Contacts of the helix formed by residues 133 - 146 (chain B) in PDB entry 5LTU
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 LYS 133 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B SER* 5.7 0.6 + - - -
45B GLN* 4.5 18.4 - - - +
46B TRP 4.6 12.3 - - - +
47B ILE* 4.1 14.2 - - + +
89B ARG* 4.5 13.2 - - - +
129B LEU* 2.9 19.9 + - + +
131B CYS 3.4 2.3 - - - +
132B HIS* 1.3 87.1 - - - +
134B PRO* 1.3 63.8 - - - +
135B VAL* 3.3 4.5 - - + +
136B HIS* 3.2 45.2 + - + +
137B ALA 3.6 2.9 + - - -
201B EDO 2.8 41.4 + - - -
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Residues in contact with PRO 134 (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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129B LEU 3.9 5.8 - - - +
130B GLN* 4.4 16.2 - - + +
132B HIS* 3.6 7.4 - - - +
133B LYS* 1.3 88.8 - - - +
135B VAL* 1.3 65.7 + - + +
136B HIS 3.2 0.2 - - - -
137B ALA* 3.2 11.9 + - + +
138B GLU* 3.1 32.5 + - - +
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PHE* 5.3 6.3 - - + -
85B GLU 5.8 1.8 - - - +
86B ASN* 4.1 35.2 - - + +
133B LYS* 3.3 2.7 - - + -
134B PRO* 1.3 79.6 - - + +
136B HIS* 1.3 69.4 + - + +
138B GLU* 3.3 34.9 - - - +
139B TYR* 3.3 29.4 - - + +
201B EDO 5.4 3.4 - - - +
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Residues in contact with HIS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ARG* 4.7 1.2 + - - -
47B ILE* 3.7 19.0 - - + +
48B VAL* 3.0 49.1 + - + +
129B LEU* 3.8 19.2 - - + +
133B LYS* 3.2 33.6 + - + +
134B PRO 3.2 0.4 - - - -
135B VAL* 1.3 78.3 - - + +
137B ALA* 1.3 65.4 + - - +
139B TYR* 3.1 46.7 + + - +
140B LEU* 3.8 3.3 + - - +
201B EDO 3.3 30.2 + - - -
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Residues in contact with ALA 137 (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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126B ILE* 4.1 14.8 - - + +
129B LEU* 4.0 24.7 - - + +
130B GLN* 4.0 24.0 - - + -
133B LYS 3.6 2.4 + - - -
134B PRO* 3.2 14.8 + - + +
136B HIS* 1.3 80.4 - - - +
138B GLU* 1.3 61.3 + - - +
140B LEU* 3.2 6.8 + - - +
141B GLU* 3.1 29.8 + - - +
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PHE* 4.1 16.3 - - + -
134B PRO* 3.1 17.9 + - + +
135B VAL* 3.3 29.9 - - - +
136B HIS 3.1 0.4 - - - -
137B ALA* 1.3 75.5 - - - +
139B TYR* 1.3 66.1 + - - +
141B GLU* 3.9 16.9 - - - +
142B LYS* 3.0 26.3 + - - +
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Residues in contact with TYR 139 (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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20B ARG* 3.8 21.4 + - - -
22B ALA* 4.5 6.1 - - + -
24B LEU* 4.0 17.0 - - + -
48B VAL* 4.3 24.7 - - + -
81B LEU* 3.3 14.2 - - - +
84B PHE* 3.6 43.8 - + + +
93B THR* 4.0 9.4 + - - +
95B VAL* 3.8 28.5 - - + -
135B VAL* 3.3 24.7 - - + +
136B HIS* 3.1 39.0 + + - +
138B GLU* 1.3 76.7 - - - +
140B LEU* 1.3 62.5 + - - +
142B LYS* 3.9 0.3 - - - +
143B LEU* 3.1 17.8 + - - +
201B EDO 4.9 0.5 + - - -
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 4.0 29.4 - - + -
26B PHE* 4.6 8.1 - - + -
34B VAL* 4.4 22.0 - - + -
36B LEU* 5.4 1.8 - - + -
48B VAL* 5.5 0.2 - - + -
122B VAL* 4.4 16.6 - - + +
125B ALA* 3.6 30.7 - - + -
126B ILE* 3.9 20.1 - - + +
129B LEU* 3.9 20.4 - - + -
136B HIS 3.8 2.7 + - - +
137B ALA 3.2 7.3 + - - +
139B TYR* 1.3 79.0 - - - +
141B GLU* 1.3 64.8 + - - +
143B LEU* 3.3 9.1 + - + +
144B LYS* 3.0 27.9 + - - +
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Residues in contact with GLU 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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145A LEU* 4.8 7.4 - - + -
126B ILE* 3.7 25.0 - - + +
130B GLN* 3.4 25.5 + - - -
137B ALA* 3.1 25.3 + - - +
138B GLU* 3.9 17.5 - - - +
140B LEU* 1.3 75.9 - - - +
142B LYS* 1.3 55.0 + - - +
145B LEU* 2.7 52.7 + - + +
147B CYS* 4.5 12.8 - - + -
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Residues in contact with LYS 142 (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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81B LEU* 4.5 9.2 - - + +
84B PHE* 4.2 19.1 - - + -
138B GLU 3.0 17.7 + - - +
139B TYR 3.9 3.4 - - - +
141B GLU* 1.3 72.7 - - - +
143B LEU* 1.3 62.8 + - - +
146B GLY* 2.8 27.1 + - - -
147B CYS* 3.8 20.3 - - + +
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Residues in contact with LEU 143 (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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24B LEU* 4.4 5.6 - - + -
26B PHE* 3.7 26.9 - - + -
31B GLU* 4.0 10.1 - - - +
79B ARG* 3.3 30.2 + - - +
81B LEU* 3.9 23.3 - - + +
97B VAL* 3.8 21.1 - - + -
139B TYR 3.1 16.0 + - - +
140B LEU* 3.5 13.5 - - + +
142B LYS* 1.3 80.3 - - - +
144B LYS* 1.3 83.2 + - + +
146B GLY 4.4 0.9 + - - -
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Residues in contact with LYS 144 (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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144A LYS* 3.6 38.3 + - - +
145A LEU* 3.7 24.0 - - + -
30B GLN 4.2 2.6 + - - -
31B GLU* 2.9 41.2 + - - +
32B ASP* 4.1 10.1 + - - -
122B VAL* 4.0 30.3 - - + -
140B LEU 3.0 15.6 + - - +
143B LEU* 1.3 92.1 - - + +
145B LEU* 1.3 64.4 + - - +
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Residues in contact with LEU 145 (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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123A GLU* 4.4 19.1 - - - +
126A ILE* 3.8 25.5 - - + +
130A GLN* 5.7 1.8 - - - +
141A GLU* 3.6 56.1 - - + +
144A LYS* 3.9 10.5 - - + -
145A LEU* 3.9 21.1 - - + -
141B GLU* 2.7 33.3 + - + +
144B LYS* 1.3 73.8 - - - +
146B GLY* 1.3 58.3 + - - +
147B CYS* 2.8 22.8 - - + +
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Residues in contact with GLY 146 (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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123A GLU* 5.7 3.6 - - - -
142B LYS* 2.8 25.6 + - - -
143B LEU 4.4 1.0 + - - -
144B LYS 3.6 0.8 - - - -
145B LEU* 1.3 75.4 - - - +
147B CYS* 1.3 67.1 - - - +
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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