Contacts of the helix formed by residues 122 - 133 (chain A) 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 VAL 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A PHE* 4.2 15.5 - - + -
31A GLU 3.6 15.0 - - - +
32A ASP* 2.9 32.4 + - - +
33A GLU 4.4 0.7 - - - +
34A VAL* 4.6 7.6 - - + -
120A PHE 3.5 0.9 + - - -
121A LYS* 1.3 72.2 - - - +
123A GLU* 1.3 65.1 + - - +
125A ALA* 3.1 9.1 + - - +
126A ILE* 3.0 33.1 + - + +
140A LEU* 4.5 13.5 - - + -
143A LEU* 5.0 0.2 - - + -
144A LYS* 3.5 37.9 - - + -
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LYS* 3.2 4.1 - - + +
122A VAL* 1.3 81.8 - - - +
124A ASP* 1.3 66.1 + - - +
126A ILE* 3.6 6.9 + - - +
127A LYS* 3.4 18.7 + - - +
145B LEU 4.4 20.6 - - - +
146B GLY* 5.7 2.5 - - - -
147B CYS 5.6 0.7 - - - +
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Residues in contact with ASP 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PHE* 4.7 10.3 - - + -
121A LYS* 3.0 26.7 + - - +
123A GLU* 1.3 80.2 - - - +
125A ALA* 1.3 62.0 + - - +
127A LYS* 3.2 7.3 + - - +
128A VAL* 2.9 37.1 + - + +
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 3.6 30.7 - - + -
36A LEU* 4.1 7.4 - - + -
120A PHE* 3.9 10.5 - - + +
121A LYS 3.0 8.6 + - - +
122A VAL 3.1 8.9 + - - +
124A ASP* 1.3 78.0 - - - +
126A ILE* 1.3 62.2 + - - +
128A VAL* 3.2 11.4 - - - +
129A LEU* 3.0 30.6 + - - +
140A LEU* 3.8 10.5 - - + -
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Residues in contact with ILE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A VAL* 3.0 25.8 + - + +
123A GLU* 3.8 8.7 - - - +
124A ASP 3.3 0.2 - - - -
125A ALA* 1.3 76.0 - - - +
127A LYS* 1.3 63.5 + - - +
129A LEU* 3.6 2.6 + - - -
130A GLN* 3.1 47.8 + - + +
137A ALA* 4.1 5.1 - - + +
140A LEU* 3.7 26.0 - - + +
141A GLU* 4.1 21.3 - - + +
144A LYS* 4.7 2.5 - - + -
145B LEU* 3.8 39.3 - - + +
147B CYS 4.1 12.3 - - - +
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Residues in contact with LYS 127 (chain A).
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 3.4 10.3 + - - +
124A ASP* 3.2 12.9 + - - +
126A ILE* 1.3 82.9 - - - +
128A VAL* 1.3 63.3 + - + +
129A LEU 3.5 0.3 + - - -
130A GLN* 3.5 18.2 + - - +
131A CYS* 3.7 13.9 + - - -
147B CYS 5.4 4.9 + - - +
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.1 17.9 - - + -
46A TRP* 5.0 15.4 - - + +
120A PHE* 4.4 21.3 - - + -
124A ASP* 2.9 22.7 + - + +
125A ALA* 3.2 22.2 - - - +
127A LYS* 1.3 78.2 - - + +
129A LEU* 1.3 62.9 + - + +
131A CYS* 3.6 12.6 + - - +
132A HIS* 3.7 11.6 + - - +
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.2 22.2 - - + -
46A TRP* 3.5 28.0 - - + +
47A ILE* 4.1 11.2 - - - +
48A VAL* 4.3 4.0 - - + -
125A ALA 3.0 22.2 + - - +
128A VAL* 1.3 74.6 - - - +
130A GLN* 1.3 59.8 + - - +
131A CYS 3.0 5.4 - - - -
132A HIS* 5.6 0.2 - - - -
133A LYS* 2.7 41.1 + - + +
136A HIS* 4.1 19.3 - - + +
137A ALA* 3.9 26.7 - - + +
140A LEU* 3.6 27.1 - - + -
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Residues in contact with GLN 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ILE* 3.1 33.5 + - - +
127A LYS* 3.7 9.9 - - - +
128A VAL 3.4 0.2 - - - -
129A LEU* 1.3 75.5 - - - +
131A CYS* 1.3 61.2 + - - +
134A PRO* 4.2 18.4 - - + +
137A ALA* 3.7 15.7 - - + -
141A GLU* 2.7 25.6 + - - +
145B LEU* 5.7 2.0 - - - +
147B CYS* 4.0 19.3 + - - +
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Residues in contact with CYS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LYS 3.7 10.0 + - - -
128A VAL* 3.6 11.1 + - - +
129A LEU 3.0 1.0 - - - -
130A GLN* 1.3 82.4 - - - +
132A HIS* 1.3 61.5 + - + +
134A PRO* 4.9 3.0 - - - +
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Residues in contact with HIS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLN* 3.1 45.0 - - + +
46A TRP 4.9 4.3 - - - +
128A VAL 3.7 8.0 + - - +
129A LEU* 3.3 1.8 + - - -
131A CYS* 1.3 79.9 - - + +
133A LYS* 1.3 66.6 + - + +
134A PRO* 3.8 5.4 - - - +
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Residues in contact with LYS 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLN* 3.9 21.2 + - - +
46A TRP 4.3 10.5 - - - +
47A ILE* 4.0 21.4 - - + +
89A ARG* 4.5 24.7 - - - +
129A LEU* 2.7 20.6 + - + +
132A HIS* 1.3 78.4 + - - +
134A PRO* 1.3 62.9 - - + +
135A VAL* 3.2 12.3 - - + -
136A HIS* 2.9 47.0 + - + +
137A ALA 3.3 5.9 + - - -
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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