAL* 1.3 77.0 - - - +
132O LYS* 1.3 66.4 + - - +
134O THR* 3.0 9.7 + - - -
135O ILE* 2.9 37.8 + - + +
158O LEU* 4.7 4.5 - - + -
162O TYR* 4.3 8.7 - - + -
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Residues in contact with LYS 132 (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 2.9 17.7 + - - +
129O GLN* 3.2 37.8 + - - +
131O THR* 1.3 74.1 - - - +
133O GLU* 1.3 88.8 + - - +
135O ILE* 3.2 9.8 + - - +
136O GLU* 3.0 37.0 + - + +
162O TYR* 3.5 29.8 - - + +
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Residues in contact with GLU 133 (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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129O GLN 3.0 16.8 + - - +
130O VAL* 3.8 6.3 - - + +
132O LYS* 1.3 95.3 + - - +
134O THR* 1.3 66.8 + - - +
136O GLU* 3.0 32.1 + - - +
137O ASP* 3.0 24.4 + - - +
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Residues in contact with THR 134 (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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101O ARG* 6.1 1.3 - - - +
115O LYS* 3.0 39.7 - - + +
118O ILE* 5.2 3.8 - - + -
119O GLY* 4.1 12.3 - - - +
122O LYS* 3.9 17.4 + - - +
130O VAL* 2.8 21.9 + - - +
131O THR* 3.3 12.0 - - - -
133O GLU* 1.3 75.3 - - - +
135O ILE* 1.3 57.1 + - - +
137O ASP* 3.3 9.4 + - - +
138O VAL* 3.0 30.2 + - + +
158O LEU* 5.4 3.1 - - + -
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Residues in contact with ILE 135 (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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131O THR* 2.9 27.5 + - + +
132O LYS* 3.5 7.6 - - - +
134O THR* 1.3 73.5 - - - +
136O GLU* 1.3 68.4 + - - +
138O VAL* 4.6 0.7 - - - -
139O GLU* 2.9 28.8 + - + +
155O PHE* 3.8 13.5 - - + -
158O LEU* 4.2 27.1 - - + -
159O SER* 3.6 24.5 - - - +
162O TYR* 3.7 40.8 - - + -
163O TYR* 5.1 10.3 - - + +
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Residues in contact with GLU 136 (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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132O LYS* 3.0 26.1 + - - +
133O GLU* 3.0 30.0 + - - +
135O ILE* 1.3 83.5 - - - +
137O ASP* 1.3 68.3 + - - +
139O GLU* 2.9 19.5 + - - +
140O GLU* 3.0 18.6 + - + +
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Residues in contact with ASP 137 (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 20.1 + - + +
133O GLU* 3.0 21.4 + - - +
134O THR* 3.8 7.0 - - + +
136O GLU* 1.3 78.5 - - - +
138O VAL* 1.3 64.2 + - - +
140O GLU* 3.0 19.5 + - - +
141O MET* 3.0 17.5 + - - +
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Residues in contact with VAL 138 (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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112O ILE* 3.5 31.6 - - + -
115O LYS* 3.4 42.8 - - + -
116O THR* 4.5 4.9 - - + -
134O THR* 3.0 18.3 + - + +
135O ILE* 5.0 0.2 - - - -
137O ASP* 1.3 75.8 - - - +
139O GLU* 1.3 64.0 + - - +
141O MET* 3.2 6.9 + - - +
142O LEU* 2.9 23.0 + - - +
155O PHE* 3.5 36.3 - - + -
158O LEU* 6.0 0.7 - - + -
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Residues in contact with GLU 139 (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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135O ILE* 2.9 22.7 + - + +
136O GLU* 2.9 13.0 + - - +
138O VAL* 1.3 77.5 - - - +
140O GLU* 1.3 68.9 + - - +
142O LEU* 3.6 10.2 + - - +
143O ASN* 3.4 29.3 + - - +
155O PHE* 3.5 23.6 - - + -
156O TYR* 5.2 1.2 - - - -
175O ASP* 5.7 0.2 - - - +
178O ARG* 4.7 13.3 + - - -
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Residues in contact with GLU 140 (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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136O GLU* 3.0 14.5 + - + +
137O ASP* 3.0 9.9 + - - +
139O GLU* 1.3 88.0 - - - +
141O MET* 1.3 60.4 + - + +
142O LEU 2.9 10.1 + - - -
143O ASN* 3.4 10.8 + - - +
144O ASN* 2.9 24.2 - - - +
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Residues in contact with MET 141 (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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105O LYS* 4.8 10.5 - - + -
109O GLU 6.0 0.2 - - - +
110O ALA* 4.2 6.6 - - - +
111O VAL* 4.1 22.0 - - + -
112O ILE* 3.9 17.9 - - + +
115O LYS* 3.6 32.3 - - - +
137O ASP* 3.0 15.3 + - + +
138O VAL* 3.2 4.9 + - - +
140O GLU* 1.3 76.8 - - + +
142O LEU* 1.3 60.2 + - - +
144O ASN* 4.0 20.7 + - - +
145O LEU* 3.9 13.5 - - - +
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Residues in contact with LEU 142 (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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112O ILE* 3.6 21.1 - - + -
138O VAL 2.9 17.0 + - - +
139O GLU* 3.7 12.3 - - - +
140O GLU 2.9 0.8 + - - -
141O MET* 1.3 77.5 - - - +
143O ASN* 1.3 76.9 + - - +
144O ASN 3.3 0.6 + - - -
145O LEU* 3.5 18.6 + - + +
146O PRO 5.2 0.2 - - - +
151O VAL* 4.2 4.3 - - + -
152O HIS* 3.6 49.8 - - + +
155O PHE* 3.9 26.5 - - + -
156O TYR* 4.5 11.7 - - + +
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Residues in contact with ASN 143 (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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139O GLU* 3.4 29.4 + - - +
140O GLU* 3.4 7.8 + - - +
142O LEU* 1.3 84.4 - - - +
144O ASN* 1.3 62.1 + - - +
145O LEU 2.9 22.5 - - - +
142U GLU* 5.3 3.8 - - - +
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Residues in contact with ASN 144 (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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140O GLU* 2.9 22.9 + - - +
141O MET* 4.0 20.2 - - - +
142O LEU 3.3 1.0 - - - -
143O ASN* 1.3 79.0 - - - +
145O LEU* 1.3 62.5 + - + +
146O PRO* 4.8 0.5 - - - +
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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
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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