Contacts of the helix formed by residues 109 - 127 (chain B) in PDB entry 2L0T
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 HIS 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B PRO* 3.5 40.7 - - + +
70B LEU* 4.7 5.1 - - + +
107B LYS 3.5 0.2 - - - -
108B ALA* 1.3 85.2 - - + +
110B PRO* 1.3 65.0 - - + +
111B LYS* 4.0 28.2 - - + +
112B VAL* 2.8 31.0 + - + +
113B CYS* 2.8 38.7 + - - -
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Residues in contact with PRO 110 (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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107B LYS* 4.8 5.8 - - + +
108B ALA 4.3 3.6 - - - +
109B HIS* 1.3 92.6 - - + +
111B LYS* 1.3 55.6 + - - +
113B CYS* 3.1 7.0 + - + -
114B GLU* 2.7 47.0 + - + +
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Residues in contact with LYS 111 (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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70B LEU* 4.0 30.3 - - + +
109B HIS* 3.3 20.8 + - + +
110B PRO* 1.3 78.9 - - - +
112B VAL* 1.3 60.0 + - - +
114B GLU* 4.1 5.8 - - - +
115B LYS* 3.5 21.7 + - - +
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Residues in contact with VAL 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 4.3 18.4 - - + +
66B PRO* 4.8 0.4 - - + +
69B ALA* 4.2 19.7 - - + -
70B LEU* 3.6 22.7 - - + -
73B LEU* 3.9 28.9 - - + +
103B VAL* 5.0 10.3 - - + -
109B HIS* 2.8 30.5 + - + +
111B LYS* 1.3 76.1 - - - +
113B CYS* 1.3 61.7 + - - +
114B GLU 3.3 0.2 - - - -
115B LYS* 3.2 3.5 + - - +
116B LEU* 2.9 28.8 + - + +
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Residues in contact with CYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B VAL* 3.8 30.3 - - - -
104B ILE* 4.3 19.2 - - + +
107B LYS* 4.3 11.0 - - - -
108B ALA 4.3 0.4 - - - -
109B HIS 2.8 32.8 + - - +
110B PRO* 3.7 6.7 - - + +
112B VAL* 1.3 80.0 - - - +
114B GLU* 1.3 57.8 + - + +
116B LEU* 3.2 8.8 + - - +
117B LYS* 2.9 39.2 + - - +
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Residues in contact with GLU 114 (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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110B PRO* 2.7 29.1 + - + +
111B LYS* 4.4 5.6 - - - +
113B CYS* 1.3 72.9 - - + +
115B LYS* 1.3 53.3 + - - +
117B LYS* 3.4 13.5 + - + +
118B SER* 2.7 31.7 + - - -
151B PRO* 4.6 3.7 - - - +
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Residues in contact with LYS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 4.0 24.0 - - + +
111B LYS 3.5 17.5 + - - +
112B VAL 3.2 5.2 + - - +
114B GLU* 1.3 76.2 - - - +
116B LEU* 1.3 64.4 + - - +
118B SER* 2.8 48.4 + - - -
119B LEU* 3.2 39.5 + - + +
122B GLU* 4.5 4.0 + - - -
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 6.1 2.7 - - + -
73B LEU* 4.5 17.7 - - + +
76B LEU* 5.1 6.3 - - + -
96B PHE* 5.0 11.4 - - + -
100B VAL* 4.0 48.5 - - + +
103B VAL* 4.3 20.6 - - + -
104B ILE* 4.2 8.5 - - + -
112B VAL* 2.9 17.5 + - + +
113B CYS* 3.2 7.4 + - - +
115B LYS* 1.3 75.3 - - - +
117B LYS* 1.3 65.1 + - - +
119B LEU* 3.3 15.6 + - + +
120B MET* 3.1 29.7 + - + +
123B TRP* 6.3 0.7 - - + -
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Residues in contact with LYS 117 (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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104B ILE* 3.6 33.1 - - + +
113B CYS* 2.9 30.4 + - - +
114B GLU* 3.6 14.6 - - + +
116B LEU* 1.3 75.5 - - - +
118B SER* 1.3 62.5 + - - +
120B MET* 3.2 6.0 + - - +
121B VAL* 3.0 25.8 + - - +
148B ILE* 3.8 12.5 - - - +
149B THR* 2.9 37.4 + - + +
150B PHE* 3.5 19.6 - - + -
151B PRO* 3.7 18.2 - - + -
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Residues in contact with SER 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU 2.7 17.9 + - - -
115B LYS* 2.8 29.7 + - - -
117B LYS* 1.3 75.7 - - - +
119B LEU* 1.3 60.8 + - - +
121B VAL* 3.1 6.0 + - - +
122B GLU* 2.9 34.3 + - - +
151B PRO* 3.8 17.9 - - - +
152B PRO 4.7 5.7 - - - +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 4.6 19.1 - - + +
76B LEU* 5.1 5.6 - - + -
77B GLY* 5.0 7.0 - - - -
115B LYS* 3.2 45.4 + - + +
116B LEU* 3.6 18.2 - - + +
118B SER* 1.3 75.8 - - - +
120B MET* 1.3 64.5 + - + +
122B GLU* 3.1 21.9 - - - +
123B TRP* 3.0 67.5 + - + +
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Residues in contact with MET 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PHE* 4.0 15.3 - - - -
97B ALA* 5.3 4.7 - - - -
100B VAL* 3.6 48.7 - - + -
116B LEU* 3.1 18.0 + - + +
117B LYS* 3.5 9.0 - - - +
119B LEU* 1.3 78.6 - - + +
121B VAL* 1.3 55.4 + - - +
123B TRP* 4.1 8.9 - - - +
124B SER* 2.7 32.9 + - - -
136B ILE* 3.7 37.8 - - + +
139B THR* 5.4 7.0 - - + -
140B ILE* 3.4 22.5 - - + +
143B MET* 5.7 2.2 - - - -
150B PHE* 4.1 5.8 - - + -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LYS 3.0 15.8 + - - +
118B SER* 3.1 6.3 + - - +
120B MET* 1.3 73.8 - - - +
122B GLU* 1.3 66.2 + - - +
124B SER* 3.0 19.6 + - - -
125B GLU* 3.4 8.2 + - + +
140B ILE* 4.1 8.3 - - + -
144B LYS* 6.2 0.2 - - - -
150B PHE* 3.5 25.6 - - + -
151B PRO* 3.2 32.5 - - + +
152B PRO* 3.6 18.6 - - + +
153B ALA* 3.9 6.3 - - + +
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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
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115B LYS* 4.5 2.9 + - - -
118B SER* 2.9 29.0 + - - +
119B LEU* 3.1 36.8 - - - +
121B VAL* 1.3 74.0 - - - +
123B TRP* 1.3 70.1 + - + +
124B SER 3.2 0.3 + - - -
125B GLU* 3.3 11.8 + - + +
126B GLU* 2.9 34.3 + - + +
153B ALA* 4.1 22.5 - - + +
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Residues in contact with TRP 123 (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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76B LEU* 4.3 17.7 - - + -
77B GLY* 4.1 8.7 + - - -
80B VAL* 3.7 37.4 - - + +
91B VAL* 3.6 29.2 - - + -
96B PHE* 4.4 17.7 - + - -
116B LEU* 6.3 1.1 - - + -
119B LEU* 3.0 51.0 + - + +
120B MET* 4.2 10.3 - - - +
122B GLU* 1.3 95.4 + - + +
124B SER* 1.3 60.6 + - - +
126B GLU* 4.1 1.3 - - + -
127B PHE* 3.3 47.8 + + + +
133B PHE* 3.5 20.5 - + + -
136B ILE* 5.2 2.9 - - + -
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Residues in contact with SER 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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120B MET 2.7 18.5 + - - -
121B VAL* 3.0 14.8 + - - -
123B TRP* 1.3 79.4 - - - +
125B GLU* 1.3 55.8 - - - +
127B PHE 4.1 0.8 - - - -
128B GLN* 3.1 26.0 + - - +
133B PHE* 5.3 0.9 - - - -
136B ILE* 3.2 20.4 - - - +
137B SER* 3.6 30.9 + - - -
140B ILE* 3.5 9.6 - - - +
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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 VAL* 3.4 4.5 + - + +
122B GLU* 3.3 11.3 - - - +
124B SER* 1.3 79.5 - - - +
126B GLU* 1.3 86.3 + - - +
127B PHE 3.2 1.8 - - - -
128B GLN* 3.2 36.5 - - - +
129B LYS* 6.1 0.2 - - - -
153B ALA* 3.7 30.6 - - + +
155B SER* 5.1 8.7 - - - -
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Residues in contact with GLU 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* 2.9 20.7 + - + +
123B TRP* 5.6 1.1 - - + -
125B GLU* 1.3 92.3 - - - +
127B PHE* 1.3 88.2 + - + +
128B GLN 3.6 0.4 - - - -
129B LYS* 5.0 11.0 - - - -
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Residues in contact with PHE 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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80B VAL* 4.7 6.3 - - + -
81B ALA* 6.0 4.3 - - + -
88B HIS* 3.4 36.3 - + - -
123B TRP* 3.3 50.3 + + + +
124B SER 4.1 2.9 - - - -
125B GLU 3.2 0.2 - - - -
126B GLU* 1.3 102.0 - - + +
128B GLN* 1.3 58.8 + - - +
129B LYS* 3.0 8.0 + - - +
130B ASP* 3.2 17.8 + - + +
133B PHE* 3.3 44.8 - + + +
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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
------------------------------------------------------------
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