Contacts of the helix formed by residues 116 - 135 (chain B) in PDB entry 2XWU
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 SER 116 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B PRO* 4.0 22.2 - - - +
75B GLN* 4.4 5.8 + - - -
112B PHE* 4.0 8.7 - - - +
115B GLY* 1.3 72.3 - - - -
117B LYS* 1.3 65.2 + - - +
118B ILE* 3.2 28.6 + - - +
119B VAL* 3.4 17.1 + - - +
120B LEU* 3.2 20.4 + - - +
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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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115B GLY 3.5 4.7 + - - +
116B SER* 1.3 72.7 + - - +
118B ILE* 1.3 64.2 + - + +
120B LEU* 3.2 19.1 + - + +
121B THR* 3.1 20.1 + - - +
168B GLU* 5.4 0.2 - - - +
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Residues in contact with ILE 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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122A GLU* 6.0 2.0 - - - +
125A ILE* 4.7 7.2 - - + -
72B PRO* 4.1 19.1 - - + +
73B GLU* 4.4 7.2 - - + +
76B TYR* 3.6 39.1 - - + -
116B SER* 3.2 14.3 + - - +
117B LYS* 1.3 78.6 - - + +
119B VAL* 1.3 68.3 + - + +
121B THR* 3.7 6.2 + - - -
122B ARG* 3.2 23.4 + - - +
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 3.8 21.8 - - + -
72B PRO 3.9 2.2 - - - +
75B GLN* 3.7 31.2 - - + +
76B TYR* 3.7 12.6 - - - +
79B ALA* 3.9 6.3 - - + -
112B PHE* 3.9 15.3 - - + -
116B SER* 3.4 18.7 + - - +
117B LYS 3.3 0.2 - - - -
118B ILE* 1.3 85.8 - - + +
120B LEU* 1.3 60.3 - - - +
122B ARG* 3.5 5.1 + - - +
123B LEU* 2.9 46.2 + - + +
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Residues in contact with LEU 120 (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 ILE* 3.6 43.7 - - + +
112B PHE* 3.7 30.0 - - + +
113B ALA* 4.3 10.1 - - - +
116B SER 3.2 7.4 + - - +
117B LYS* 3.2 15.6 + - + +
119B VAL* 1.3 77.1 - - - +
121B THR* 1.3 57.6 + - - +
123B LEU* 3.0 5.2 + - - +
124B CYS* 2.8 39.4 + - - -
161B GLY 5.6 0.4 - - - +
164B LEU* 5.4 2.0 - - + +
165B ALA* 4.3 21.3 - - + +
168B GLU* 4.7 11.7 - - + +
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Residues in contact with THR 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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117B LYS* 3.1 14.8 + - - +
118B ILE* 4.0 7.4 + - - -
120B LEU* 1.3 77.5 - - - +
122B ARG* 1.3 60.0 + - - +
124B CYS* 2.9 4.7 + - - +
125B VAL* 2.9 36.6 + - + +
168B GLU* 3.4 41.4 + - - +
172B VAL* 4.1 12.6 - - + -
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Residues in contact with ARG 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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124A ASN* 6.1 1.0 - - - +
76B TYR* 2.9 36.1 + - + -
79B ALA* 3.4 10.3 - - + +
80B SER* 3.3 50.0 + - - +
83B HIS* 3.8 27.0 + - - +
118B ILE 3.2 16.7 + - - +
119B VAL 3.7 4.0 - - - +
121B THR* 1.3 80.8 - - - +
123B LEU* 1.3 62.7 + - - +
125B VAL* 3.5 15.1 + - - +
126B ALA* 3.3 18.7 + - - +
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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
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66B LEU* 4.1 9.9 - - + -
79B ALA* 3.8 20.2 - - + +
82B LEU* 4.0 26.2 - - + -
105B LEU* 4.6 10.5 - - + +
108B GLN* 3.9 22.9 - - + +
109B ILE* 4.1 16.3 - - + +
112B PHE* 3.7 24.9 - - + -
119B VAL* 2.9 37.1 + - + +
120B LEU* 3.0 4.0 + - - +
122B ARG* 1.3 76.9 - - - +
124B CYS* 1.3 61.7 + - - +
126B ALA* 3.3 5.8 + - + +
127B LEU* 3.1 21.7 + - - +
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Residues in contact with CYS 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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109B ILE* 4.1 16.8 - - - -
120B LEU* 2.8 33.4 + - - -
121B THR* 2.9 11.6 + - - +
123B LEU* 1.3 75.4 - - - +
125B VAL* 1.3 59.6 + - - +
127B LEU 3.3 1.2 + - - -
128B ALA* 3.0 25.5 + - - +
165B ALA 4.2 3.1 - - - -
168B GLU* 4.0 14.8 - - + +
169B LEU* 3.5 50.3 - - - +
172B VAL* 4.6 4.9 - - + -
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Residues in contact with VAL 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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83B HIS* 3.2 32.8 - - + +
121B THR* 2.9 25.8 + - + +
122B ARG* 3.8 20.2 - - - +
123B LEU 3.3 0.2 - - - -
124B CYS* 1.3 75.0 - - - +
126B ALA* 1.3 63.2 + - - +
128B ALA* 3.2 2.5 + - - +
129B SER* 3.0 22.5 + - - -
172B VAL* 3.0 31.6 - - + -
176B GLU* 3.6 17.5 - - + +
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Residues in contact with ALA 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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79B ALA 4.8 0.4 - - - +
82B LEU* 4.5 6.5 - - + -
83B HIS* 3.8 33.6 - - + +
86B ILE* 4.0 9.1 - - + +
105B LEU* 4.0 16.4 - - + -
122B ARG 3.3 11.0 + - - +
123B LEU* 3.5 12.8 - - + +
124B CYS 3.2 0.6 - - - -
125B VAL* 1.3 81.0 - - - +
127B LEU* 1.3 61.1 + - - +
129B SER* 3.2 5.1 + - - -
130B LEU* 3.2 21.0 + - - +
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Residues in contact with LEU 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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102B LYS* 4.7 2.2 - - + +
105B LEU* 3.6 25.3 - - + +
106B PHE* 3.8 42.4 - - + -
109B ILE* 3.6 20.4 - - + -
123B LEU 3.1 10.9 + - - +
124B CYS 3.7 6.5 - - - +
126B ALA* 1.3 78.9 - - - +
128B ALA* 1.3 59.0 + - - +
130B LEU* 3.4 8.9 + - + +
131B ALA* 3.0 23.9 + - - +
139B TRP* 4.5 8.7 - - + -
146B MET* 4.3 7.2 - - + -
169B LEU* 3.6 32.8 - - + -
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Residues in contact with ALA 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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124B CYS 3.0 16.8 + - - +
125B VAL* 3.6 7.9 - - - +
127B LEU* 1.3 75.2 - - - +
129B SER* 1.3 64.3 + - - +
131B ALA* 3.6 4.5 - - - +
132B LEU* 3.1 30.6 + - - +
146B MET* 5.3 0.7 - - - -
169B LEU* 4.3 8.5 - - + +
172B VAL* 4.6 3.6 - - + +
173B LEU* 3.8 39.1 - - + +
176B GLU* 4.6 5.4 - - + -
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Residues in contact with SER 129 (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 HIS* 4.1 9.9 - - - -
86B ILE* 4.2 5.9 - - - +
87B SER* 3.3 29.5 + - - -
125B VAL 3.0 9.9 + - - -
126B ALA 3.5 9.2 - - - -
128B ALA* 1.3 76.0 - - - +
130B LEU* 1.3 63.9 + - - +
132B LEU* 3.5 6.9 + - - +
133B SER* 3.0 30.0 + - - -
176B GLU* 3.5 22.1 + - - -
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Residues in contact with LEU 130 (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 ILE* 3.8 8.5 - - + +
90B TRP* 3.5 28.0 - - + -
98B TYR* 4.6 4.0 - - - +
101B LEU* 3.4 39.5 - - + -
102B LYS* 4.3 19.5 - - + +
105B LEU* 4.5 9.4 - - + -
126B ALA 3.2 7.3 + - - +
127B LEU* 3.7 10.8 - - + +
128B ALA 3.3 0.2 - - - -
129B SER* 1.3 81.3 - - - +
131B ALA* 1.3 63.8 - - - +
133B SER 3.4 0.5 + - - -
134B MET* 3.0 47.9 + - - +
139B TRP* 4.2 11.7 - - + -
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Residues in contact with ALA 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 LEU 3.0 17.2 + - - +
128B ALA* 3.6 7.4 - - - +
129B SER 3.3 0.2 - - - -
130B LEU* 1.3 74.0 - - - +
132B LEU* 1.3 66.2 + - - +
134B MET* 3.0 12.5 + - - +
135B MET* 3.1 17.7 + - - +
139B TRP* 3.9 33.1 - - + +
142B ALA* 4.5 8.6 - - + +
146B MET* 4.1 15.3 - - + -
173B LEU* 4.7 6.7 - - + -
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Residues in contact with LEU 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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128B ALA 3.1 18.4 + - - +
129B SER* 3.9 5.2 - - - +
131B ALA* 1.3 75.4 - - - +
133B SER* 1.3 66.2 + - - +
134B MET 2.9 2.8 + - - -
135B MET* 3.1 33.9 + - - +
173B LEU* 3.9 14.6 - - + +
176B GLU* 4.0 13.7 - - + +
177B PHE* 3.6 33.0 - - + +
180B SER* 4.8 7.9 - - - -
182B LEU* 6.1 2.5 - - + -
186B ARG* 3.1 12.6 + - - -
190B VAL* 3.9 17.2 - - + +
194B LEU* 3.7 29.6 - - + -
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Residues in contact with SER 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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86B ILE 4.8 2.9 + - - -
87B SER* 5.8 0.5 - - - -
90B TRP* 3.5 48.0 + - - +
129B SER* 3.0 22.5 + - - -
130B LEU 3.7 1.6 - - - -
132B LEU* 1.3 75.3 - - - +
134B MET* 1.3 61.6 + - - +
135B MET 3.8 0.5 - - - +
186B ARG* 3.0 21.7 + - - +
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Residues in contact with MET 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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90B TRP* 3.9 15.7 - - + -
98B TYR* 4.7 17.0 - - + +
99B GLU* 4.0 8.5 - - - +
102B LYS* 3.7 23.1 - - - +
130B LEU* 3.0 41.5 + - - +
131B ALA 3.2 9.2 - - - +
132B LEU 2.9 1.8 + - - -
133B SER* 1.3 77.6 - - - +
135B MET* 1.3 66.3 + - - +
137B ASP 4.0 0.2 + - - -
138B ALA* 3.1 64.1 + - + +
139B TRP* 3.7 19.5 - - + -
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Residues in contact with MET 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 ALA* 3.1 12.8 + - - +
132B LEU* 3.3 40.4 - - - +
133B SER 3.8 0.5 - - - +
134B MET* 1.3 79.9 - - - +
136B PRO* 1.3 76.0 - - + +
139B TRP* 4.4 10.4 - - + +
142B ALA* 5.5 6.5 - - + -
173B LEU* 5.9 1.1 - - - -
186B ARG* 3.4 25.1 + - - -
190B VAL* 3.8 19.1 - - + +
193B SER* 3.6 23.8 - - - -
194B LEU* 3.5 33.2 - - + +
197B GLU* 4.2 12.3 - - + +
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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