Contacts of the helix formed by residues 106 - 125 (chain C) in PDB entry 3QN3
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
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Residue Dist Surf HB Arom Phob DC
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49C LEU 3.6 5.4 - - - -
51C LEU* 4.2 12.1 - - - -
102C TYR* 2.9 21.1 + - - -
104C ASN 3.4 1.4 - - - -
105C LEU* 1.3 82.1 - - - +
107C ALA* 1.3 61.8 + - - -
108C ASN* 3.1 11.9 - - - -
109C ALA 3.0 15.5 + - - -
110C THR* 3.1 13.2 + - - +
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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
----------------------------------------------------------
37C VAL* 4.7 1.1 - - - +
48C ALA* 3.8 20.4 - - + +
49C LEU 2.8 22.1 + - - +
50C GLU* 4.6 2.0 - - + +
102C TYR* 3.7 6.4 - - + +
106C GLY* 1.3 71.7 - - - -
108C ASN* 1.3 57.9 + - - +
109C ALA 3.2 0.2 - - - -
110C THR* 3.5 10.0 + - - -
111C LEU* 3.0 32.6 + - - +
334C ASN* 3.7 23.6 - - - +
337C GLY* 4.2 7.1 - - - +
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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
----------------------------------------------------------
20C THR* 5.0 4.2 + - - +
21C VAL* 3.6 21.2 - - + +
37C VAL* 3.4 39.4 - - + +
50C GLU* 3.5 22.2 + - + +
51C LEU 2.9 45.5 + - - +
52C ARG* 5.3 0.4 - - - +
63C VAL* 3.7 15.0 - - - +
66C ALA* 3.6 17.4 - - - +
106C GLY* 3.7 4.7 - - - -
107C ALA* 1.3 73.2 - - - +
109C ALA* 1.3 63.4 + - - +
112C GLY 4.1 0.7 + - - -
334C ASN* 6.2 0.4 - - - +
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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* 4.9 0.4 - - - -
66C ALA* 3.6 23.7 - - - +
69C ASN* 4.2 2.7 - - + -
70C VAL* 3.6 18.2 - - + +
74C ILE* 3.9 12.9 - - + +
105C LEU 3.3 26.2 - - - +
106C GLY 3.0 3.0 + - - +
108C ASN* 1.3 81.4 + - - +
110C THR* 1.3 63.7 + - - +
111C LEU 3.5 0.2 - - - -
112C GLY* 3.9 0.7 + - - -
113C VAL* 3.5 25.8 + - - +
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Residues in contact with THR 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ILE* 4.3 7.4 - - + -
93C LEU* 3.7 21.3 - - + +
102C TYR* 3.8 29.9 - - + -
105C LEU* 3.8 25.8 - - + -
106C GLY 3.1 11.1 + - - +
107C ALA* 3.5 14.4 + - - -
109C ALA* 1.3 76.3 - - - +
111C LEU* 1.3 66.4 + - - +
113C VAL* 3.4 2.0 + - - +
114C SER* 3.0 22.9 + - - -
337C GLY* 2.9 23.9 + - - -
338C THR* 4.5 0.7 - - - -
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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
----------------------------------------------------------
37C VAL* 4.2 8.7 - - + -
38C PRO* 4.4 5.4 - - + -
107C ALA 3.0 17.8 + - - +
110C THR* 1.3 78.0 - - - +
112C GLY* 1.3 57.9 + - - +
114C SER* 3.5 1.2 - - - -
115C MET* 2.8 52.2 + - + +
333C PRO* 4.0 16.8 - - + +
334C ASN* 3.5 35.0 - - + +
337C GLY* 2.9 31.5 + - - +
338C THR 3.9 7.4 - - - -
339C ILE* 3.6 29.4 - - + -
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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* 5.8 0.9 - - - -
23C ALA* 3.6 16.5 - - - +
35C ALA* 3.9 7.0 - - - +
37C VAL* 3.6 24.8 - - - +
108C ASN 4.1 1.3 + - - -
109C ALA 3.9 4.1 + - - -
110C THR 3.3 1.0 - - - -
111C LEU* 1.3 79.4 - - - +
113C VAL* 1.3 56.1 + - - +
115C MET* 3.5 7.1 + - - -
116C ALA* 2.8 31.5 + - - +
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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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7C VAL* 3.9 10.8 - - + -
23C ALA* 3.8 7.2 - - + +
25C VAL* 4.6 2.2 - - + -
70C VAL* 3.7 30.3 - - + -
74C ILE* 4.2 13.0 - - + -
78C ILE* 3.5 31.4 - - + -
89C LEU* 4.5 2.5 - - + -
93C LEU* 4.4 11.2 - - + -
109C ALA 3.5 15.7 + - - +
110C THR* 3.8 6.3 - - - +
112C GLY* 1.3 74.4 - - - +
114C SER* 1.3 59.7 + - - +
116C ALA* 4.1 4.0 - - - +
117C THR* 2.7 41.9 + - - +
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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 21.6 + - - +
89C LEU* 4.1 5.2 - - - -
90C ASP* 2.6 32.0 + - - -
93C LEU* 4.2 2.2 - - - +
110C THR 3.0 18.8 + - - -
111C LEU 3.5 5.6 - - - -
113C VAL* 1.3 79.7 - - - +
115C MET* 1.3 62.4 + - - +
117C THR* 3.6 0.9 + - - -
118C ALA* 3.4 10.7 + - - +
338C THR* 4.0 5.8 - - - -
339C ILE* 3.0 27.6 + - - +
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Residues in contact with MET 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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35C ALA* 3.5 16.8 - - + -
36C ILE 3.7 23.3 - - - +
37C VAL* 4.0 6.1 - - + -
38C PRO* 4.8 2.2 - - + -
111C LEU* 2.8 49.1 + - + +
112C GLY* 3.9 12.1 - - - -
114C SER* 1.3 73.5 - - - +
116C ALA* 1.3 59.2 + - - +
118C ALA* 3.3 4.1 + - - +
119C ARG* 2.9 26.0 + - - +
333C PRO* 5.9 1.6 - - - -
339C ILE* 3.1 26.5 - - + -
367C ASP* 5.2 0.4 - - - +
369C PHE* 3.4 46.5 - - + -
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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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23C ALA 3.7 16.8 - - - +
25C VAL* 3.6 19.1 - - + +
33C GLY* 3.5 28.2 - - - +
34C ALA* 4.0 2.9 - - - -
35C ALA* 4.0 5.2 - - - +
112C GLY 2.8 23.7 + - - +
113C VAL* 4.3 0.2 - - - -
115C MET* 1.3 71.1 - - - +
117C THR* 1.3 61.7 + - - +
119C ARG* 3.3 1.2 + - - +
120C ALA* 2.9 29.6 + - - +
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Residues in contact with THR 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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4C ILE* 3.9 23.8 - - + +
25C VAL* 3.6 22.9 - - + +
27C LEU* 5.0 2.7 - - + -
82C ASP 5.7 0.2 - - - +
83C ALA* 3.8 21.3 - - - +
86C GLN* 4.3 4.3 - - - +
89C LEU* 3.3 28.6 - - + +
113C VAL* 2.7 25.2 + - - +
114C SER 3.9 0.4 - - - -
115C MET 3.3 0.2 - - - -
116C ALA* 1.3 77.6 - - - +
118C ALA* 1.3 56.1 + - - +
120C ALA* 3.2 2.3 + - - +
121C ALA* 2.9 28.5 + - - +
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Residues in contact with ALA 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* 3.6 20.0 + - - +
114C SER 3.4 8.4 + - - +
115C MET* 3.3 11.4 + - - +
116C ALA 3.3 0.4 - - - -
117C THR* 1.3 77.4 - - - +
119C ARG* 1.3 62.5 + - - +
122C ALA* 3.0 24.9 + - - +
129C LEU* 3.9 16.7 - - + +
132C TYR* 3.7 13.9 - - + -
133C LEU* 4.2 16.8 - - + -
339C ILE* 5.5 1.3 - - + -
369C PHE* 4.6 4.3 - - + -
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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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33C GLY* 3.9 12.3 - - - -
34C ALA 3.0 24.3 + - - +
35C ALA* 3.6 8.5 - - - +
115C MET 2.9 17.8 + - - +
116C ALA 3.3 3.8 + - - +
118C ALA* 1.3 75.5 - - - +
120C ALA* 1.3 57.3 + - - +
122C ALA* 3.4 4.4 + - - +
123C ALA* 2.9 29.5 + - - +
129C LEU* 3.9 26.2 - - + +
367C ASP* 2.8 43.3 + - - -
368C ALA* 4.0 5.9 - - - +
369C PHE* 3.3 30.1 - - + +
372C ASP* 5.3 2.0 + - - -
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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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25C VAL* 3.6 11.4 - - + +
27C LEU* 3.4 30.6 - - + +
31C SER* 3.8 3.7 - - - +
32C VAL 4.0 4.7 - - - -
33C GLY* 3.4 23.2 - - - +
116C ALA 2.9 16.6 + - - +
117C THR* 3.5 7.0 - - - +
119C ARG* 1.3 75.4 - - - +
121C ALA* 1.3 59.6 + - - +
123C ALA* 3.4 2.2 + - - +
124C ALA* 2.9 23.9 + - - +
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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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27C LEU* 3.7 7.7 - - + +
83C ALA* 3.8 11.7 - - + +
84C PHE* 3.4 29.6 - - + -
117C THR 2.9 15.2 + - - +
120C ALA* 1.3 76.2 - - - +
122C ALA* 1.3 62.9 + - - +
124C ALA* 3.3 2.1 + - - +
125C LEU* 3.2 18.5 + - - +
132C TYR* 3.5 34.8 - - + +
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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 ALA 3.0 18.9 + - - +
119C ARG* 3.7 5.8 - - - +
121C ALA* 1.3 76.4 - - - +
123C ALA* 1.3 59.2 + - - +
125C LEU* 3.2 5.6 + - - -
127C MET* 2.8 50.7 + - - +
129C LEU* 4.1 12.6 - - + +
132C TYR* 3.7 27.3 - - + -
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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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31C SER* 4.4 8.3 - - - -
32C VAL 4.2 16.6 - - - +
119C ARG 2.9 17.8 + - - +
120C ALA 3.8 4.3 - - - +
122C ALA* 1.3 71.7 - - - +
124C ALA* 1.3 67.7 + - - +
126C GLY* 3.0 15.5 + - - -
127C MET 4.9 1.3 - - - +
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Residues in contact with ALA 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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2C LEU* 3.4 30.5 - - + -
27C LEU* 4.0 2.5 - - + -
29C ASP* 3.5 5.3 - - - +
31C SER* 3.4 23.7 + - - +
84C PHE* 4.3 4.5 - - + -
120C ALA 2.9 15.6 + - - +
121C ALA 3.3 5.8 + - - +
123C ALA* 1.3 78.4 - - - +
125C LEU* 1.3 59.7 + - - +
126C GLY 3.2 1.0 + - - -
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Residues in contact with LEU 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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1B MET* 4.1 7.4 - - - +
125B LEU* 3.5 55.0 - - + +
127B MET* 4.2 14.6 - - + -
1C MET* 4.3 5.6 - - + -
84C PHE* 3.4 37.7 - - + -
121C ALA 3.2 10.9 + - - +
122C ALA 3.2 6.1 + - - +
123C ALA 3.2 0.8 - - - -
124C ALA* 1.3 76.6 - - - +
126C GLY* 1.3 60.9 - - - +
127C MET* 3.4 19.2 + - + +
132C TYR* 3.9 19.7 - - + -
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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