Contacts of the helix formed by residues 105 - 117 (chain A) in PDB entry 1LWW
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 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLU* 3.7 16.4 - - - +
102A LEU 5.2 1.1 - - - -
103A ASP 3.4 8.7 + - - -
104A VAL* 1.3 70.3 - - - +
106A LEU* 1.3 63.7 + - - +
107A ALA* 3.9 5.6 - - + +
108A GLN* 3.2 43.1 + - + +
109A LEU* 3.3 14.6 + - - +
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Residues in contact with LEU 106 (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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31A SER 4.3 3.6 - - - +
32A GLU* 2.9 42.7 + - - +
104A VAL* 3.2 3.2 + - - -
105A THR* 1.3 72.3 - - - +
107A ALA* 1.3 58.1 + - - +
109A LEU* 3.2 19.9 + - + +
110A TYR* 2.9 54.6 + - + -
113A TRP* 4.5 5.4 - - + -
129A GLY* 3.5 7.6 - - - +
130A VAL 3.3 46.2 - - - +
131A ARG* 3.7 16.6 - - + +
313A TRP* 4.4 7.4 - - + -
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 4.9 10.9 + - - +
32A GLU* 2.9 16.1 + - - +
105A THR* 3.2 7.4 - - + -
106A LEU* 1.3 77.7 - - - +
108A GLN* 1.3 61.5 + - + +
110A TYR* 4.1 5.8 - - - +
111A HIS* 3.2 23.9 + - - +
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Residues in contact with GLN 108 (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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105A THR* 3.2 31.8 + - + +
107A ALA* 1.3 76.9 - - + +
109A LEU* 1.3 66.4 + - + +
111A HIS* 3.6 12.7 + - - +
112A HIS* 3.2 22.0 + - - +
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Residues in contact with LEU 109 (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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104A VAL* 3.6 29.6 - - + -
105A THR 3.3 9.1 + - - +
106A LEU* 3.2 11.7 + - + +
108A GLN* 1.3 78.6 - - + +
110A TYR* 1.3 64.6 + - - +
112A HIS* 3.2 10.0 + - + +
113A TRP* 3.0 54.5 + - + +
310A TYR* 4.1 35.2 - - + -
313A TRP* 4.0 17.9 - - + -
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Residues in contact with TYR 110 (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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106A LEU* 2.9 50.9 + - + +
107A ALA* 4.1 6.5 - - - +
109A LEU* 1.3 75.7 - - - +
111A HIS* 1.3 64.7 + - - +
113A TRP* 3.7 15.1 - + - +
114A GLY* 2.9 23.0 + - - -
120A PHE* 4.2 4.8 - + - -
121A GLN* 5.1 1.4 - - - +
124A ALA* 3.5 34.5 - - + +
127A PHE 2.6 28.8 + - - -
128A GLN* 3.5 16.9 - - + -
129A GLY 4.1 1.8 - - - -
130A VAL* 3.3 23.0 + - - +
317A VAL* 3.6 20.7 - - + +
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Residues in contact with HIS 111 (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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107A ALA 3.2 17.3 + - - +
108A GLN* 3.6 14.4 - - - +
110A TYR* 1.3 80.7 - - - +
112A HIS* 1.3 62.5 + - + +
114A GLY* 3.3 1.6 + - - -
115A SER* 2.9 47.3 + - - -
121A GLN* 5.1 2.7 - - - +
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Residues in contact with HIS 112 (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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108A GLN 3.2 10.2 + - - +
109A LEU* 3.2 14.2 + - + +
111A HIS* 1.3 87.8 - - + +
113A TRP* 1.3 83.1 + + - +
115A SER* 2.9 21.8 + - - -
116A VAL* 3.3 26.1 + - + +
307A TRP 3.8 15.4 + - - -
308A GLY* 5.3 1.6 - - - -
309A PRO* 5.4 5.7 - - + +
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Residues in contact with TRP 113 (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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106A LEU* 4.5 5.2 - - + -
109A LEU* 3.0 45.7 + - + +
110A TYR* 3.7 24.7 - + - -
112A HIS* 1.3 85.6 - + - +
114A GLY* 1.3 59.0 + - - +
116A VAL* 3.2 9.6 + - - +
117A ASP* 2.9 33.3 + - - +
120A PHE* 3.2 44.9 - + + -
307A TRP* 3.7 37.6 + - + +
310A TYR* 3.4 36.0 + - + +
313A TRP* 3.5 16.4 - - + -
314A ALA* 3.4 28.1 - - + +
317A VAL* 4.1 3.4 - - + -
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Residues in contact with GLY 114 (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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110A TYR 2.9 18.5 + - - -
111A HIS 3.7 1.6 - - - -
113A TRP* 1.3 77.7 - - - +
115A SER* 1.3 59.7 + - - +
117A ASP 3.5 20.3 + - - +
118A SER* 4.3 1.9 + - - -
120A PHE* 3.9 2.1 - - - -
121A GLN* 3.8 38.1 - - - +
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Residues in contact with SER 115 (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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111A HIS* 2.9 38.6 + - - -
112A HIS* 2.9 16.4 + - - -
114A GLY* 1.3 78.9 - - - +
116A VAL* 1.3 63.1 + - - +
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Residues in contact with VAL 116 (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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112A HIS* 3.7 32.3 - - + +
113A TRP* 3.4 16.6 - - - +
115A SER* 1.3 82.9 - - - +
117A ASP* 1.3 60.6 + - + +
118A SER 4.2 0.9 - - - -
306A LEU* 3.5 33.4 - - - +
307A TRP* 4.9 3.6 - - + -
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Residues in contact with ASP 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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113A TRP 2.9 12.9 + - - +
114A GLY 3.5 7.6 - - - +
115A SER 3.5 1.2 - - - -
116A VAL* 1.3 81.8 - - + +
118A SER* 1.3 63.5 + - - +
119A HIS* 3.1 13.5 + - - +
120A PHE* 3.0 22.1 + - + +
121A GLN 3.0 10.7 + - - -
279A TYR* 2.6 39.9 + - - -
306A LEU* 3.4 10.0 - - + +
307A TRP* 2.9 26.7 + - + +
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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