Contacts of the helix formed by residues 94 - 117 (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 THR 94 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B LYS* 2.7 32.9 + - + +
76B LEU 3.1 7.5 + - - -
77B ILE 3.8 21.8 - - - +
78B TYR* 4.0 15.7 - - + -
92B GLY 3.9 0.4 + - - -
93B LEU* 1.3 75.8 - - - +
95B THR* 1.3 60.1 + - - +
96B SER* 2.9 13.1 + - - -
97B GLY 3.0 6.1 + - - -
98B ILE* 2.9 30.6 + - - +
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Residues in contact with THR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B THR* 1.3 72.7 - - - +
96B SER* 1.3 63.3 + - - +
98B ILE* 3.4 10.6 + - - +
99B LYS* 3.1 47.7 + - + +
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Residues in contact with SER 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LYS 4.6 2.1 + - - -
75B LYS 3.0 13.9 + - - -
76B LEU* 3.6 14.3 - - - +
94B THR* 2.9 19.6 + - - -
95B THR* 1.3 78.5 - - - +
97B GLY* 1.3 57.0 + - - +
99B LYS* 3.4 9.8 + - - +
100B LEU* 2.9 30.1 + - - +
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Residues in contact with GLY 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.9 2.4 - - - +
76B LEU* 3.4 33.6 - - - +
93B LEU* 4.2 10.7 - - - +
94B THR* 3.0 12.8 + - - -
96B SER* 1.3 73.5 + - - +
98B ILE* 1.3 66.1 + - - +
100B LEU* 3.3 3.3 + - - +
101B VAL* 3.1 28.8 + - - +
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TYR* 4.0 11.6 - - + -
44B GLN* 4.3 14.8 - - - +
93B LEU* 3.8 27.3 - - + +
94B THR 2.9 22.4 + - - +
95B THR* 3.7 8.5 - - - +
97B GLY* 1.3 75.2 - - - +
99B LYS* 1.3 66.3 + - + +
101B VAL* 3.3 3.6 + - - +
102B GLU* 3.1 45.5 + - - +
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Residues in contact with LYS 99 (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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95B THR* 3.1 41.7 + - + +
96B SER* 3.7 7.4 - - - +
97B GLY 3.3 0.2 - - - -
98B ILE* 1.3 81.9 - - + +
100B LEU* 1.3 56.5 + - - +
102B GLU* 3.5 9.6 + - - +
103B ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 3.8 42.5 - - + +
29B ILE* 3.9 29.3 - - + +
37B LEU* 4.0 6.7 - - + -
76B LEU* 3.7 34.5 - - + -
96B SER 2.9 17.0 + - - +
97B GLY 3.8 5.8 - - - +
98B ILE 3.2 0.4 - - - -
99B LYS* 1.3 75.1 - - - +
101B VAL* 1.3 61.5 + - - +
103B ALA* 3.2 4.9 + - + +
104B PHE* 2.9 28.6 + - - +
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLY 5.4 0.4 - - - +
37B LEU* 3.5 42.0 - - + +
38B GLY* 4.2 9.0 - - - +
41B TYR* 3.7 35.9 - - + -
93B LEU* 4.4 1.8 - - + -
97B GLY 3.1 14.8 + - - +
98B ILE 3.7 7.0 - - - +
100B LEU* 1.3 75.3 - - - +
102B GLU* 1.3 58.7 + - - +
104B PHE* 3.2 7.4 + - + +
105B THR* 3.0 40.4 + - - +
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B TYR* 2.6 37.3 + - + +
98B ILE* 3.1 29.4 + - - +
99B LYS* 3.9 8.5 - - - +
101B VAL* 1.3 75.7 - - - +
103B ALA* 1.3 57.3 + - - +
105B THR* 3.5 7.7 + - - -
106B SER* 3.0 28.8 + - - -
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Residues in contact with ALA 103 (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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23B LYS* 3.4 16.9 - - - +
27B LEU* 4.3 17.0 - - + -
99B LYS 2.9 20.0 + - - +
100B LEU* 3.6 7.9 - - + +
102B GLU* 1.3 76.3 - - - +
104B PHE* 1.3 64.5 + - - +
106B SER* 2.7 25.3 + - - -
107B ILE 3.9 0.2 + - - -
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Residues in contact with PHE 104 (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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20B ALA* 3.2 42.8 - - + -
23B LYS* 4.0 12.8 - - + -
24B LEU* 3.6 34.5 - - + -
27B LEU* 3.9 14.3 - - + +
29B ILE* 5.6 2.2 - - + -
34B GLY* 6.4 0.9 - - - -
100B LEU 2.9 13.6 + - - +
101B VAL* 3.8 8.5 - - + +
103B ALA* 1.3 75.1 - - - +
105B THR* 1.3 71.6 + - - +
107B ILE* 3.0 30.7 + - + +
108B PHE* 4.2 20.4 - + - -
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Residues in contact with THR 105 (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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101B VAL* 3.0 25.1 + - - +
102B GLU* 3.7 8.1 - - - -
104B PHE* 1.3 86.5 - - - +
106B SER* 1.3 58.5 + - - +
107B ILE 3.0 6.1 + - - -
108B PHE* 3.3 29.6 + - + +
109B ASP* 4.4 2.1 + - - +
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Residues in contact with SER 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LYS* 4.7 6.2 + - - -
102B GLU 3.0 15.9 + - - -
103B ALA* 2.7 20.9 + - - -
104B PHE 3.1 0.2 - - - -
105B THR* 1.3 75.1 - - - +
107B ILE* 1.3 61.3 + - - +
108B PHE 3.2 0.8 + - - -
109B ASP* 3.4 12.5 + - - +
110B GLU* 3.0 27.2 + - - +
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Residues in contact with ILE 107 (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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19B LYS* 4.0 36.3 - - - +
20B ALA* 4.3 4.9 - - - -
23B LYS* 4.1 26.9 - - + -
103B ALA 3.9 0.6 + - - -
104B PHE* 3.0 33.8 + - + +
105B THR 3.0 1.4 + - - -
106B SER* 1.3 79.9 + - - +
108B PHE* 1.3 83.0 + - + +
110B GLU* 3.6 28.1 - - + +
111B MET* 2.9 37.6 + - + +
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Residues in contact with PHE 108 (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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6A SER* 4.5 7.9 + - - +
16B MET 5.1 1.3 - - - -
20B ALA* 4.3 11.4 - - + -
104B PHE* 4.2 25.4 - + - -
105B THR* 3.3 28.9 + - + +
106B SER 3.2 0.6 - - - -
107B ILE* 1.3 88.9 - - + +
109B ASP* 1.3 69.2 + - - +
111B MET* 3.3 27.5 + - + +
112B GLU* 3.0 22.2 + - - +
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Residues in contact with ASP 109 (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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105B THR 4.4 1.2 + - - +
106B SER* 3.4 14.3 + - - +
108B PHE* 1.3 79.6 - - - +
110B GLU* 1.3 62.7 + - - +
112B GLU* 3.3 8.5 + - - +
113B GLN* 3.0 30.8 + - + +
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Residues in contact with GLU 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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19B LYS* 4.7 10.5 + - - -
23B LYS* 4.6 10.7 + - - -
106B SER* 3.0 21.1 + - - +
107B ILE* 3.6 26.3 - - + +
109B ASP* 1.3 77.4 - - - +
111B MET* 1.3 63.8 + - + +
113B GLN* 3.3 7.9 + - - +
114B THR* 3.0 30.2 + - - +
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Residues in contact with MET 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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6A SER* 5.4 2.0 - - - +
138A LEU* 4.1 14.3 - - + +
16B MET* 3.7 49.6 - - + +
19B LYS* 3.6 36.6 - - + -
20B ALA 5.1 0.2 - - - +
107B ILE* 2.9 27.8 + - + +
108B PHE* 3.7 35.0 - - + +
110B GLU* 1.3 73.7 - - + +
112B GLU* 1.3 60.2 + - - +
114B THR* 3.2 9.1 + - - -
115B LEU* 2.9 35.9 + - + +
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Residues in contact with GLU 112 (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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4A THR* 3.4 24.4 - - + +
5A TYR* 2.9 34.3 + - - +
6A SER* 2.6 42.7 + - - +
108B PHE 3.0 13.1 + - - +
109B ASP* 3.5 12.1 - - - +
111B MET* 1.3 76.2 - - - +
113B GLN* 1.3 69.5 + - - +
115B LEU* 3.3 4.3 + - - +
116B VAL* 2.9 43.3 + - + +
128B LYS* 3.9 3.8 + - - -
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Residues in contact with GLN 113 (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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109B ASP* 3.0 21.0 + - + +
110B GLU* 3.8 6.5 - - - +
111B MET 3.2 0.2 - - - -
112B GLU* 1.3 87.6 + - - +
114B THR* 1.3 64.4 + - - +
116B VAL* 3.9 16.3 - - - +
117B SER* 3.0 26.9 + - - -
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Residues in contact with THR 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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137A SER* 3.6 37.7 - - - +
138A LEU* 4.7 7.6 - - + -
110B GLU* 3.0 21.0 + - - +
111B MET* 3.2 11.7 + - - -
113B GLN* 1.3 75.0 - - - +
115B LEU* 1.3 61.4 + - - +
117B SER* 2.9 21.7 + - - +
118B GLN* 2.9 20.8 + - - +
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Residues in contact with LEU 115 (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* 3.9 35.4 - - + -
6A SER* 4.6 2.0 - - - +
9A PHE* 4.0 13.2 - - + -
134A MET* 3.7 52.2 - - + +
137A SER* 4.1 2.0 - - - +
138A LEU* 4.0 18.8 - - + -
12B ILE* 5.9 0.4 - - + -
16B MET* 4.4 20.2 - - - -
111B MET 2.9 22.0 + - - +
112B GLU* 3.5 11.2 - - - +
114B THR* 1.3 76.7 - - - +
116B VAL* 1.3 63.2 + - - +
118B GLN* 3.2 21.6 + - - +
119B LEU 4.4 0.5 + - - -
124B ASN* 4.6 0.3 - - - +
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Residues in contact with VAL 116 (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* 4.1 10.5 - - + -
112B GLU* 2.9 40.9 + - + +
113B GLN* 3.9 18.2 - - - +
115B LEU* 1.3 76.3 - - - +
117B SER* 1.3 60.2 + - - +
118B GLN 3.2 1.0 + - - -
119B LEU 3.1 11.8 + - - +
124B ASN* 3.0 41.9 + - + +
128B LYS* 4.8 6.7 - - - +
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Residues in contact with SER 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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113B GLN 3.0 15.9 + - - -
114B THR* 2.9 20.3 + - - +
115B LEU 3.2 0.2 - - - -
116B VAL* 1.3 74.3 - - - +
118B GLN* 1.3 70.1 + - - +
119B LEU 3.2 5.0 + - - +
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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