Contacts of the helix formed by residues 102 - 123 (chain B) in PDB entry 5XOU
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 ASP 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B ASP* 3.3 6.8 + - + +
100B PRO 4.5 0.2 - - - -
101B LYS* 1.3 75.6 - - + +
103B PRO* 1.4 60.5 - - - +
104B GLY* 2.6 26.7 + - - -
105B GLU* 2.7 44.0 + - + +
106B ARG 3.1 8.8 + - - -
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Residues in contact with PRO 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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100B PRO 4.9 0.4 - - - +
101B LYS 2.7 20.4 - - - +
102B ASP* 1.4 71.9 - - - +
104B GLY* 1.3 63.1 + - - +
106B ARG* 3.8 19.0 - - + +
107B SER* 3.2 20.3 + - - -
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Residues in contact with GLY 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ASP* 2.6 17.9 + - - -
103B PRO* 1.3 74.7 - - - +
105B GLU* 1.3 62.8 + - - +
107B SER* 3.1 20.0 + - - -
108B VAL* 3.4 10.9 + - - +
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Residues in contact with GLU 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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96B ARG* 5.0 9.9 + - - -
97B PRO 3.3 8.3 - - - +
98B LEU* 3.0 32.3 - - + +
99B ASP* 2.5 44.0 + - - +
102B ASP* 2.7 41.9 + - + +
104B GLY* 1.3 70.0 - - - -
106B ARG* 1.3 64.7 + - - +
108B VAL* 2.8 18.1 + - - +
109B LEU* 3.0 14.6 + - - +
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Residues in contact with ARG 106 (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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99B ASP 4.0 1.6 + - - -
100B PRO* 2.7 37.8 + - + +
102B ASP 3.1 7.1 + - - +
103B PRO* 3.9 18.7 + - + +
105B GLU* 1.3 75.5 - - - +
107B SER* 1.3 58.0 + - - +
109B LEU* 3.0 10.1 + - - +
110B SER* 2.7 37.3 + - - -
156B TRP* 4.2 15.0 - - - +
157B VAL* 2.7 47.5 + - + +
158B SER* 3.9 13.3 - - - +
159B ASP* 4.0 6.6 - - - +
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Residues in contact with SER 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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103B PRO 3.2 10.5 + - - -
104B GLY* 3.1 12.2 + - - -
105B GLU 3.1 0.6 - - - -
106B ARG* 1.3 76.6 - - - +
108B VAL* 1.3 60.1 + - - +
110B SER* 3.3 7.5 + - - -
111B ALA* 3.0 28.2 + - - +
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Residues in contact with VAL 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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58B VAL* 4.4 7.0 - - + -
59B ARG 4.8 2.5 - - - +
60B MET* 4.1 41.3 - - + -
61B GLY 5.8 0.7 - - - +
65B ALA* 4.3 4.9 - - + -
98B LEU* 4.0 19.5 - - + -
104B GLY 3.7 12.3 - - - +
105B GLU* 2.8 11.5 + - - +
107B SER* 1.3 78.6 - - - +
109B LEU* 1.3 55.5 + - - +
111B ALA* 3.2 7.2 + - - +
112B LEU* 2.9 37.2 + - + +
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Residues in contact with LEU 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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19B LEU* 4.1 15.0 - - + -
23B GLU 3.7 23.8 - - - +
24B LEU* 4.4 2.0 - - + -
67B TRP* 4.0 8.0 - - + -
98B LEU* 3.8 34.8 - - + +
99B ASP 4.4 0.4 - - - -
100B PRO* 4.1 38.1 - - + -
105B GLU 3.0 12.0 + - - +
106B ARG* 3.5 8.7 - - - +
108B VAL* 1.3 77.5 - - - +
110B SER* 1.3 56.3 + - - +
112B LEU* 3.4 9.5 + - + +
113B ALA* 2.8 27.0 + - - +
157B VAL* 3.5 24.6 - - + +
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Residues in contact with SER 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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106B ARG* 2.7 24.5 + - - -
107B SER* 3.7 7.8 - - - -
109B LEU* 1.3 70.3 - - - +
111B ALA* 1.3 59.3 + - - +
113B ALA* 3.1 9.0 + - - +
114B ARG* 2.9 36.7 + - - +
155B LEU 3.5 0.6 - - - +
156B TRP* 3.1 30.3 - - - +
157B VAL* 3.2 12.7 + - - +
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Residues in contact with ALA 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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58B VAL* 3.6 26.8 - - + +
59B ARG 5.6 2.0 - - - +
107B SER 3.0 14.7 + - - +
108B VAL* 3.2 10.5 + - - +
110B SER* 1.3 73.9 - - - +
112B LEU* 1.3 64.9 + - - +
114B ARG* 3.3 11.8 + - - +
115B ARG* 3.0 18.4 + - - +
6F A 5.7 8.1 - - - +
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Residues in contact with LEU 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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26B PRO* 4.1 15.0 - - + -
56B VAL* 3.4 36.2 - - + +
58B VAL* 3.7 15.5 - - + +
65B ALA* 3.6 22.4 - - + +
67B TRP* 3.5 47.1 - - + +
108B VAL* 2.9 29.7 + - + +
109B LEU* 3.5 13.9 - - + +
111B ALA* 1.3 77.7 - - - +
113B ALA* 1.3 56.8 + - - +
115B ARG 3.3 0.9 + - - -
116B LEU* 2.8 26.3 + - - +
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Residues in contact with ALA 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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67B TRP* 4.0 8.7 - - - -
109B LEU 2.8 18.0 + - - +
110B SER* 3.1 8.9 + - - +
112B LEU* 1.3 73.9 - - - +
114B ARG* 1.3 60.5 + - - +
116B LEU* 3.3 4.5 + - - +
117B LEU* 2.9 28.6 + - - +
155B LEU* 3.5 24.7 - - + +
156B TRP* 4.0 6.1 - - - +
157B VAL* 4.4 1.1 - - + -
163B PHE* 3.9 22.0 - - + -
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Residues in contact with ARG 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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110B SER* 2.9 18.6 + - - +
111B ALA* 3.9 9.4 - - - +
113B ALA* 1.3 72.1 - - - +
115B ARG* 1.3 67.5 - - - +
117B LEU* 3.2 8.0 + - - +
118B GLN* 3.0 25.5 + - - +
132B LEU* 3.7 29.8 - - + +
154B ASP* 2.7 46.8 + - - +
155B LEU* 3.3 18.4 - - - +
6F A 3.8 36.7 + - - +
7F A 3.2 25.3 + - - -
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Residues in contact with ARG 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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47B ALA* 4.6 4.4 + - - +
50B ALA* 3.6 15.0 + - - +
51B ARG* 3.5 39.7 - - - +
55B GLY 5.4 0.8 + - - -
56B VAL* 4.2 9.0 - - + -
57B THR 2.8 27.8 + - - +
58B VAL* 3.7 20.5 - - + +
59B ARG 4.8 0.8 - - - +
111B ALA 3.0 17.6 + - - +
112B LEU 3.8 3.6 - - - +
114B ARG* 1.3 78.1 - - - +
116B LEU* 1.3 65.1 + - - +
118B GLN* 3.2 15.8 + - - +
119B GLU* 2.8 65.8 + - + +
5F C 5.0 11.6 + - - -
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Residues in contact with LEU 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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17B ARG* 5.3 0.2 - - - +
23B GLU* 4.4 4.5 - - - +
56B VAL* 3.7 22.9 - - + +
67B TRP* 3.5 28.9 - - + -
112B LEU 2.8 13.7 + - - +
113B ALA 3.4 7.9 - - - +
115B ARG* 1.3 74.6 - - - +
117B LEU* 1.3 64.2 + - - +
120B ARG* 2.8 83.3 + - + +
155B LEU* 4.5 11.4 - - + -
163B PHE* 4.0 16.6 - - + -
301B LEU* 5.7 0.7 - - + -
303B LEU* 4.6 12.8 - - + -
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Residues in contact with LEU 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 ALA 2.9 17.6 + - - +
114B ARG* 3.6 3.8 - - - +
116B LEU* 1.3 81.4 - - - +
118B GLN* 1.3 63.7 + - - +
120B ARG* 3.9 1.6 - - - +
121B LEU* 3.0 43.3 + - + +
132B LEU* 4.2 11.2 - - + -
153B LEU* 3.8 25.6 - - + -
154B ASP* 3.8 32.5 - - - +
155B LEU* 3.6 19.1 - - + +
165B LEU* 4.5 7.9 - - + -
297B ILE* 5.3 0.9 - - + -
301B LEU* 3.5 28.9 - - + -
303B LEU* 5.5 0.2 - - + -
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Residues in contact with GLN 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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114B ARG 3.0 15.4 + - - +
115B ARG* 3.6 22.6 - - - +
117B LEU* 1.3 76.9 - - - +
119B GLU* 1.4 63.0 + - + +
121B LEU* 3.2 5.1 + - - +
122B ARG* 3.0 30.6 + - + +
129B VAL* 5.1 0.9 - - - +
131B GLY* 4.0 32.6 - - - +
132B LEU* 3.7 21.3 - - + +
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Residues in contact with GLU 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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54B GLY* 5.7 0.3 - - - -
55B GLY* 2.5 33.1 - - - +
56B VAL* 3.6 8.0 - - + -
115B ARG* 2.8 46.8 + - + +
116B LEU* 3.7 4.9 - - - +
118B GLN* 1.4 78.9 - - + +
120B ARG* 1.3 66.4 + - + +
122B ARG* 2.0 61.8 + - - +
123B ARG* 3.4 23.3 + - - +
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Residues in contact with ARG 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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17B ARG* 4.9 9.7 - - - +
23B GLU* 5.5 0.4 + - - -
116B LEU* 2.8 57.8 + - + +
117B LEU 4.1 2.2 - - - +
119B GLU* 1.3 73.8 - - + +
121B LEU* 1.3 62.3 + - - +
123B ARG* 3.1 23.0 + - - +
124B LEU* 3.5 8.8 + - - +
301B LEU* 2.8 55.8 + - + +
302B GLY* 4.4 4.9 + - - -
303B LEU* 4.4 9.2 - - - +
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Residues in contact with LEU 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 LEU* 3.0 34.3 + - + +
118B GLN 3.4 4.9 - - - +
120B ARG* 1.3 74.4 - - - +
122B ARG* 1.3 64.2 + - - +
123B ARG 3.0 2.4 + - - -
124B LEU* 3.2 24.3 + - + +
129B VAL* 3.3 23.6 - - + +
131B GLY 4.3 13.7 - - - +
132B LEU* 4.4 10.1 - - - -
134B VAL* 3.7 23.6 - - + -
153B LEU* 3.6 28.7 - - + -
297B ILE* 4.6 9.2 - - + -
301B LEU* 3.7 25.6 - - + -
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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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54B GLY* 6.0 1.2 - - - -
55B GLY 5.0 4.9 + - - +
118B GLN* 3.0 18.7 + - + +
119B GLU* 2.0 61.0 + - - +
121B LEU* 1.3 76.8 - - - +
123B ARG* 1.3 79.8 + - + +
124B LEU 3.3 5.2 + - - +
129B VAL* 4.6 12.8 - - + +
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Residues in contact with ARG 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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55B GLY* 5.3 11.1 - - - +
119B GLU* 3.4 21.4 + - - +
120B ARG* 3.1 14.8 + - - +
121B LEU 3.0 1.0 - - - -
122B ARG* 1.3 105.3 - - + +
124B LEU* 1.3 60.1 + - - +
125B GLU* 3.7 4.2 + - - +
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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