Contacts of the helix formed by residues 104 - 119 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C LEU 3.4 8.5 - - - +
76C TRP* 3.6 31.4 - - + +
102C TYR 3.7 2.2 - - - +
103C PRO* 1.3 89.6 - - + +
105C ARG* 1.3 57.2 + - - +
106C GLU 4.6 0.9 - - - +
107C VAL* 2.8 31.1 + - + +
108C LEU 3.2 6.8 + - - -
442C ASP 5.7 0.4 - - - +
443C ASP* 3.7 28.0 - - + +
448C TYR* 3.4 39.0 - - + -
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Residues in contact with ARG 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C TRP* 3.1 35.8 + - + +
54C TYR* 3.2 41.0 - - - +
71C MET* 3.8 33.7 - - - -
72C TYR 5.0 6.1 + - - +
73C ARG* 6.1 2.6 - - - +
75C LEU* 2.9 28.4 + - + +
76C TRP* 4.2 0.8 - - - +
103C PRO 3.8 0.6 + - - -
104C PRO* 1.3 69.3 - - - +
106C GLU* 1.3 86.8 + - - +
107C VAL 3.2 0.2 + - - -
108C LEU* 3.2 2.7 + - - +
109C TRP* 3.0 47.4 + - - +
443C ASP* 5.3 6.7 + - - -
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Residues in contact with GLU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C PRO* 3.1 1.6 + - - +
105C ARG* 1.3 102.0 + - - +
107C VAL* 1.3 58.6 + - + +
109C TRP* 3.4 9.2 - - + +
110C ASP* 3.1 26.3 + - - +
443C ASP* 4.2 10.5 + - - +
444C SER* 3.6 17.8 - - - -
445C LEU* 3.5 29.2 - - + +
446C GLU* 3.2 20.4 - - - +
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Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C PHE* 3.5 33.2 - - + -
99C ILE* 4.3 3.8 - - + -
103C PRO* 3.6 21.3 - - + -
104C PRO* 2.8 17.3 + - + +
106C GLU* 1.3 74.8 - - - +
108C LEU* 1.3 64.2 + - + +
110C ASP* 3.4 1.9 + - - +
111C TYR* 3.3 15.8 + - - +
445C LEU* 3.9 34.3 - - + +
448C TYR* 3.9 30.7 - - + -
449C LEU* 4.9 2.5 - - + -
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Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C TRP* 3.6 39.0 - - + -
77C SER* 3.9 28.5 - - - +
81C LYS* 4.8 2.0 - - + -
84C LEU* 4.3 22.9 - - + -
91C PHE* 4.1 25.8 - - + -
103C PRO* 4.1 31.9 - - + +
104C PRO 3.2 3.6 + - - +
105C ARG 3.2 3.4 + - - +
107C VAL* 1.3 75.6 - - + +
109C TRP* 1.3 61.2 + - - +
111C TYR* 3.1 7.5 + - + +
112C ILE* 2.9 37.8 + - + +
327C PHE* 5.4 1.8 - - + -
500C FAD 4.9 0.2 - - - +
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Residues in contact with TRP 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C MET* 5.2 0.2 - - + -
47C ASP* 4.5 7.6 - - - -
48C TRP* 3.1 33.7 - + - -
49C GLY* 4.2 1.6 - - - -
52C TRP* 3.0 40.2 + - + -
53C ASN* 3.7 16.3 + - + +
105C ARG* 3.0 35.4 + - - +
106C GLU* 3.4 9.2 - - + +
108C LEU* 1.3 70.3 - - - +
110C ASP* 1.3 67.6 + - - +
111C TYR 3.2 0.2 + - - -
112C ILE* 3.2 18.1 + - + -
113C LYS* 2.0 76.1 + - + +
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Residues in contact with ASP 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C HIS* 2.8 32.2 + - - +
95C PHE* 4.3 6.8 - - + -
106C GLU 3.1 15.3 + - - +
107C VAL 3.6 8.7 - - - +
108C LEU 3.2 0.6 - - - -
109C TRP* 1.3 76.8 - - - +
111C TYR* 1.3 62.1 + - - +
113C LYS* 3.4 14.6 + - - +
114C GLY 3.1 17.8 + - - -
445C LEU* 4.0 19.6 - - + +
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Residues in contact with TYR 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU* 4.5 10.1 - - + -
85C GLU* 3.7 7.6 - - - +
86C PHE* 3.0 42.7 + + - -
89C TYR* 2.9 37.4 + + - -
90C THR 3.9 7.6 - - - -
91C PHE* 3.6 57.0 - + + -
94C HIS* 3.7 24.6 + + + -
95C PHE* 4.0 9.6 - + + -
107C VAL 3.3 9.9 + - - +
108C LEU* 3.1 15.0 + - + +
110C ASP* 1.3 76.8 - - - +
112C ILE* 1.3 71.3 + - + +
114C GLY 3.3 8.0 + - - -
115C ARG* 3.6 7.8 + - - +
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Residues in contact with ILE 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C PRO* 4.2 25.6 - - + -
20C MET* 4.2 20.8 - - + +
49C GLY* 4.6 3.6 - - - -
52C TRP* 4.3 18.8 - - + +
86C PHE* 4.1 21.4 - - + -
108C LEU* 2.9 25.6 + - + +
109C TRP* 3.2 13.4 + - + +
111C TYR* 1.3 81.8 - - + +
113C LYS* 1.3 64.1 + - - +
115C ARG* 3.6 11.1 + - - +
116C VAL* 3.6 12.8 + - - +
327C PHE* 4.3 22.9 - - + -
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Residues in contact with LYS 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C MET* 4.7 1.1 - - + -
47C ASP* 4.6 7.0 + - - +
48C TRP* 3.3 26.7 - - + +
109C TRP* 2.0 80.4 + - + +
110C ASP* 3.6 13.0 + - - +
112C ILE* 1.3 76.3 - - - +
114C GLY* 1.3 60.4 + - - +
116C VAL* 3.2 8.0 - - - +
117C GLU* 2.9 47.5 + - - +
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Residues in contact with GLY 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C TYR* 3.8 18.8 + - - -
94C HIS* 4.0 8.3 - - - -
110C ASP 3.1 15.0 + - - -
111C TYR 3.3 5.0 + - - -
113C LYS* 1.3 76.9 - - - +
115C ARG* 1.3 59.0 + - - +
117C GLU* 3.5 11.7 + - - +
118C LYS* 3.1 25.1 + - - +
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Residues in contact with ARG 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PRO 5.6 0.6 + - - -
20C MET* 4.8 2.8 + - - +
21C ALA* 4.2 9.1 - - - +
24C ARG* 3.1 46.5 + - - +
86C PHE* 3.1 37.7 - - + -
88C ASP* 3.0 22.3 + - - +
89C TYR* 3.6 46.0 - - + -
111C TYR 3.6 4.2 + - - -
112C ILE 3.6 8.8 + - - +
113C LYS 3.3 0.8 - - - -
114C GLY* 1.3 74.6 - - - +
116C VAL* 1.3 64.2 + - - +
118C LYS* 3.5 5.7 + - + +
119C ALA* 3.2 20.6 + - - +
331C ASP* 2.8 42.0 + - - -
335C TRP* 5.6 0.2 - - - -
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Residues in contact with VAL 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C MET* 3.2 60.6 - - + +
24C ARG* 4.8 9.2 - - + -
48C TRP* 3.6 21.0 - - + -
112C ILE 3.6 7.2 + - - +
113C LYS* 3.2 17.5 - - - +
115C ARG* 1.3 76.7 - - - +
117C GLU* 1.3 64.4 + - - +
119C ALA* 3.3 12.4 + - - +
120C GLY* 3.4 9.0 + - - -
121C VAL* 3.7 27.3 + - + +
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Residues in contact with GLU 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C TRP* 4.0 18.5 + - + -
113C LYS* 2.9 38.7 + - - +
114C GLY* 3.9 12.0 - - - +
116C VAL* 1.3 75.4 - - - +
118C LYS* 1.3 64.4 + - - +
120C GLY* 3.1 14.1 + - - -
122C ARG* 6.3 0.7 - - - -
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Residues in contact with LYS 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ARG* 5.8 3.1 - - - +
27C GLN* 5.6 0.2 + - - -
88C ASP 5.1 4.6 + - - -
89C TYR* 4.2 22.3 - - + +
93C GLU* 3.1 22.6 + - - +
114C GLY 3.1 15.4 + - - +
115C ARG* 3.7 5.4 - - + +
117C GLU* 1.3 80.3 - - - +
119C ALA* 1.3 60.3 + - - +
120C GLY 3.4 0.5 + - - -
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Residues in contact with ALA 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ARG* 3.1 33.4 - - + +
27C GLN* 3.3 37.5 + - - +
115C ARG 3.2 9.4 + - - +
116C VAL* 3.6 9.9 - - - +
117C GLU 3.1 0.6 - - - -
118C LYS* 1.3 79.1 - - - +
120C GLY* 1.3 61.6 + - - +
121C VAL* 4.3 11.9 - - + -
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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
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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