Contacts of the helix formed by residues 115 - 125 (chain A) in PDB entry 1L2L
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 GLY 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ASN* 3.4 22.9 - - - -
35A ASN* 3.3 12.2 + - - -
114A GLY* 1.3 72.4 - - - +
116A GLN* 1.3 65.2 + - - -
117A VAL 3.2 3.3 + - - -
118A GLY 3.3 0.3 + - - -
119A ILE* 3.0 32.0 + - - +
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Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LEU* 5.0 0.2 - - - +
33A ASN* 3.5 10.4 + - - +
115A GLY* 1.3 71.7 - - - -
117A VAL* 1.3 55.7 + - - +
119A ILE* 3.9 22.5 - - - +
120A MET* 3.0 60.7 + - + +
235A SER* 3.3 29.8 - - - +
441A ILE* 4.1 5.1 - - - +
443A ASP* 2.8 55.0 + - - +
447A SER* 5.0 0.6 + - - -
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Residues in contact with VAL 117 (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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30A LEU* 3.5 29.6 - - + +
31A ALA 3.3 40.4 - - - +
32A TYR 3.7 1.3 - - - +
33A ASN 3.2 16.3 + - - +
34A THR* 3.1 20.4 - - - +
116A GLN* 1.3 76.4 - - - +
118A GLY* 1.3 59.6 + - - +
121A ALA* 3.0 28.4 + - - +
134A ALA* 3.7 15.3 - - + -
135A HIS 3.5 10.3 - - - +
136A VAL* 5.1 0.2 - - + -
233A ILE 5.7 0.2 - - - +
235A SER* 3.8 6.3 - - - +
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Residues in contact with GLY 118 (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 THR* 3.7 9.3 + - - +
113A MET* 3.4 37.7 - - - +
115A GLY 3.3 5.7 + - - -
117A VAL* 1.3 81.8 - - - +
119A ILE* 1.3 60.6 + - - +
121A ALA* 3.4 2.1 + - - +
122A ASN* 3.2 23.0 + - - -
147A PHE* 4.1 9.4 - - - -
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Residues in contact with ILE 119 (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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37A ASP* 5.8 0.4 - - - +
112A ARG* 6.1 2.7 - - - +
113A MET* 3.7 29.4 - - + +
114A GLY* 4.4 0.9 - - - -
115A GLY 3.0 27.1 + - - +
116A GLN* 3.9 24.0 - - - +
118A GLY* 1.3 75.3 - - - +
120A MET* 1.3 65.4 + - - +
122A ASN* 3.5 6.9 + - - +
123A LEU* 3.2 21.6 + - + +
375A LYS* 5.3 5.6 - - - +
441A ILE* 4.4 17.9 - - + -
444A THR* 5.8 0.4 - - - +
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Residues in contact with MET 120 (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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30A LEU* 3.8 17.5 - - + -
116A GLN* 3.0 45.2 + - + +
119A ILE* 1.3 79.8 - - - +
121A ALA* 1.3 57.1 + - - +
123A LEU* 3.5 26.9 - - + -
124A LEU* 2.7 66.1 + - + +
233A ILE* 5.3 5.2 - - + -
441A ILE* 5.6 0.2 - - - -
443A ASP* 3.9 9.2 - - - +
444A THR* 4.5 2.5 - - - -
447A SER* 3.3 39.0 - - - +
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Residues in contact with ALA 121 (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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30A LEU* 3.4 7.6 - - - +
117A VAL 3.0 19.3 + - - +
118A GLY 3.6 6.1 - - - +
119A ILE 3.3 0.2 - - - -
120A MET* 1.3 78.9 - - - +
122A ASN* 1.3 55.6 + - - +
125A GLY* 2.7 33.8 + - - -
126A GLY 3.2 1.2 + - - -
132A VAL* 3.9 22.9 - - + -
134A ALA* 4.7 2.9 - - + -
147A PHE* 3.9 22.4 - - + -
152A ILE* 3.6 10.1 - - + +
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Residues in contact with ASN 122 (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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113A MET* 3.8 16.8 - - - +
118A GLY 3.2 15.8 + - - +
119A ILE* 3.8 6.4 - - - +
120A MET 3.3 0.2 - - - -
121A ALA* 1.3 80.8 - - - +
123A LEU* 1.3 55.7 + - - +
126A GLY* 2.7 32.2 + - - +
127A VAL* 3.1 4.0 + - - +
146A LEU 3.2 20.4 + - - -
147A PHE* 3.2 8.9 - - - +
148A LEU* 2.7 49.5 + - + +
152A ILE* 3.7 6.0 - - - +
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Residues in contact with LEU 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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119A ILE* 3.2 18.8 + - + +
120A MET* 3.5 29.6 - - + +
122A ASN* 1.3 73.5 - - - +
124A LEU* 1.3 61.9 + - - +
127A VAL* 2.9 41.8 + - + +
128A TYR* 2.9 37.2 + - + +
381A ILE* 4.6 17.9 - - + +
444A THR* 3.9 28.7 - - + +
448A SER* 4.1 10.5 - - - +
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A VAL* 4.1 20.4 - - + -
30A LEU* 4.3 8.7 - - + -
120A MET* 2.7 50.2 + - + +
123A LEU* 1.3 73.8 - - - +
125A GLY* 1.3 56.8 + - - +
128A TYR* 3.3 34.0 - - + +
129A GLY 3.2 8.8 + - - -
130A ILE* 2.9 31.4 + - + +
132A VAL* 4.0 8.7 - - + -
233A ILE* 3.9 22.2 - - + -
447A SER* 4.6 4.0 - - - +
451A VAL* 4.2 22.7 - - + -
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Residues in contact with GLY 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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121A ALA 2.7 18.9 + - - -
124A LEU* 1.3 75.7 - - - +
126A GLY* 1.3 61.5 + - - -
127A VAL 3.3 1.1 + - - -
129A GLY* 3.5 10.6 + - - -
130A ILE 3.2 17.7 - - - -
132A VAL* 3.7 5.7 - - - +
150A GLY* 4.3 0.9 - - - -
151A PRO* 3.4 23.5 - - - +
152A ILE* 4.1 10.3 - - - -
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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