Contacts of the helix formed by residues 106 - 125 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU 3.6 5.8 - - - -
51B LEU* 4.1 12.3 - - - +
102B TYR* 2.9 20.8 + - - -
103B SER 5.3 0.2 - - - -
104B ASN 3.4 1.4 - - - -
105B LEU* 1.3 77.0 - - - +
107B ALA* 1.3 60.8 + - - -
108B ASN* 3.2 12.8 - - - -
109B ALA* 2.9 20.6 + - - +
110B THR* 3.1 11.3 + - - +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 4.7 1.2 - - - +
48B ALA* 4.1 18.4 - - + +
49B LEU 2.8 22.7 + - - +
50B GLU* 4.6 2.0 - - + +
102B TYR* 3.7 5.8 - - + +
106B GLY* 1.3 71.5 - - - -
108B ASN* 1.3 56.6 + - - +
109B ALA 3.3 0.2 - - - -
110B THR* 3.4 10.3 + - - -
111B LEU* 2.9 34.3 + - - +
334B ASN* 3.6 24.4 - - + +
337B GLY* 4.1 7.6 - - - +
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Residues in contact with ASN 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B THR* 5.0 4.4 + - - +
21B VAL* 3.7 21.3 - - + +
37B VAL* 3.3 41.8 - - + +
38B PRO 5.4 0.2 - - - +
50B GLU* 3.4 21.4 + - + +
51B LEU 2.9 46.8 + - - +
52B ARG* 5.3 0.2 - - - -
63B VAL* 3.4 20.4 - - - +
66B ALA* 3.7 12.8 - - - +
106B GLY* 3.6 5.4 - - - -
107B ALA* 1.3 76.6 - - - +
109B ALA* 1.3 63.1 + - - +
112B GLY 3.8 0.3 + - - -
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 5.0 0.6 - - - +
66B ALA* 3.8 22.6 - - - +
69B ASN* 4.4 1.3 - - + -
70B VAL* 3.8 16.2 - - + +
74B ILE* 4.0 13.9 - - + -
105B LEU 3.3 17.9 - - - +
106B GLY 2.9 12.3 + - - +
108B ASN* 1.3 79.4 + - - +
110B THR* 1.3 63.0 + - - +
112B GLY* 4.4 0.3 - - - -
113B VAL* 3.3 28.4 + - - +
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Residues in contact with THR 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 4.6 5.6 - - + -
93B LEU* 3.8 16.2 - - + +
102B TYR* 3.7 33.8 - - + -
105B LEU* 3.9 24.5 - - + -
106B GLY 3.1 8.1 + - - +
107B ALA* 3.4 14.9 + - - -
109B ALA* 1.3 75.7 - - - +
111B LEU* 1.3 65.8 + - - +
113B VAL* 3.4 3.5 + - - +
114B SER* 2.9 23.9 + - - -
337B GLY* 2.7 25.1 + - - -
338B THR* 4.3 6.7 - - - -
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 4.3 7.9 - - + -
38B PRO* 4.4 5.2 - - + -
107B ALA 2.9 18.5 + - - +
110B THR* 1.3 76.5 - - - +
112B GLY* 1.3 64.2 + - - +
114B SER* 3.2 1.4 + - - -
115B MET* 2.8 48.2 + - + +
333B PRO* 3.9 20.0 - - + +
334B ASN* 3.5 34.3 - - + +
337B GLY* 3.0 9.6 + - - +
338B THR* 3.9 19.7 - - - -
339B ILE* 3.7 27.6 - - + +
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Residues in contact with GLY 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 5.6 1.1 - - - -
23B ALA* 3.6 16.2 - - - +
35B ALA* 4.0 7.3 - - - +
37B VAL* 3.3 26.1 - - - +
108B ASN 4.4 1.1 - - - -
109B ALA 3.8 3.7 + - - -
110B THR 3.3 0.6 - - - -
111B LEU* 1.3 79.0 - - - +
113B VAL* 1.3 57.5 + - - +
115B MET* 3.9 7.7 - - - +
116B ALA* 2.9 32.6 + - - +
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Residues in contact with VAL 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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7B VAL* 4.1 6.5 - - + -
23B ALA* 4.2 5.6 - - + -
25B VAL* 4.5 5.4 - - + -
70B VAL* 3.5 31.9 - - + -
74B ILE* 4.1 13.5 - - + -
78B ILE* 3.5 30.5 - - + -
89B LEU* 4.5 8.3 - - + -
93B LEU* 4.5 5.6 - - + -
109B ALA 3.3 19.3 + - - +
110B THR* 3.4 5.1 + - - +
111B LEU 3.2 0.4 - - - -
112B GLY* 1.3 74.4 - - - +
114B SER* 1.3 59.5 + - - +
116B ALA* 4.0 2.6 - - - +
117B THR* 2.8 40.2 + - - +
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLN* 3.2 19.5 + - - +
89B LEU* 4.3 5.4 - - - -
90B ASP* 2.5 31.5 + - - -
93B LEU* 4.4 1.7 - - - +
110B THR 2.9 18.5 + - - -
111B LEU* 3.4 5.6 - - - -
113B VAL* 1.3 77.9 - - - +
115B MET* 1.3 60.4 + - - +
117B THR* 3.6 0.9 + - - -
118B ALA* 3.4 14.6 + - - +
338B THR* 4.1 5.8 - - - -
339B ILE* 3.0 28.0 + - - +
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Residues in contact with MET 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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35B ALA* 3.5 17.5 - - + -
36B ILE 3.8 21.5 - - - +
37B VAL* 4.0 5.4 - - + -
38B PRO* 4.9 1.8 - - + -
111B LEU* 2.8 54.8 + - + +
112B GLY* 3.9 8.3 - - - +
114B SER* 1.3 70.9 - - - +
116B ALA* 1.3 65.5 + - - +
118B ALA* 3.4 2.5 + - - +
119B ARG* 3.1 27.7 + - - +
333B PRO* 6.0 2.0 - - - -
339B ILE* 3.3 24.0 - - + -
367B ASP* 5.1 0.4 - - - +
369B PHE* 3.5 43.5 - - + -
370B ILE* 6.4 0.4 - - - -
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Residues in contact with ALA 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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23B ALA* 3.7 20.0 - - + +
25B VAL* 3.8 18.2 - - + -
33B GLY* 3.7 21.7 - - - +
34B ALA* 4.0 4.9 - - - -
35B ALA* 3.8 6.3 - - - +
112B GLY 2.9 21.0 + - - +
113B VAL 4.0 0.9 - - - +
115B MET* 1.3 76.6 - - - +
117B THR* 1.3 63.2 + - - +
119B ARG* 3.4 2.8 + - - +
120B ALA* 3.0 23.4 + - - +
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Residues in contact with THR 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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4B ILE* 3.9 23.4 - - + +
25B VAL* 3.5 24.3 - - + +
27B LEU* 5.1 2.8 - - + +
83B ALA* 3.8 21.1 - - - +
86B GLN* 4.5 4.0 - - - +
89B LEU* 3.4 31.0 - - + +
113B VAL* 2.8 22.3 + - - +
114B SER 4.0 1.1 - - - -
116B ALA* 1.3 77.0 - - - +
118B ALA* 1.3 55.0 + - - +
120B ALA* 3.2 2.8 + - - +
121B ALA* 2.9 27.2 + - - +
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Residues in contact with ALA 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B GLN* 3.6 21.7 + - - +
114B SER 3.4 8.5 + - - +
115B MET* 3.6 11.2 - - - +
116B ALA 3.3 0.4 - - - -
117B THR* 1.3 77.6 - - - +
119B ARG* 1.3 57.8 + - - +
121B ALA* 3.4 3.7 + - - +
122B ALA* 2.9 28.8 + - - +
129B LEU* 4.1 15.9 - - + +
132B TYR* 3.7 11.7 - - + -
133B LEU* 4.3 15.7 - - + -
339B ILE* 5.4 1.3 - - + -
369B PHE* 4.5 3.1 - - + -
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Residues in contact with ARG 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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33B GLY* 4.1 10.9 - - - -
34B ALA 2.9 30.7 + - - +
35B ALA* 3.4 10.5 - - - +
115B MET 3.1 20.0 + - - +
116B ALA 3.6 4.7 - - - +
117B THR 3.3 0.2 - - - -
118B ALA* 1.3 77.6 - - - +
120B ALA* 1.3 55.3 + - - +
122B ALA* 3.4 3.9 + - - +
123B ALA* 2.9 28.9 + - - +
129B LEU* 4.0 28.2 - - + +
367B ASP* 2.8 43.9 + - - +
368B ALA* 4.0 5.9 - - - +
369B PHE* 3.2 28.9 - - + +
372B ASP* 5.4 1.8 + - - -
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Residues in contact with ALA 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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25B VAL* 3.7 13.2 - - + +
27B LEU* 3.6 25.2 - - + +
31B SER* 3.8 3.7 - - - +
32B VAL 4.0 5.2 - - - -
33B GLY* 3.5 26.2 - - - +
116B ALA 3.0 14.3 + - - +
117B THR 3.2 6.0 + - - +
119B ARG* 1.3 73.8 - - - +
121B ALA* 1.3 60.8 + - - +
123B ALA* 3.4 2.8 + - - +
124B ALA* 3.0 29.1 + - - +
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Residues in contact with ALA 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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27B LEU* 3.9 7.7 - - + +
83B ALA 3.9 10.1 - - - +
84B PHE* 3.6 16.8 - - + -
117B THR 2.9 13.5 + - - +
118B ALA* 3.5 6.1 - - - +
120B ALA* 1.3 73.4 - - - +
122B ALA* 1.3 64.8 + - - +
124B ALA* 3.2 4.0 + - - +
125B LEU* 3.2 25.1 + - - +
132B TYR* 3.4 35.9 - - + +
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Residues in contact with ALA 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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118B ALA 2.9 16.5 + - - +
119B ARG* 3.8 5.8 - - - +
121B ALA* 1.3 76.4 - - - +
123B ALA* 1.3 60.5 + - - +
125B LEU* 3.1 5.5 + - - +
126B GLY 3.0 3.6 + - - -
127B MET* 2.9 45.8 + - - +
129B LEU* 4.1 13.2 - - + +
132B TYR* 3.7 27.9 - - + -
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Residues in contact with ALA 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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31B SER* 4.3 7.8 + - - -
32B VAL 4.0 17.3 - - - +
119B ARG 2.9 18.5 + - - +
120B ALA 3.5 5.8 - - - +
122B ALA* 1.3 73.5 - - - +
124B ALA* 1.3 58.6 + - - +
126B GLY* 2.9 20.1 + - - +
127B MET 4.9 1.1 - - - -
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Residues in contact with ALA 124 (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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2B LEU* 3.6 20.8 - - + +
27B LEU* 4.2 4.7 - - + -
29B ASP* 3.5 12.9 - - - +
31B SER* 3.2 24.2 + - - +
84B PHE* 4.4 4.5 - - + -
120B ALA 3.0 15.3 + - - +
121B ALA 3.2 5.6 + - - +
123B ALA* 1.3 76.8 - - - +
125B LEU* 1.3 63.2 + - - +
126B GLY 3.3 0.2 - - - -
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Residues in contact with LEU 125 (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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1B MET* 5.3 3.8 - - - -
84B PHE* 3.6 35.7 - - + -
121B ALA 3.2 9.8 + - - +
122B ALA 3.1 8.6 + - - +
123B ALA 3.1 0.8 - - - -
124B ALA* 1.3 78.8 - - - +
126B GLY* 1.3 61.4 + - - +
127B MET* 3.4 14.7 + - + +
132B TYR* 4.1 13.0 - - + -
1C MET* 3.4 16.7 - - - +
125C LEU* 3.5 42.5 - - + +
127C MET* 3.4 31.2 - - + -
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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