Contacts of the helix formed by residues 120 - 139 (chain B) in PDB entry 4L9T
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 SER 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119B LEU* 1.3 76.2 - - - +
121B GLU* 1.3 61.0 + - - +
122B GLU* 4.4 2.2 + - - +
123B GLU* 2.8 33.1 + - - +
124B ASN* 2.9 27.9 + - - -
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Residues in contact with GLU 121 (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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120B SER* 1.3 75.0 - - - +
122B GLU* 1.3 63.6 + - - +
124B ASN* 3.4 9.6 + - - +
125B GLU* 3.2 18.9 + - - +
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B SER* 3.4 2.8 + - - +
121B GLU* 1.3 77.6 - - - +
123B GLU* 1.3 62.8 + - - +
125B GLU* 3.0 13.3 + - - +
126B GLN* 3.0 23.3 + - - +
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Residues in contact with GLU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ASN* 4.7 12.0 + - - +
119B LEU* 3.7 28.3 - - + +
120B SER* 2.8 41.0 + - - +
122B GLU* 1.3 78.8 - - - +
124B ASN* 1.3 57.4 + - - +
126B GLN* 3.4 5.8 + - - +
127B MET* 2.9 29.6 + - - +
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Residues in contact with ASN 124 (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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5A TYR* 2.5 37.9 + - + +
116B VAL* 3.0 39.8 + - + +
119B LEU* 3.4 18.7 + - - +
120B SER 2.9 21.5 + - - -
121B GLU* 3.6 10.4 - - - +
123B GLU* 1.3 75.5 - - - +
125B GLU* 1.3 58.6 + - - +
128B LYS* 2.9 40.7 + - + +
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Residues in contact with GLU 125 (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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121B GLU 3.2 11.5 + - - +
122B GLU* 3.0 15.1 + - - +
124B ASN* 1.3 76.7 - - - +
126B GLN* 1.3 57.9 + - - +
128B LYS* 4.0 5.0 - - - +
129B ALA* 3.0 28.1 + - + +
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Residues in contact with GLN 126 (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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122B GLU 3.0 11.8 + - - +
123B GLU* 3.9 8.3 - - - +
125B GLU* 1.3 72.8 - - - +
127B MET* 1.3 61.2 + - - +
129B ALA* 3.3 5.8 + - - +
130B ASN* 2.9 43.6 + - - +
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Residues in contact with MET 127 (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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5A TYR* 3.3 28.7 - - + +
127A MET* 3.5 30.8 - - - +
130A ASN* 3.9 28.3 - - + +
131A LEU* 3.4 35.2 - - + -
134A MET* 3.7 22.0 - - + -
119B LEU* 4.2 4.5 - - + -
123B GLU 2.9 18.5 + - - +
124B ASN 3.5 0.2 - - - +
126B GLN* 1.3 77.5 - - - +
128B LYS* 1.3 57.5 + - - +
130B ASN* 3.3 2.5 + - - +
131B LEU* 2.9 41.4 + - + +
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Residues in contact with LYS 128 (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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3A PHE 3.1 28.6 + - - +
4A THR* 3.9 3.0 - - - +
5A TYR* 3.6 46.6 - - + +
8A LEU* 4.1 12.9 - - + +
112B GLU* 3.9 11.3 + - - -
116B VAL* 4.8 6.5 - - - +
124B ASN* 2.9 26.1 + - + +
125B GLU* 4.1 4.3 - - - +
127B MET* 1.3 73.6 - - - +
129B ALA* 1.3 60.9 + - - +
131B LEU* 3.8 2.8 - - - +
132B THR* 2.6 35.4 + - - +
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Residues in contact with ALA 129 (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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125B GLU* 3.0 21.4 + - + +
126B GLN* 3.6 7.0 - - - +
127B MET 3.3 0.2 - - - -
128B LYS* 1.3 77.0 - - - +
130B ASN* 1.3 61.6 + - - +
132B THR* 3.2 8.4 + - - -
133B LYS* 3.0 31.5 + - - +
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Residues in contact with ASN 130 (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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119A LEU* 3.4 27.0 - - + +
123A GLU* 3.9 20.8 + - - +
127A MET* 3.3 23.8 - - + +
126B GLN* 2.9 27.8 + - - +
127B MET* 5.2 0.2 - - - +
129B ALA* 1.3 77.7 - - - +
131B LEU* 1.3 59.4 + - - +
133B LYS* 3.0 32.0 + - - +
134B MET* 2.8 31.7 + - - +
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Residues in contact with LEU 131 (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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5A TYR* 3.6 27.1 - - + -
8A LEU* 4.2 19.7 - - + +
9A PHE* 3.6 22.2 - - + -
12A ILE* 3.8 11.5 - - + +
127A MET* 3.9 20.4 - - - +
131A LEU* 4.7 0.9 - - + -
9B PHE* 3.8 36.1 - - + -
127B MET* 2.9 24.9 + - + +
128B LYS 3.8 4.0 - - - +
130B ASN* 1.3 76.4 - - - +
132B THR* 1.3 58.3 + - - +
134B MET* 3.2 7.6 + - - +
135B LEU* 2.8 29.3 + - - +
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Residues in contact with THR 132 (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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3A PHE* 4.4 23.3 - - + -
8A LEU* 3.9 16.7 - - + +
128B LYS* 2.6 24.4 + - - +
129B ALA* 3.4 8.8 - - - -
130B ASN 3.2 0.4 - - - -
131B LEU* 1.3 75.2 - - - +
133B LYS* 1.3 59.9 + - - +
135B LEU* 3.4 6.5 + - + +
136B SER* 2.8 30.7 + - - -
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Residues in contact with LYS 133 (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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118A GLN* 3.8 27.0 + - + +
119A LEU* 3.8 18.0 - - - +
123A GLU* 4.6 6.3 + - - -
129B ALA* 3.0 16.2 + - - +
130B ASN* 3.0 33.0 + - - +
132B THR* 1.3 77.4 - - - +
134B MET* 1.3 62.1 + - - +
136B SER* 3.4 6.9 + - - -
137B SER* 3.0 23.2 + - - -
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Residues in contact with MET 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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12A ILE* 4.6 5.2 - - + -
115A LEU* 3.7 32.3 - - + +
118A GLN* 4.5 8.5 - - + -
119A LEU* 4.6 9.4 - - + -
127A MET* 4.0 25.1 - - - +
5B TYR* 3.8 28.5 - - + -
9B PHE* 3.6 33.4 - - + -
130B ASN 2.8 18.5 + - - +
131B LEU* 3.5 15.5 - - - +
132B THR 3.2 0.2 - - - -
133B LYS* 1.3 73.2 - - - +
135B LEU* 1.3 63.5 + - - +
137B SER* 2.7 25.1 + - - -
138B LEU* 3.3 12.1 + - - +
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Residues in contact with LEU 135 (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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3A PHE* 5.7 3.6 - - + -
7A TYR* 4.6 10.3 - - + +
8A LEU* 4.2 17.5 - - + -
11A MET* 3.7 36.3 - - + +
12A ILE* 3.9 16.7 - - + +
15A GLU* 3.7 26.7 - - + -
131B LEU 2.8 21.0 + - - +
132B THR* 3.7 9.0 - - + +
134B MET* 1.3 72.8 - - - +
136B SER* 1.3 64.0 + - - +
138B LEU* 3.2 13.6 + - + +
139B GLN* 3.3 35.7 + - - +
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Residues in contact with SER 136 (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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132B THR* 2.8 20.1 + - - -
133B LYS* 3.5 8.5 - - - -
135B LEU* 1.3 77.1 - - - +
137B SER* 1.3 58.3 + - - +
139B GLN* 3.0 36.9 + - - +
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Residues in contact with SER 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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19A LYS* 5.5 1.6 - - - -
114A THR* 3.5 26.8 - - - +
115A LEU* 4.0 5.4 - - - +
118A GLN* 3.4 40.8 - - - +
133B LYS 3.0 8.2 + - - -
134B MET* 2.7 20.4 + - - -
136B SER* 1.3 76.4 - - - +
138B LEU* 1.3 59.5 + - - +
139B GLN 3.6 2.6 + - - -
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Residues in contact with LEU 138 (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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12A ILE* 3.9 28.0 - - + +
15A GLU* 3.9 23.1 - - + +
16A MET* 3.6 32.1 - - + -
19A LYS* 3.4 36.7 + - + +
111A MET* 4.4 23.8 - - + +
114A THR* 4.8 6.3 - - + -
115A LEU* 4.0 23.6 - - + -
134B MET 3.6 13.7 - - - +
135B LEU* 3.2 7.8 + - - +
136B SER 3.2 0.8 - - - -
137B SER* 1.3 79.1 + - - +
139B GLN* 1.3 59.9 + - - +
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Residues in contact with GLN 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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11A MET* 5.7 4.2 - - - -
15A GLU* 3.6 33.7 + - + +
19A LYS* 5.0 5.0 + - - -
135B LEU* 3.3 39.8 - - - +
136B SER* 3.0 25.4 + - - +
137B SER 4.6 2.9 - - - -
138B LEU* 1.3 82.4 - - - +
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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