Contacts of the helix formed by residues 119 - 137 (chain B) in PDB entry 4XZC
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 GLU 119 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B VAL 3.7 5.6 + - - +
118B PRO* 1.3 77.5 - - - +
120B PRO* 1.3 83.9 - - + +
121B GLU* 3.2 19.5 - - + +
122B GLN* 3.1 35.3 + - + +
123B LEU* 3.2 12.7 + - - +
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Residues in contact with PRO 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PRO 4.6 0.9 - - - +
119B GLU* 1.3 100.6 - - + +
121B GLU* 1.3 66.7 + - - +
123B LEU* 3.4 16.6 - - + +
124B VAL* 3.2 31.1 + - + +
293B LYS 5.2 10.3 - - - +
299B ARG* 6.0 6.1 - - + -
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 4.2 16.6 - - + -
119B GLU* 3.4 25.3 - - + +
120B PRO* 1.3 84.4 - - - +
122B GLN* 1.3 61.2 + - + +
123B LEU 3.1 1.6 - - - -
124B VAL* 3.6 7.0 - - - +
125B ALA* 2.6 39.6 + - - +
128B ARG* 5.2 0.5 + - - -
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Residues in contact with GLN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 3.2 45.7 + - + +
106B TRP* 3.9 10.9 - - + +
109B LYS* 3.4 25.9 - - - +
113B LEU* 3.4 20.3 - - - +
117B VAL 4.7 0.7 - - - +
118B PRO* 4.4 2.2 - - + -
119B GLU* 3.1 42.8 + - + +
121B GLU* 1.3 78.4 - - + +
123B LEU* 1.3 56.3 + - - +
125B ALA* 3.7 1.6 - - - +
126B TYR* 3.0 23.0 + - - +
377B HIS* 3.2 21.9 + - + -
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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
----------------------------------------------------------
118B PRO* 3.5 20.9 - - + +
119B GLU 3.2 10.5 + - - +
120B PRO* 3.4 19.7 - - + +
121B GLU 3.1 0.4 - - - -
122B GLN* 1.3 75.3 - - - +
124B VAL* 1.3 65.2 + - + +
126B TYR* 3.1 4.5 + - - +
127B GLN* 3.1 27.6 + - - +
298B LEU 5.4 0.2 - - - +
299B ARG* 4.0 32.8 - - + +
302B GLY* 3.6 35.3 - - - +
303B ALA* 3.8 6.1 - - + -
377B HIS* 3.5 22.9 - - - +
378B PRO* 3.6 11.2 - - + -
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PRO* 3.2 16.1 + - + +
121B GLU* 3.1 7.9 + - - +
123B LEU* 1.3 77.4 - - + +
125B ALA* 1.3 62.6 + - - +
127B GLN* 3.2 16.0 + - - +
128B ARG* 3.2 43.4 + - + +
302B GLY* 6.0 1.1 - - - -
471B TYR* 4.0 20.2 - - + +
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Residues in contact with ALA 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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102B VAL* 4.1 9.3 - - - +
105B LEU* 3.6 33.9 - - + -
106B TRP* 3.3 7.7 - - + -
121B GLU 2.6 22.5 + - - +
122B GLN 3.7 4.0 - - - +
124B VAL* 1.3 74.2 - - - +
126B TYR* 1.3 59.5 + - - +
128B ARG* 3.9 14.8 - - - +
129B ALA* 3.2 24.6 + - - +
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Residues in contact with TYR 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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106B TRP* 3.3 23.1 - + + -
122B GLN 3.0 15.5 + - - +
123B LEU 3.1 6.7 + - - +
125B ALA* 1.3 77.4 - - - +
127B GLN* 1.3 87.6 + - - +
129B ALA* 3.5 2.6 - - - +
130B ALA* 3.0 25.2 + - + +
304B GLN 3.9 5.6 - - - -
305B ILE* 3.9 1.6 - - - -
306B ASP* 3.1 22.2 + - + +
309B PHE* 3.4 34.7 - + - -
310B SER* 2.5 28.2 + - - -
313B TYR* 6.1 0.4 - + - -
377B HIS* 3.5 22.4 - - + +
378B PRO* 3.5 20.2 - - + -
379B GLY* 3.9 13.7 - - - -
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Residues in contact with GLN 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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123B LEU 3.1 13.2 + - - +
124B VAL 3.2 5.8 + - - +
126B TYR* 1.3 95.9 - - - +
128B ARG* 1.3 62.5 + - - +
130B ALA* 3.2 8.3 + - - +
131B GLN* 3.0 30.3 + - - +
302B GLY 2.8 25.8 + - - +
304B GLN* 3.3 23.2 + - - +
306B ASP* 5.7 0.3 - - - +
469B ASN* 4.5 8.0 + - - -
471B TYR* 3.4 61.9 - - + +
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Residues in contact with ARG 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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102B VAL* 5.0 2.5 - - + -
121B GLU 5.2 0.4 + - - -
124B VAL* 3.2 46.9 + - + +
125B ALA* 3.9 11.2 - - - +
127B GLN* 1.3 78.1 - - + +
129B ALA* 1.3 56.8 + - - +
131B GLN* 2.9 14.5 + - + +
132B LYS* 2.7 36.0 + - - +
471B TYR* 5.4 5.4 - - + -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B TRP* 3.8 2.6 - - + -
102B VAL* 3.7 26.3 - - + +
103B ILE* 4.3 4.7 - - + -
106B TRP* 3.3 26.9 - - + -
125B ALA 3.2 22.1 + - - +
126B TYR 3.5 1.6 - - - +
127B GLN 3.3 0.2 - - - -
128B ARG* 1.3 75.5 - - - +
130B ALA* 1.3 57.2 + - - +
132B LYS* 3.0 3.3 + - - +
133B TRP* 2.8 30.1 + - - +
309B PHE* 3.9 7.6 - - + -
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TYR* 3.0 13.0 + - + +
127B GLN* 3.2 13.2 - - - +
129B ALA* 1.3 80.3 - - - +
131B GLN* 1.3 56.7 + - - +
133B TRP* 3.7 2.4 - - - +
134B ARG* 2.9 30.2 + - - +
306B ASP* 3.6 29.0 - - + +
309B PHE* 3.5 29.7 - - + -
469B ASN* 4.9 4.3 - - - +
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Residues in contact with GLN 131 (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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127B GLN 3.0 19.6 + - - +
128B ARG* 2.9 19.7 + - + +
130B ALA* 1.3 77.4 - - - +
132B LYS* 1.3 54.1 + - - +
134B ARG* 3.4 6.7 + - - +
135B GLN* 2.8 38.4 + - - +
147B SER* 3.1 18.8 + - - -
469B ASN* 3.0 36.9 + - - +
471B TYR* 4.0 16.3 - - + +
472B LYS* 3.8 29.4 - - - +
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Residues in contact with LYS 132 (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 TRP* 4.1 2.9 - - + -
99B ASN* 2.8 27.4 + - - +
102B VAL* 3.5 29.4 - - + -
128B ARG 2.7 11.8 + - - +
129B ALA* 3.4 9.4 - - - +
131B GLN* 1.3 75.6 - - - +
133B TRP* 1.3 56.7 + - - +
135B GLN* 2.9 7.3 + - + +
136B ASP* 2.6 75.0 + - - +
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Residues in contact with TRP 133 (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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88B MET* 4.2 7.9 - - - -
92B GLY* 3.2 22.0 + - - -
95B TRP* 3.3 27.2 - + + +
96B PHE* 3.5 27.3 - + - -
129B ALA 2.8 18.7 + - - +
130B ALA 3.7 2.2 - - - +
132B LYS* 1.3 72.2 - - - +
134B ARG* 1.3 73.5 + - + +
137B ASN* 3.0 51.6 + - - +
139B PHE* 3.8 40.2 - + + -
308B ILE* 3.9 21.3 - - + -
309B PHE* 3.6 24.7 - + + -
312B TYR* 3.3 36.9 - + + +
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Residues in contact with ARG 134 (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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130B ALA 2.9 17.1 + - - +
131B GLN* 3.4 8.9 - - - +
133B TRP* 1.3 88.8 - - + +
135B GLN* 1.3 62.2 - - - +
138B LYS* 3.4 2.1 + - - -
139B PHE* 3.1 43.5 + - + -
140B GLU* 3.2 37.3 + - + +
145B THR 3.4 13.9 + - - -
146B ARG 4.0 1.2 + - - -
147B SER* 3.6 9.0 - - - -
306B ASP* 2.4 46.6 + - - -
308B ILE* 3.8 10.4 - - - +
467B PHE 3.0 27.3 + - - -
468B GLN 4.3 1.2 - - - -
469B ASN* 3.5 25.7 - - - +
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Residues in contact with GLN 135 (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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131B GLN* 2.8 22.1 + - - +
132B LYS* 2.9 10.1 + - + +
134B ARG* 1.3 74.7 - - - +
136B ASP* 1.3 70.3 + - - +
138B LYS* 3.2 16.1 + - - +
140B GLU* 6.1 0.7 - - - -
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Residues in contact with ASP 136 (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 TRP* 2.6 31.2 + - + +
99B ASN* 3.9 0.4 + - - -
132B LYS* 2.6 53.8 + - - +
135B GLN* 1.3 73.1 - - - +
137B ASN* 1.3 60.1 + - - +
138B LYS* 2.9 21.1 + - - +
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Residues in contact with ASN 137 (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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82B TRP* 4.9 0.5 - - - -
88B MET* 3.5 30.1 - - - +
91B ASN* 3.2 40.6 + - + +
92B GLY* 3.8 3.7 - - - -
95B TRP* 3.8 14.6 - - - +
133B TRP* 3.0 60.5 + - + +
136B ASP* 1.3 74.0 - - - +
138B LYS* 1.3 71.0 + - - +
139B PHE 3.2 2.7 + - - +
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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