Contacts of the helix formed by residues 126 - 149 (chain B) in PDB entry 4I7Z
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 ARG 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A TYR* 2.8 48.5 + - - -
106A LEU* 4.3 4.6 - - - +
108A GLY* 3.4 13.8 - - - +
110A PHE* 4.2 4.1 - - - -
111A LYS* 3.8 20.4 - - - +
115B GLU* 3.1 24.5 + - - -
118B ASN* 3.6 13.7 - - - +
120B PHE* 3.6 11.6 + - + -
121B GLN 2.9 28.4 + - - -
122B ASN 3.4 10.5 + - - +
123B PRO* 3.0 11.6 + - + +
124B PHE 3.2 1.2 - - - -
125B ARG* 1.3 82.2 - - - +
127B PRO* 1.3 59.6 - - - +
128B VAL* 3.5 2.2 - - - -
129B ALA* 3.9 10.1 + - + +
130B THR* 2.6 35.4 + - - -
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Residues in contact with PRO 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PRO 3.9 2.2 - - - +
124B PHE* 4.6 8.3 - - - +
125B ARG 4.1 4.3 - - - +
126B ARG* 1.3 86.0 - - - +
128B VAL* 1.3 69.2 + - + +
130B THR* 3.8 7.3 - - - -
131B THR* 2.5 40.8 + - - +
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ARG 3.5 0.4 - - - -
127B PRO* 1.3 82.5 - - + +
129B ALA* 1.3 67.3 + - - +
131B THR* 3.1 7.2 + - - -
132B ILE* 2.9 45.5 + - + +
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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
----------------------------------------------------------
105A TYR* 3.4 22.1 + - - +
115B GLU* 3.5 22.7 - - + +
126B ARG* 3.9 19.6 + - + +
128B VAL* 1.3 79.7 - - - +
130B THR* 1.3 53.0 + - - +
132B ILE* 3.2 11.7 + - - +
133B PHE* 2.8 35.2 + - - +
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Residues in contact with THR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A TYR* 5.2 3.1 - - - -
106A LEU* 5.2 6.1 - - + +
123B PRO* 2.9 33.8 + - + +
126B ARG* 2.6 25.3 + - - +
127B PRO* 3.8 6.7 - - - -
128B VAL 3.2 0.2 - - - -
129B ALA* 1.3 78.9 - - - +
131B THR* 1.3 57.2 + - - +
133B PHE* 3.2 6.8 + - - +
134B LEU* 2.9 50.2 + - + +
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Residues in contact with THR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B PRO* 2.5 28.2 + - - +
128B VAL* 3.1 6.7 + - - -
130B THR* 1.3 77.1 - - - +
132B ILE* 1.3 59.9 + - + +
134B LEU* 3.3 6.9 + - - +
135B PHE* 2.8 34.6 + - + +
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 2.9 38.2 + - + +
129B ALA* 3.6 9.9 - - - +
131B THR* 1.3 77.7 - - + +
133B PHE* 1.3 57.9 + - - +
135B PHE* 3.5 11.7 + - + +
136B GLY* 2.8 26.0 + - - -
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Residues in contact with PHE 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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101A VAL* 6.3 1.8 - - + -
102A PHE* 3.8 32.8 - + - -
105A TYR* 3.6 37.5 - + + -
106A LEU* 3.7 37.9 - - + -
129B ALA 2.8 20.6 + - - +
130B THR* 3.5 4.7 - - - +
132B ILE* 1.3 71.0 - - - +
134B LEU* 1.3 80.4 + - + +
136B GLY* 3.2 2.6 + - - -
137B THR* 2.9 49.2 + - + -
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 5.3 4.0 - - + -
130B THR* 2.9 36.5 + - + +
131B THR* 3.8 5.8 - - - +
133B PHE* 1.3 97.0 - - + +
135B PHE* 1.3 58.0 + - - +
137B THR* 3.2 7.7 + - - +
138B LEU* 2.8 32.3 + - - +
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Residues in contact with PHE 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 THR* 2.8 21.9 + - + +
132B ILE* 3.5 12.3 - - + +
134B LEU* 1.3 74.6 - - - +
136B GLY* 1.3 61.4 + - - +
138B LEU* 3.1 12.4 + - + +
139B VAL* 2.8 56.9 + - + +
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Residues in contact with GLY 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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132B ILE 2.8 18.3 + - - -
133B PHE* 3.2 3.8 + - - -
135B PHE* 1.3 78.8 - - - +
137B THR* 1.3 49.6 + - - +
139B VAL* 3.2 6.9 + - - +
140B THR* 2.7 42.5 + - - -
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Residues in contact with THR 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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102A PHE* 4.7 19.2 - - + -
133B PHE* 2.9 41.6 + - + -
134B LEU* 3.5 10.8 - - - -
136B GLY* 1.3 71.5 - - - +
138B LEU* 1.3 59.5 + - + +
140B THR* 3.1 8.4 + - - -
141B ILE* 2.9 48.3 + - + +
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Residues in contact with LEU 138 (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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134B LEU 2.8 17.4 + - - +
135B PHE* 3.5 10.8 - - + +
137B THR* 1.3 77.5 - - + +
139B VAL* 1.3 58.8 + - + +
141B ILE* 3.4 9.8 + - + +
142B TRP* 2.8 32.4 + - + +
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PHE* 2.8 52.7 + - + +
136B GLY* 3.6 6.1 - - - +
138B LEU* 1.3 76.5 - - + +
140B THR* 1.3 57.7 + - - +
142B TRP* 3.4 16.5 + - + +
143B LEU* 2.9 48.3 + - + +
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Residues in contact with THR 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PRO* 3.7 26.7 - - + +
136B GLY 2.7 22.9 + - - -
137B THR* 3.1 11.9 + - - -
139B VAL* 1.3 78.4 - - - +
141B ILE* 1.3 60.6 + - + +
143B LEU* 3.2 8.0 + - - +
144B GLY* 2.8 26.0 + - - -
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B THR* 2.9 41.4 + - + +
138B LEU* 3.9 10.5 - - + +
140B THR* 1.3 73.7 - - + +
142B TRP* 1.3 58.5 + - - +
144B GLY* 3.1 2.4 + - - +
145B ILE* 2.8 49.4 + - + +
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Residues in contact with TRP 142 (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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138B LEU* 2.8 20.6 + - + +
139B VAL* 3.4 19.1 - - + +
141B ILE* 1.3 78.6 - - - +
143B LEU* 1.3 77.0 + - + +
145B ILE* 3.3 7.5 + - - +
146B GLY* 2.8 26.5 + - - -
154B THR 5.6 0.7 - - - -
155B LEU* 2.8 54.6 + - + -
157B LEU* 3.9 30.0 - - + +
159B LEU* 6.1 0.6 - - - +
160B PHE* 4.9 16.7 - + - -
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Residues in contact with LEU 143 (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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83B PRO* 4.0 16.8 - - + +
86B GLN* 3.4 32.8 - - + +
87B ILE* 3.9 32.8 - - + -
90B SER* 5.8 0.4 - - - +
139B VAL* 2.9 39.4 + - + +
140B THR* 3.6 5.2 - - - +
142B TRP* 1.3 90.2 - - + +
144B GLY* 1.3 58.0 + - - +
146B GLY* 3.1 1.9 + - - +
147B ALA* 2.8 26.5 + - - +
155B LEU* 4.6 9.2 - - + -
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Residues in contact with GLY 144 (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 TYR* 3.4 33.7 - - - +
83B PRO* 3.9 8.2 - - - +
140B THR 2.8 15.0 + - - -
141B ILE* 3.1 5.1 + - - -
143B LEU* 1.3 76.6 - - - +
145B ILE* 1.3 62.5 + - - +
147B ALA* 3.2 18.2 + - - +
148B THR* 3.9 1.0 + - - +
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Residues in contact with ILE 145 (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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141B ILE* 2.8 40.8 + - + +
142B TRP* 3.8 7.2 - - + +
144B GLY* 1.3 71.0 - - - -
146B GLY* 1.3 62.4 + - - +
148B THR* 2.5 32.7 + - - +
149B PHE* 3.7 20.1 + - + -
157B LEU* 4.0 24.0 - - + -
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Residues in contact with GLY 146 (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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86B GLN* 3.4 8.5 - - - -
89B ARG* 3.2 1.4 + - - -
142B TRP 2.8 16.0 + - - -
143B LEU* 3.1 5.8 + - - -
145B ILE* 1.3 76.7 - - - +
147B ALA* 1.3 61.2 + - - +
148B THR 3.0 1.4 + - - -
149B PHE* 3.1 14.0 + - - +
154B THR* 2.8 35.7 + - - -
157B LEU* 3.7 7.8 - - - +
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Residues in contact with ALA 147 (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* 4.5 9.0 - - + +
82B TYR* 3.4 38.8 - - + +
85B PHE* 4.0 21.9 - - + -
86B GLN* 3.4 13.0 + - + -
89B ARG* 3.3 16.3 + - - +
143B LEU 2.8 7.9 + - - +
144B GLY 3.3 12.1 - - - +
145B ILE 3.1 0.6 + - - -
146B GLY* 1.3 74.7 - - - +
148B THR* 1.3 60.1 + - - +
149B PHE 3.8 0.2 - - - +
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Residues in contact with THR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 4.1 20.5 - - + +
82B TYR* 3.9 28.9 - - + +
144B GLY 4.1 4.3 - - - +
145B ILE* 2.5 25.8 + - - +
147B ALA* 1.3 75.2 - - - +
149B PHE* 1.3 81.6 + - - +
150B PRO* 4.0 1.2 - - - +
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Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ARG* 2.8 27.0 + - - -
145B ILE* 4.0 19.7 - - + -
146B GLY 3.1 8.8 + - - +
147B ALA 3.8 0.3 - - - +
148B THR* 1.3 95.1 - - - +
150B PRO* 1.3 72.6 - - + +
153B LYS* 3.6 28.7 - - + +
154B THR* 4.2 0.2 - - - -
157B LEU* 3.3 41.5 - - + -
158B GLY* 4.6 0.9 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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