Contacts of the helix formed by residues 133 - 149 (chain D) in PDB entry 5CLQ
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 THR 133 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ARG* 4.2 4.0 - - - -
131D PHE* 3.8 4.3 - - - +
132D LYS* 1.3 90.6 - - + +
134D PRO* 1.3 72.3 - - + +
135D GLU* 3.7 13.4 + - - +
136D GLU* 2.3 51.4 + - - +
137D ALA* 3.2 8.5 + - - +
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Residues in contact with PRO 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ASP* 3.6 46.5 - - + +
108D ARG* 4.1 11.6 - - + -
132D LYS 4.5 1.1 - - - +
133D THR* 1.3 85.0 - - + +
135D GLU* 1.3 65.6 + - - +
136D GLU 3.3 0.2 - - - -
137D ALA* 3.7 2.3 - - + +
138D ALA* 2.9 30.3 + - - +
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Residues in contact with GLU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D THR* 3.2 19.0 - - - +
134D PRO* 1.3 81.2 - - - +
136D GLU* 1.3 59.2 + - + +
138D ALA* 3.4 5.6 + - - +
139D LEU* 2.9 29.6 + - - +
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Residues in contact with GLU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D PHE* 4.0 5.6 - - - -
43D ASN* 2.3 44.9 + - - +
44D ARG* 4.2 3.8 - - - +
131D PHE* 4.0 10.8 - - + -
132D LYS* 4.5 8.8 + - - +
133D THR* 2.3 42.6 + - - +
135D GLU* 1.3 75.5 - - + +
137D ALA* 1.3 60.4 + - - +
139D LEU* 3.5 9.6 + - + +
140D PHE* 2.9 28.2 + - - +
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Residues in contact with ALA 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ASP 3.6 23.6 - - - +
108D ARG* 4.0 10.1 - - - +
110D PHE* 3.3 27.2 - - + -
131D PHE* 3.7 19.9 - - + +
133D THR 3.2 8.2 + - - +
134D PRO 3.7 3.1 - - - +
135D GLU 3.3 0.2 - - - -
136D GLU* 1.3 77.9 - - - +
138D ALA* 1.3 67.4 + - - +
140D PHE* 3.0 2.1 + - - +
141D LYS 2.9 20.4 + - - -
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D PHE* 4.5 2.4 - - - -
134D PRO 2.9 17.5 + - - +
135D GLU* 3.8 6.1 - - - +
137D ALA* 1.3 75.7 - - - +
139D LEU* 1.3 58.2 + - - +
141D LYS* 3.9 5.5 - - - +
142D CYS* 2.9 31.2 + - - +
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Residues in contact with LEU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D PHE* 3.5 24.9 - - + -
43D ASN* 5.9 2.0 - - - +
135D GLU 2.9 18.5 + - - +
136D GLU* 3.7 8.1 - - + +
138D ALA* 1.3 73.4 - - - +
140D PHE* 1.3 61.3 + - - +
142D CYS* 3.8 7.4 - - + +
143D LYS* 2.9 47.5 + - + +
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Residues in contact with PHE 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D PHE* 3.7 29.3 - + + -
65D VAL* 4.2 11.4 - - + -
67D ILE* 4.1 14.4 - - + -
78D LEU* 3.5 33.2 - - + -
100D LEU* 3.4 26.5 - - + -
110D PHE* 4.1 7.2 - + - -
112D TRP* 5.1 2.9 - + - -
129D ILE* 3.7 24.9 - - + -
131D PHE* 3.4 35.4 - + + -
136D GLU 2.9 8.9 + - - +
137D ALA 3.0 4.7 + - - +
139D LEU* 1.3 74.5 - - - +
141D LYS* 1.3 69.0 + - - +
143D LYS* 3.3 1.6 + - - +
144D PHE* 2.8 34.3 + + - +
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Residues in contact with LYS 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LYS* 5.3 5.9 - - - +
100D LEU* 3.9 33.1 + - + +
102D PRO* 4.7 11.1 - - - +
110D PHE* 3.7 35.2 - - + -
137D ALA 2.9 7.8 + - - +
138D ALA* 3.9 4.3 - - - +
140D PHE* 1.3 79.1 - - - +
142D CYS* 1.3 65.8 + - - +
144D PHE* 3.1 0.5 + - - +
145D GLU* 2.9 63.2 + - + +
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Residues in contact with CYS 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D ALA 2.9 20.5 + - - +
139D LEU* 3.8 10.5 - - + +
141D LYS* 1.3 76.8 - - - +
143D LYS* 1.3 63.1 + - + +
145D GLU* 3.5 5.9 + - - +
146D GLU* 2.8 35.9 + - - +
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Residues in contact with LYS 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D PHE* 4.2 24.3 + - + +
41D PHE* 4.0 20.0 - - + -
67D ILE* 3.9 18.9 - - + +
139D LEU* 2.9 39.7 + - + +
140D PHE 3.9 0.2 - - - +
142D CYS* 1.3 76.6 - - - +
144D PHE* 1.3 56.1 + - - +
146D GLU* 3.1 29.1 + - - +
147D ALA* 2.6 35.5 + - - +
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Residues in contact with PHE 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D ILE* 3.7 9.9 - - + +
78D LEU* 4.1 14.6 - - + -
92D HIS* 5.5 0.4 - - - -
94D ILE* 3.9 35.0 - - + +
98D MET* 4.1 24.9 - - + -
99D LYS 5.4 0.2 - - - -
100D LEU* 3.9 30.5 - - + -
112D TRP* 4.4 17.3 - + - -
140D PHE* 2.8 41.3 + + + +
141D LYS 3.3 4.0 - - - +
143D LYS* 1.3 71.7 - - - +
145D GLU* 1.3 67.5 + - + +
147D ALA* 3.1 20.8 + - - +
148D GLN* 3.2 34.6 + - - +
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Residues in contact with GLU 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LYS* 5.1 6.6 - - - +
100D LEU* 4.6 13.0 + - + +
141D LYS* 2.9 60.2 + - + +
142D CYS* 4.0 5.0 - - - +
144D PHE* 1.3 75.5 - - + +
146D GLU* 1.3 64.3 + - - +
148D GLN* 3.0 29.4 + - - +
149D SER* 3.0 14.4 + - - -
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Residues in contact with GLU 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D PHE* 5.2 11.1 - - - -
142D CYS* 2.8 25.9 + - - +
143D LYS* 3.1 41.0 + - - +
145D GLU* 1.3 75.3 - - - +
147D ALA* 1.3 58.4 - - - +
149D SER* 2.9 31.6 - - - +
150D ILE* 3.2 15.0 - - + +
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Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D PHE* 5.4 6.3 - - + -
67D ILE* 4.3 6.1 - - + -
76D ILE* 3.4 30.2 - - + +
94D ILE* 4.1 13.5 - - + -
143D LYS 2.6 16.9 + - - +
144D PHE 3.1 13.5 - - - +
146D GLU* 1.3 74.2 - - - +
148D GLN* 1.3 58.8 + - - +
149D SER 3.3 0.3 + - - -
150D ILE* 3.3 16.5 - - - +
151D LEU* 3.3 22.3 - - - +
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Residues in contact with GLN 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ILE* 3.6 16.2 - - + -
95D SER 2.3 37.2 + - - +
96D PRO* 3.3 18.1 + - + +
98D MET* 2.9 33.0 + - - +
99D LYS* 5.5 0.3 - - - -
100D LEU 5.9 0.2 + - - -
144D PHE* 3.2 17.7 + - - +
145D GLU* 3.0 28.0 + - - +
147D ALA* 1.3 76.1 - - - +
149D SER* 1.3 53.6 - - - +
150D ILE 3.2 0.2 - - - -
151D LEU* 2.8 31.9 + - - +
152D LYS 3.0 8.3 + - - +
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Residues in contact with SER 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D GLU 3.0 14.8 + - - -
146D GLU* 2.9 24.8 + - - +
148D GLN* 1.3 70.7 - - - +
150D ILE* 1.3 56.8 + - - +
152D LYS* 2.7 24.9 - - - +
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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