Contacts of the helix formed by residues 106 - 125 (chain C) in PDB entry 2XH2
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 GLY 106 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU* 3.8 7.0 - - - -
48C MET* 3.8 14.2 - - - +
97C ASP* 4.2 0.2 + - - -
102C LYS* 2.9 18.4 + - - -
103C SER* 5.0 0.2 - - - -
104C LYS 3.7 1.4 - - - -
105C LEU* 1.3 79.9 - - - +
107C ALA* 1.3 67.0 + - - -
108C ASN* 3.1 11.7 - - - -
109C ALA 3.1 10.3 + - - -
110C ILE* 3.1 14.6 + - - +
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Residues in contact with ALA 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C VAL* 5.6 0.2 - - - -
45C ALA* 3.7 29.6 - - + +
46C LEU 2.8 20.3 + - - +
47C GLU* 5.3 0.2 - - - -
102C LYS* 3.4 22.1 + - + -
106C GLY* 1.3 71.9 - - - -
108C ASN* 1.3 56.6 + - - +
109C ALA 3.2 0.4 - - - -
110C ILE* 4.0 1.1 - - - +
111C LEU* 2.9 34.3 + - - +
347C ASN* 4.5 9.4 - - + +
350C GLY* 4.2 8.6 - - - +
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Residues in contact with ASN 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C THR* 5.5 2.4 + - - +
19C VAL* 3.3 32.0 - - + +
34C VAL* 3.7 34.6 - - + +
46C LEU 4.0 0.6 + - - -
47C GLU* 3.9 18.3 - - + +
48C MET* 3.0 52.0 + - - +
49C ARG* 5.7 0.2 - - - -
61C VAL* 3.8 15.2 - - - +
64C ALA* 3.7 12.2 - - - +
106C GLY 3.9 2.8 - - - -
107C ALA* 1.3 77.2 - - - +
109C ALA* 1.3 61.3 + - - +
111C LEU 4.5 0.2 - - - -
112C GLY 4.7 0.2 + - - -
347C ASN* 6.2 0.7 - - - +
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Residues in contact with ALA 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C VAL* 4.7 0.9 - - - +
64C ALA* 3.5 24.9 - - + +
67C ASN* 4.1 6.5 - - + -
68C VAL* 3.5 26.5 - - + +
72C ILE* 3.8 8.8 - - + +
105C LEU 3.2 26.7 - - - +
106C GLY 3.1 2.3 + - - +
108C ASN* 1.3 82.3 + - - +
110C ILE* 1.3 63.7 + - - +
111C LEU 3.5 0.2 - - - -
112C GLY* 4.0 4.0 + - - -
113C VAL* 3.7 11.3 + - - +
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Residues in contact with ILE 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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72C ILE* 4.4 7.6 - - + -
93C LEU* 3.9 27.8 - - + +
94C ILE* 5.5 1.3 - - + -
97C ASP* 3.8 26.9 - - + +
102C LYS* 3.8 30.7 - - + -
105C LEU* 4.2 16.6 - - + -
106C GLY 3.1 15.6 + - - +
107C ALA* 4.0 4.5 - - - +
109C ALA* 1.3 76.5 - - - +
111C LEU* 1.3 64.3 + - - +
113C VAL* 3.2 6.8 + - - +
114C SER* 3.1 17.8 + - - -
350C GLY 3.4 17.3 - - - +
351C THR* 3.7 18.4 - - + -
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Residues in contact with LEU 111 (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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34C VAL* 4.2 16.4 - - + -
35C PRO* 4.4 4.5 - - + -
107C ALA 2.9 22.3 + - - +
109C ALA 3.5 0.2 - - - -
110C ILE* 1.3 73.6 - - - +
112C GLY* 1.3 58.6 + - - +
114C SER* 3.1 3.9 + - - -
115C LEU* 2.9 57.3 + - + +
346C VAL* 4.0 21.5 - - + +
347C ASN* 3.5 37.7 - - + +
350C GLY* 3.2 27.1 + - - +
351C THR* 4.2 8.5 - - - +
352C LEU 4.5 0.7 - - - +
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Residues in contact with GLY 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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21C VAL* 3.6 24.7 - - - +
32C SER* 3.7 13.0 - - - -
34C VAL* 3.7 20.5 - - - +
109C ALA 4.0 3.4 + - - -
110C ILE 3.3 0.8 - - - -
111C LEU* 1.3 78.3 - - - +
113C VAL* 1.3 56.9 + - - +
115C LEU* 4.7 1.6 - - - -
116C ALA* 3.0 31.0 + - - +
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Residues in contact with VAL 113 (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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5C VAL* 4.1 8.1 - - + -
21C VAL* 4.0 19.0 - - + +
23C LEU* 4.6 8.9 - - + +
68C VAL* 4.1 14.1 - - + -
72C ILE* 4.1 19.3 - - + -
76C PHE* 3.9 34.8 - - + -
89C VAL* 5.3 0.2 - - + -
93C LEU* 4.0 13.0 - - + -
109C ALA 3.7 15.5 - - - +
110C ILE 3.2 6.6 + - - +
112C GLY* 1.3 72.4 - - - +
114C SER* 1.3 67.8 + - - +
116C ALA* 4.1 0.6 - - - +
117C ALA* 3.0 24.3 + - - +
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Residues in contact with SER 114 (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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86C GLN* 3.0 25.5 + - - +
89C VAL* 4.5 2.0 - - - -
90C ASP* 2.6 28.9 + - - -
93C LEU* 3.8 6.6 - - - +
110C ILE 3.1 12.6 + - - -
111C LEU* 3.1 10.7 + - - -
113C VAL* 1.3 79.0 - - - +
115C LEU* 1.3 62.6 + - - +
117C ALA* 3.6 1.2 + - - +
118C SER* 3.5 9.2 + - - -
350C GLY 4.5 0.2 - - - -
351C THR* 4.1 7.6 - - - -
352C LEU* 3.0 25.7 + - - +
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Residues in contact with LEU 115 (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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32C SER* 3.3 23.6 + - - +
33C ILE 4.6 13.2 - - - +
35C PRO* 5.8 0.7 - - + -
111C LEU* 2.9 52.2 + - + +
112C GLY* 5.1 1.1 - - - -
114C SER* 1.3 78.2 - - - +
116C ALA* 1.3 61.7 + - - +
118C SER* 2.7 24.4 + - - -
119C ARG* 3.3 7.4 + - - +
346C VAL* 4.7 9.6 - - + -
352C LEU* 4.4 15.3 - - + -
380C ASP* 5.4 1.3 - - - +
382C PHE* 3.6 49.1 - - + -
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Residues in contact with ALA 116 (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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21C VAL* 4.2 9.9 - - + -
23C LEU* 4.0 14.8 - - + -
30C PHE* 3.6 27.1 - - - +
32C SER* 3.1 17.5 + - - +
112C GLY 3.0 19.8 + - - +
113C VAL* 4.1 2.0 - - - +
115C LEU* 1.3 74.8 - - - +
117C ALA* 1.3 63.0 + - - +
119C ARG* 3.3 7.5 + - - +
120C ALA* 3.0 22.9 + - - +
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Residues in contact with ALA 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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23C LEU* 4.1 15.3 - - + +
76C PHE* 4.8 1.6 - - + -
83C VAL* 3.7 22.2 - - + +
86C GLN* 4.2 2.9 - - - +
89C VAL* 3.9 25.4 - - + -
113C VAL 3.0 17.8 + - - +
114C SER 3.7 6.3 - - - +
116C ALA* 1.3 77.8 - - - +
118C SER* 1.3 56.2 + - - +
120C ALA* 3.3 5.5 + - - +
121C ALA* 2.8 28.2 + - - +
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Residues in contact with SER 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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86C GLN* 3.3 19.9 + - - -
114C SER 3.5 3.5 + - - -
115C LEU 2.7 20.4 + - - -
117C ALA* 1.3 76.8 - - - +
119C ARG* 1.3 56.6 + - - +
121C ALA* 3.4 5.6 + - - -
122C ALA* 3.0 25.3 + - - +
129C LEU* 3.8 4.0 - - - +
132C HIS* 3.3 20.1 - - - -
133C LEU* 4.4 2.5 - - - -
352C LEU* 3.5 18.0 - - - +
382C PHE* 3.3 22.3 - - - -
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Residues in contact with ARG 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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30C PHE* 4.0 21.3 - - + -
31C ARG* 2.8 49.2 + - - +
32C SER* 3.7 9.6 - - - +
115C LEU 3.3 12.1 + - - +
116C ALA* 3.3 7.5 + - - +
118C SER* 1.3 75.4 + - - +
120C ALA* 1.3 64.1 + - - +
122C ALA* 3.3 5.4 + - - +
123C ALA* 3.1 21.7 + - - +
129C LEU* 4.2 30.0 - - + +
380C ASP* 5.4 2.9 + - - -
381C THR* 5.8 2.3 + - - -
382C PHE* 4.9 3.8 - - + -
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Residues in contact with ALA 120 (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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23C LEU* 3.6 24.9 - - + -
25C THR* 3.9 13.6 + - + +
27C LYS* 5.2 0.5 - - - +
30C PHE* 3.6 30.8 - - + -
83C VAL* 4.2 7.5 - - + +
116C ALA 3.0 8.6 + - - +
117C ALA 3.6 8.1 - - - +
119C ARG* 1.3 77.2 - - - +
121C ALA* 1.3 55.7 + - - +
123C ALA* 3.2 4.7 + - - +
124C GLU* 3.0 26.7 + - - +
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Residues in contact with ALA 121 (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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83C VAL* 3.5 32.0 - - - +
84C LYS* 3.8 9.4 - - + -
117C ALA 2.8 12.2 + - - +
118C SER 3.5 1.3 - - - +
120C ALA* 1.3 73.2 - - - +
122C ALA* 1.3 66.5 + - - +
124C GLU* 3.2 5.3 + - - +
125C LYS* 3.0 30.1 + - - +
132C HIS* 3.3 29.2 - - + +
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Residues in contact with ALA 122 (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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118C SER 3.0 13.3 + - - +
119C ARG* 3.3 8.9 + - - +
121C ALA* 1.3 76.4 - - - +
123C ALA* 1.3 58.0 + - - +
125C LYS 3.3 1.9 + - - -
126C ASN 3.0 21.8 + - - -
127C VAL* 3.0 36.2 + - - +
129C LEU* 4.0 19.1 - - + +
132C HIS* 3.8 20.1 - - + -
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Residues in contact with ALA 123 (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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27C LYS* 3.6 25.5 - - + +
30C PHE* 3.4 39.9 - - + -
119C ARG 3.1 5.8 + - - +
120C ALA 3.5 4.7 - - - +
121C ALA 3.1 0.2 - - - -
122C ALA* 1.3 75.6 - - - +
124C GLU* 1.3 64.6 + - - +
126C ASN* 3.2 13.4 + - - +
127C VAL 5.0 1.3 - - - -
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Residues in contact with GLU 124 (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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1C ALA 5.2 4.0 + - - -
26C GLU* 4.3 18.0 - - - +
27C LYS* 4.1 16.6 - - + +
82C ASP* 4.3 1.7 - - - +
83C VAL* 3.9 15.5 + - + +
84C LYS* 2.8 45.4 + - + +
120C ALA 3.0 13.1 + - - +
121C ALA* 3.2 8.7 + - - +
123C ALA* 1.3 76.0 - - - +
125C LYS* 1.3 59.3 + - - +
126C ASN* 3.2 2.8 + - - +
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Residues in contact with LYS 125 (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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84C LYS* 3.7 28.0 - - + -
121C ALA 3.0 16.9 + - - +
122C ALA 3.7 4.0 - - - +
124C GLU* 1.3 74.9 - - - +
126C ASN* 1.3 69.9 + - - +
127C VAL* 3.4 23.0 + - + +
132C HIS* 3.0 39.2 + - + +
135C ASP* 3.0 35.2 + - - +
136C LEU* 5.7 0.4 - - - +
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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