Contacts of the helix formed by residues 104 - 120 (chain B) in PDB entry 2XLR
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 PRO 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B LEU 3.4 8.7 - - - +
76B TRP* 3.6 29.4 - - + +
102B TYR 3.6 1.7 - - - +
103B PRO* 1.3 92.5 - - + +
105B ARG* 1.3 60.5 + - - +
106B GLU 4.5 1.3 - - - +
107B VAL* 2.9 29.2 + - + +
108B LEU* 3.3 7.2 + - - -
443B ASP* 3.7 28.0 - - + +
448B TYR* 3.4 39.0 - - + -
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Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TRP* 3.0 40.3 + - + +
54B TYR* 3.3 42.3 - - - +
71B MET* 3.7 34.3 - - - -
72B TYR 4.9 5.5 + - - -
73B ARG* 6.3 1.4 - - - +
75B LEU* 2.9 27.2 + - + +
76B TRP* 4.2 0.8 - - - +
103B PRO 3.7 1.2 + - - -
104B PRO* 1.3 70.1 - - - +
106B GLU* 1.3 89.9 + - - +
108B LEU* 3.4 2.1 + - - +
109B TRP* 2.9 44.3 + - - +
443B ASP* 5.5 5.1 + - - -
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Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PRO* 3.2 1.6 + - - +
105B ARG* 1.3 106.3 + - - +
107B VAL* 1.3 57.4 + - + +
109B TRP* 3.6 11.2 - - + +
110B ASP* 3.1 26.0 + - - +
443B ASP* 4.1 8.5 + - - +
444B SER* 3.4 12.8 - - - -
445B LEU* 3.2 38.6 + - + +
446B GLU* 3.4 16.0 - - - +
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Residues in contact with VAL 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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95B PHE* 3.6 31.6 - - + -
99B ILE* 4.4 4.9 - - + -
103B PRO* 3.7 19.3 - - + -
104B PRO* 2.9 20.4 + - + +
106B GLU* 1.3 74.4 - - - +
108B LEU* 1.3 68.0 + - + +
110B ASP* 3.2 4.7 + - - +
111B TYR* 3.1 16.6 + - - +
445B LEU* 3.9 33.2 - - + +
448B TYR* 3.8 29.2 - - + -
449B LEU* 4.9 3.1 - - + -
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TRP* 3.7 40.4 - - + -
77B SER* 3.7 26.5 - - - -
81B LYS* 4.8 1.3 - - + -
84B LEU* 4.3 23.1 - - + -
91B PHE* 4.1 28.0 - - + -
103B PRO* 4.0 31.0 - - + +
104B PRO 3.3 5.1 + - - +
105B ARG 4.0 2.0 - - - +
107B VAL* 1.3 78.9 - - + +
109B TRP* 1.3 62.0 + - - +
111B TYR* 3.1 6.3 + - + +
112B ILE* 3.0 32.1 + - + +
327B PHE* 5.3 1.8 - - + -
500B FAD 5.3 0.2 - - - +
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Residues in contact with TRP 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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47B ASP* 4.0 12.6 - - + -
48B TRP 3.4 27.9 + - - -
49B GLY* 3.6 9.5 - - - -
52B TRP* 3.3 38.8 - - + +
53B ASN* 3.8 20.6 - - - -
105B ARG* 2.9 35.7 + - - +
106B GLU* 3.6 12.6 - - + +
108B LEU* 1.3 75.4 - - - +
110B ASP* 1.3 66.4 + - - +
112B ILE* 3.5 12.6 + - + +
113B LYS* 2.9 65.3 + - + +
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Residues in contact with ASP 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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94B HIS* 2.9 33.5 + - - +
95B PHE* 4.3 5.1 - - + -
106B GLU 3.1 12.4 + - - +
107B VAL 3.2 8.9 + - - +
109B TRP* 1.3 79.6 - - + +
111B TYR* 1.3 61.8 + - - +
113B LYS* 3.4 15.1 + - - +
114B GLY 3.1 18.2 + - - -
445B LEU* 4.0 20.6 - - + +
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Residues in contact with TYR 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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84B LEU* 4.5 9.0 - - + -
85B GLU* 3.7 7.1 - - - +
86B PHE* 3.0 44.2 + + - -
89B TYR* 2.7 38.1 + + - -
90B THR 3.7 19.3 - - - -
91B PHE* 3.6 45.1 - + + -
94B HIS* 3.7 24.6 + + + -
95B PHE* 4.1 9.4 - - + -
107B VAL 3.1 11.6 + - - +
108B LEU* 3.1 13.6 + - + +
110B ASP* 1.3 75.9 - - - +
112B ILE* 1.3 70.7 + - + +
114B GLY 3.2 9.0 + - - -
115B ARG 3.6 7.4 + - - -
327B PHE* 5.5 0.2 - + - -
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Residues in contact with ILE 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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17B PRO* 4.3 23.6 - - + -
20B MET* 4.1 15.9 - - + +
49B GLY* 4.5 8.7 - - - -
52B TRP* 4.3 11.9 - - + +
86B PHE* 4.1 19.5 - - + -
108B LEU* 3.0 18.1 + - + +
109B TRP* 3.9 25.4 - - + +
111B TYR* 1.3 82.5 - - + +
113B LYS* 1.3 65.0 + - - +
115B ARG* 3.6 10.0 + - - +
116B VAL* 3.5 15.6 + - - +
327B PHE* 4.1 28.5 - - + -
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B MET* 4.3 5.2 - - + -
47B ASP* 4.7 3.7 + - - +
48B TRP* 3.5 30.1 - - + +
109B TRP* 2.9 84.7 + - + +
110B ASP* 3.8 14.1 + - - +
112B ILE* 1.3 78.2 - - - +
114B GLY* 1.3 58.8 - - - +
116B VAL* 3.2 7.4 - - - +
117B GLU* 2.9 46.9 + - - +
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Residues in contact with GLY 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR* 3.6 20.0 + - - -
94B HIS* 4.1 7.2 - - - -
110B ASP 3.1 13.9 + - - -
111B TYR 3.2 3.9 + - - -
113B LYS* 1.3 76.4 - - - +
115B ARG* 1.3 62.5 + - - +
117B GLU* 3.7 13.8 + - - +
118B LYS* 3.0 26.9 + - - +
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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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17B PRO 5.5 0.4 + - - -
20B MET* 5.0 2.6 + - - +
21B ALA* 4.1 12.5 - - - +
24B ARG* 3.7 39.8 + - - +
86B PHE* 3.4 33.4 - - + -
88B ASP* 3.0 29.3 + - - -
89B TYR* 3.5 49.3 - - + -
111B TYR 3.6 0.2 + - - -
112B ILE 3.6 9.3 + - - +
113B LYS 3.3 0.6 - - - -
114B GLY* 1.3 77.2 - - - +
116B VAL* 1.3 60.6 + - - +
118B LYS* 3.5 3.7 + - + +
119B ALA* 3.1 25.3 + - - +
331B ASP* 3.0 38.6 + - - -
335B TRP* 5.1 0.8 - - - -
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Residues in contact with VAL 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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20B MET* 3.3 61.2 - - + +
24B ARG* 4.7 8.7 - - + -
48B TRP* 3.6 24.2 - - + -
112B ILE 3.5 6.3 - - - +
113B LYS* 3.2 15.5 - - - +
115B ARG* 1.3 78.4 - - + +
117B GLU* 1.3 64.1 + - - +
119B ALA* 3.3 6.1 + - - +
120B GLY 3.2 16.1 + - - -
121B VAL* 3.6 25.9 + - + +
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Residues in contact with GLU 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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48B TRP* 4.1 18.2 + - + -
113B LYS* 2.9 42.2 + - - +
114B GLY* 3.7 11.8 - - - +
116B VAL* 1.3 77.6 - - - +
118B LYS* 1.3 60.5 + - - +
120B GLY* 3.3 13.0 + - - -
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Residues in contact with LYS 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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24B ARG* 5.6 4.7 - - - +
27B GLN* 5.5 0.3 + - - -
88B ASP 5.1 5.5 + - - -
89B TYR* 4.2 20.5 - - + -
93B GLU* 3.0 23.6 + - - +
114B GLY 3.0 18.5 + - - +
115B ARG* 3.7 5.2 - - + +
117B GLU* 1.3 76.0 - - - +
119B ALA* 1.3 61.2 + - - +
120B GLY 3.3 0.7 + - - -
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Residues in contact with ALA 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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24B ARG* 3.3 31.2 - - - +
27B GLN* 3.5 39.1 + - - +
115B ARG 3.1 11.7 + - - +
116B VAL* 3.6 10.3 - - - +
117B GLU 3.3 0.4 - - - -
118B LYS* 1.3 77.2 - - - +
120B GLY* 1.3 59.1 + - - +
121B VAL* 4.2 12.8 - - + -
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Residues in contact with GLY 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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116B VAL 3.2 4.7 + - - -
117B GLU* 3.3 8.8 + - - -
118B LYS 3.2 5.7 + - - -
119B ALA* 1.3 77.2 - - - +
121B VAL* 1.3 59.0 + - - +
122B ARG* 3.2 7.5 + - - -
123B LYS* 3.7 24.8 + - - +
124B TYR* 4.6 0.5 - - - -
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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
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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