Contacts of the helix formed by residues 120 - 138 (chain A) in PDB entry 2L5E
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 ASP 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A ASN* 4.2 10.1 - - + +
117A LYS* 2.9 33.4 + - + +
119A THR* 1.3 81.6 - - - +
121A ASP* 1.3 70.3 + - - +
122A ILE* 3.7 24.9 + - + +
123A VAL* 3.3 4.2 + - - +
124A LEU* 3.0 27.9 + - - +
312B ALY 4.1 1.6 - - - +
313B GLY* 3.3 22.6 + - - -
314B LYS* 2.7 31.0 + - - +
315B ALY 4.5 1.2 + - - +
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Residues in contact with ASP 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A THR 4.7 1.6 - - - +
120A ASP* 1.3 77.7 + - - +
122A ILE* 1.3 58.5 + - - +
124A LEU* 3.2 12.9 + - - +
125A MET* 2.8 47.5 + - + +
314B LYS* 3.2 16.1 - - - +
315B ALY 3.4 30.6 - - + +
316B LYS* 2.8 47.1 + - - +
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO* 3.6 28.9 - - + -
59A PHE* 3.6 29.8 - - + -
112A CYS* 3.5 11.2 - - - -
116A ASN* 3.5 28.9 - - + +
120A ASP* 3.7 17.2 + - - +
121A ASP* 1.3 80.2 - - - +
123A VAL* 1.3 58.6 + - - +
125A MET* 3.4 11.2 + - + +
126A ALA* 2.8 26.9 + - - +
312B ALY 3.4 26.0 - - + +
313B GLY 5.6 0.9 - - - +
315B ALY 4.2 16.6 - - + +
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A CYS* 3.6 33.0 - - - +
113A TYR* 4.0 19.9 - - + -
116A ASN* 4.0 8.1 - - + +
117A LYS 3.3 23.1 - - - +
118A PRO* 3.6 27.4 - - + +
120A ASP 3.3 7.4 + - - +
121A ASP 3.2 0.4 - - - -
122A ILE* 1.3 78.1 - - - +
124A LEU* 1.3 67.5 + - - +
126A ALA* 3.1 2.8 + - - +
127A GLN* 2.9 35.6 + - + +
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Residues in contact with LEU 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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55A PHE* 5.1 7.5 - - + -
118A PRO 5.3 5.2 - - - +
119A THR* 4.7 10.5 - - + +
120A ASP 3.0 19.3 + - - +
121A ASP* 3.4 15.3 - - - +
123A VAL* 1.3 79.5 - - - +
125A MET* 1.3 64.1 + - + +
127A GLN* 3.6 15.5 + - - +
128A ALA* 3.5 16.6 + - - +
316B LYS* 6.3 0.2 - - - +
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Residues in contact with MET 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PHE* 3.2 62.4 - - + +
57A TRP* 3.4 28.0 - - + +
58A PRO* 3.6 19.7 - - + -
59A PHE* 6.1 0.2 - - + -
121A ASP* 2.8 37.4 + - + +
122A ILE* 3.5 7.0 - - + +
124A LEU* 1.3 74.7 - - + +
126A ALA* 1.3 55.1 + - - +
128A ALA* 2.9 4.2 + - - -
129A LEU* 2.8 41.3 + - + +
315B ALY 4.4 13.5 - - + +
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Residues in contact with ALA 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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59A PHE* 4.1 7.0 - - + -
109A PHE* 3.4 21.1 - - + -
112A CYS* 3.8 19.3 - - + -
113A TYR* 3.5 13.9 - - + +
122A ILE 2.8 21.2 + - - +
123A VAL 3.5 5.2 - - - +
125A MET* 1.3 71.6 - - - +
127A GLN* 1.3 57.5 + - - +
129A LEU* 3.9 12.7 - - - +
130A GLU* 2.9 29.6 + - - +
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Residues in contact with GLN 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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113A TYR* 3.4 24.1 - - + +
118A PRO 5.4 2.4 + - - -
123A VAL* 2.9 30.9 + - + +
124A LEU* 3.6 16.8 - - - +
125A MET 3.2 0.2 - - - -
126A ALA* 1.3 77.7 - - - +
128A ALA* 1.3 56.7 + - - +
130A GLU* 3.6 9.2 - - - +
131A LYS* 2.7 36.0 + - - +
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Residues in contact with ALA 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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53A HIS* 4.4 18.5 + - + +
55A PHE* 5.0 6.7 - - + -
124A LEU 3.5 8.2 + - - +
125A MET* 2.9 9.0 + - - +
127A GLN* 1.3 76.2 - - - +
129A LEU* 1.3 66.6 + - - +
130A GLU 3.1 2.0 - - - -
131A LYS* 3.0 29.1 + - + +
132A ILE* 3.9 5.2 + - - +
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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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50A LEU* 3.3 22.1 - - + +
53A HIS* 3.1 28.9 - - + +
55A PHE* 3.6 21.1 - - + +
56A ALA* 3.5 31.0 - - + +
59A PHE* 3.6 30.7 - - + -
108A MET* 5.1 2.0 - - + -
109A PHE* 3.7 11.9 - - + -
125A MET* 2.8 25.4 + - + +
126A ALA* 3.4 7.2 - - - +
128A ALA* 1.3 76.3 - - - +
130A GLU* 1.3 62.4 + - - +
131A LYS 3.1 1.0 + - - -
132A ILE* 3.2 20.4 - - - +
133A PHE* 3.3 4.7 + - - +
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Residues in contact with GLU 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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109A PHE* 3.6 31.1 - - + -
113A TYR* 3.2 24.1 + - - +
126A ALA 2.9 15.8 + - - +
127A GLN* 3.6 9.2 - - - +
128A ALA 3.1 0.2 - - - -
129A LEU* 1.3 76.4 - - - +
131A LYS* 1.3 65.1 + - - +
133A PHE* 3.2 10.2 - - + +
134A LEU* 3.1 39.9 + - + +
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Residues in contact with LYS 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 GLN* 2.7 39.6 + - - +
128A ALA* 3.0 19.3 + - - +
130A GLU* 1.3 85.0 + - - +
132A ILE* 1.3 58.1 + - + +
134A LEU* 3.3 17.9 - - + +
135A GLN* 3.0 31.3 + - - +
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Residues in contact with ILE 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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46A VAL* 5.3 1.3 - - - +
49A THR* 4.1 11.7 - - + +
50A LEU* 3.6 32.1 - - + -
53A HIS* 3.5 42.6 - - + +
128A ALA 4.1 4.9 - - - +
129A LEU* 3.2 15.3 - - - +
131A LYS* 1.3 71.8 - - + +
133A PHE* 1.3 66.6 + - - +
135A GLN* 3.6 24.0 - - - +
136A LYS* 3.2 37.4 + - + +
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Residues in contact with PHE 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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42A MET* 4.7 2.7 - - - -
46A VAL* 3.6 20.3 - - + +
50A LEU* 4.6 7.3 - - + +
102A MET* 4.6 14.4 - - + -
105A PHE* 3.5 47.8 - + + -
106A ASN* 5.3 4.0 - - + -
109A PHE* 3.9 24.7 - + + -
129A LEU 3.3 9.5 + - - +
130A GLU* 3.2 23.8 + - + +
131A LYS 3.1 0.2 - - - -
132A ILE* 1.3 79.7 - - - +
134A LEU* 1.3 69.4 + - + +
136A LYS* 3.3 2.3 + - - +
137A VAL* 3.0 46.4 + - + +
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Residues in contact with LEU 134 (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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130A GLU* 3.2 32.1 - - + +
131A LYS* 3.3 20.6 - - + +
133A PHE* 1.3 83.7 - - + +
135A GLN* 1.3 67.5 + - + +
137A VAL* 4.0 8.5 - - + -
138A ALA* 2.8 36.7 + - + +
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Residues in contact with GLN 135 (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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131A LYS 3.0 20.1 + - - +
132A ILE* 3.4 21.0 - - - +
134A LEU* 1.3 85.7 - - + +
136A LYS* 1.3 87.2 + - + +
138A ALA* 3.8 4.3 + - - +
139A GLN* 3.2 28.0 + - - +
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Residues in contact with LYS 136 (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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41A TYR* 3.0 27.7 + - - +
45A VAL* 3.7 25.8 - - + +
46A VAL* 3.7 24.2 - - + +
49A THR* 3.6 34.1 - - + -
132A ILE* 3.2 27.3 + - - +
133A PHE 4.1 0.7 - - - +
135A GLN* 1.3 104.2 + - - +
137A VAL* 1.3 64.3 + - - +
139A GLN* 3.3 8.8 + - - +
140A MET 3.3 2.4 + - - -
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Residues in contact with VAL 137 (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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42A MET* 3.9 18.2 - - - -
46A VAL* 4.1 2.9 - - + -
102A MET* 3.6 22.9 - - + -
133A PHE* 3.0 50.6 + - + +
134A LEU* 3.2 8.5 + - + +
136A LYS* 1.3 74.9 - - - +
138A ALA* 1.3 57.5 + - - +
139A GLN 3.0 5.2 - - - -
140A MET* 3.0 33.6 + - + +
142A GLN* 4.2 3.5 + - - -
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Residues in contact with ALA 138 (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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134A LEU* 2.8 19.8 + - + +
135A GLN* 4.0 6.1 - - - +
136A LYS 3.4 0.2 - - - -
137A VAL* 1.3 77.3 - - - +
139A GLN* 1.3 59.2 + - + +
140A MET 3.3 0.7 - - - -
142A GLN* 3.2 21.7 + - - +
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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
------------------------------------------------------------
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