Contacts of the helix formed by residues 111 - 128 (chain B) in PDB entry 4TXQ
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 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B TYR* 3.3 26.5 - - - -
104B GLU* 2.7 26.6 + - - +
109B ARG* 3.6 21.4 + - + -
110B PHE* 1.3 76.1 - - - +
112B LYS* 1.3 67.0 + - - +
113B ASN* 3.1 12.9 + - + +
114B MET* 3.2 38.0 + - + +
115B ILE* 3.1 27.0 + - - +
156B LEU* 3.9 8.4 - - - +
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Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B HIS* 1.3 73.8 - - - +
113B ASN* 1.3 56.6 + - - +
115B ILE* 3.5 15.6 - - + +
116B LYS* 2.8 31.8 + - - +
153B HIS* 6.2 3.6 - - - +
156B LEU* 4.9 2.6 - - + +
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Residues in contact with ASN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B TYR* 3.9 14.6 + - - -
111B HIS* 3.1 16.7 + - + +
112B LYS* 1.3 79.5 - - - +
114B MET* 1.3 58.3 + - - +
116B LYS* 3.3 10.0 + - - +
117B SER* 3.0 32.2 + - - -
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Residues in contact with MET 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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100B TYR* 3.9 10.1 - - - -
101B ALA* 3.3 25.5 - - - +
104B GLU* 3.8 15.5 - - + -
105B ASP* 3.6 23.1 - - + +
109B ARG 3.8 13.0 - - - +
110B PHE* 4.0 5.2 - - + -
111B HIS* 3.2 35.1 + - + +
113B ASN* 1.3 76.9 - - - +
115B ILE* 1.3 69.9 + - - +
117B SER* 4.3 1.3 - - - -
118B PHE* 3.1 53.8 + - + -
152B ILE* 3.6 25.1 - - + -
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Residues in contact with ILE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B HIS 3.1 17.9 + - - +
112B LYS* 3.5 15.3 - - + +
114B MET* 1.3 86.9 - - + +
116B LYS* 1.3 60.0 + - - +
118B PHE* 3.4 2.0 + - - -
119B TYR* 3.0 27.2 + - + +
149B ALA* 3.6 29.2 - - + +
152B ILE* 3.8 21.5 - - + -
153B HIS* 3.7 39.9 - - + +
156B LEU* 3.8 20.2 - - + -
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Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLU* 3.5 34.3 + - - -
112B LYS 2.8 16.2 + - - +
113B ASN* 3.6 11.0 - - - +
115B ILE* 1.3 79.8 - - + +
117B SER* 1.3 52.5 + - - +
119B TYR* 3.2 7.5 + - + +
120B THR* 2.8 52.1 + - - +
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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
----------------------------------------------------------
97B MET* 3.6 39.1 - - - +
100B TYR* 3.3 23.1 - - - -
101B ALA* 3.8 2.7 - - - -
113B ASN* 3.0 21.3 + - - -
114B MET 3.8 4.3 - - - -
115B ILE 3.3 0.2 - - - -
116B LYS* 1.3 73.2 - - - +
118B PHE* 1.3 65.8 + - - +
120B THR* 4.6 0.2 - - - -
121B ALA* 3.0 25.5 + - - +
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Residues in contact with PHE 118 (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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98B PHE* 4.2 12.8 - + - +
101B ALA* 3.6 13.6 - - + +
102B ASP* 3.6 26.2 - - + -
105B ASP* 4.3 4.5 - - + -
114B MET* 3.1 52.5 + - + -
115B ILE* 3.7 7.2 - - - +
117B SER* 1.3 75.5 - - - +
119B TYR* 1.3 63.6 + - - +
121B ALA* 3.5 1.6 + - - +
122B SER* 3.2 17.5 + - - -
144B TYR* 4.2 13.2 - + - -
145B ALA* 3.3 43.9 - - + +
148B LYS* 3.6 37.9 - - + -
149B ALA* 4.0 5.6 - - + -
152B ILE* 4.1 5.8 - - + -
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Residues in contact with TYR 119 (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 HIS* 2.6 39.8 + + - -
115B ILE* 3.0 18.8 + - + +
116B LYS* 3.2 7.8 + - + +
118B PHE* 1.3 76.9 - - - +
120B THR* 1.3 60.9 + - - +
122B SER* 2.6 27.4 + - - -
123B LEU* 3.0 39.8 + - + +
145B ALA 4.8 0.4 - - - -
146B ARG* 4.0 28.7 + - + -
149B ALA* 3.7 17.0 - - + -
150B THR* 5.7 2.5 - - - -
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Residues in contact with THR 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B THR* 4.3 23.4 + - + +
27B HIS* 4.9 6.3 - - + -
97B MET* 3.6 28.5 - - + -
116B LYS* 2.8 40.9 + - - +
119B TYR* 1.3 71.0 - - - +
121B ALA* 1.3 59.8 + - - +
123B LEU* 3.1 13.0 + - - +
124B LEU* 2.9 34.9 + - + +
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Residues in contact with ALA 121 (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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94B ALA* 3.9 14.7 - - + +
97B MET* 3.6 18.5 - - + -
98B PHE* 4.3 15.0 - - + +
117B SER 3.0 20.1 + - - +
118B PHE* 3.6 5.8 - - - +
120B THR* 1.3 77.0 - - - +
122B SER* 1.3 61.4 + - - +
124B LEU* 3.4 8.6 + - - +
125B ILE* 3.1 31.3 + - + +
145B ALA* 4.7 5.8 - - + -
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Residues in contact with SER 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PHE 3.2 10.3 + - - -
119B TYR* 2.6 25.3 + - - -
121B ALA* 1.3 79.4 - - - +
123B LEU* 1.3 60.7 + - - +
125B ILE* 3.4 9.1 + - - +
126B ASP* 3.2 16.3 + - - -
142B ARG* 3.8 30.2 - - - +
145B ALA* 4.4 2.2 - - - +
146B ARG* 3.3 42.1 + - - +
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B HIS* 3.8 15.7 - - + +
20B HIS* 3.5 33.0 - - + +
23B THR* 3.5 27.4 - - + +
119B TYR* 3.0 54.7 + - + +
120B THR* 3.1 13.7 + - + +
122B SER* 1.3 80.0 + - - +
124B LEU* 1.3 64.8 + - + +
126B ASP* 3.1 10.9 + - - +
127B VAL* 3.0 24.7 + - + +
146B ARG* 4.0 11.0 - - - +
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Residues in contact with LEU 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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23B THR* 4.7 7.9 - - + -
34B VAL* 4.0 26.7 - - + -
38B CYS* 4.4 12.1 - - - -
90B LEU* 4.8 13.4 - - + +
93B TYR* 3.6 28.3 - - + -
94B ALA* 3.8 25.4 - - + +
97B MET* 3.7 20.4 - - + -
120B THR* 2.9 22.4 + - + +
121B ALA 3.6 4.7 - - - +
123B LEU* 1.3 75.1 - - - +
125B ILE* 1.3 56.3 + - - +
127B VAL* 3.1 8.7 + - + +
128B ILE* 3.0 35.6 + - + +
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Residues in contact with ILE 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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94B ALA* 4.7 8.3 - - + -
98B PHE* 6.2 1.1 - - + -
121B ALA* 3.1 20.8 + - + +
122B SER 3.6 7.0 - - - +
123B LEU 3.2 0.2 - - - -
124B LEU* 1.3 74.9 - - - +
126B ASP* 1.3 67.3 + - - +
128B ILE* 3.3 21.0 + - + +
129B THR* 3.9 0.7 - - - +
134B LEU* 3.6 27.8 - - + +
138B ASN* 3.6 34.5 - - + +
141B HIS* 4.0 13.7 - - + +
142B ARG* 3.6 41.5 - - + +
145B ALA* 5.8 0.7 - - + -
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Residues in contact with ASP 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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20B HIS* 2.8 32.1 + - + +
41B TYR* 3.3 19.4 - - + -
122B SER 3.2 4.4 + - - +
123B LEU* 3.1 9.4 + - - +
125B ILE* 1.3 74.5 - - - +
127B VAL* 1.3 58.2 + - - +
129B THR* 2.6 33.3 + - - +
142B ARG* 2.9 36.1 + - - +
146B ARG* 2.8 29.7 + - - -
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B HIS* 4.1 13.5 - - + -
37B TYR* 3.4 29.4 - - + +
38B CYS* 3.8 24.9 - - - +
41B TYR* 3.9 19.1 - - + -
90B LEU* 3.5 24.2 - - + -
123B LEU* 3.0 15.6 + - + +
124B LEU* 3.1 12.0 + - + +
126B ASP* 1.3 75.9 - - - +
128B ILE* 1.3 57.2 + - - +
129B THR 3.0 5.2 + - - -
130B VAL* 3.0 25.3 + - - +
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Residues in contact with ILE 128 (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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87B CYS* 4.5 14.6 - - - +
90B LEU* 3.8 23.6 - - + +
91B GLU* 3.8 40.4 - - + +
94B ALA* 4.6 3.8 - - + -
124B LEU 3.0 22.1 + - - +
125B ILE* 3.6 21.3 - - + +
126B ASP 3.2 0.8 - - - -
127B VAL* 1.3 74.6 - - - +
129B THR* 1.3 61.8 + - - +
130B VAL 3.1 0.4 - - - -
131B PHE* 3.0 26.9 + - + +
132B GLY 4.0 3.5 - - - +
134B LEU* 3.9 15.3 - - + -
138B ASN* 4.0 13.9 - - - +
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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