Contacts of the helix formed by residues 106 - 125 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU 3.6 5.4 - - - -
51A LEU* 4.3 12.3 - - - -
102A TYR* 3.0 20.6 + - - +
103A SER* 5.4 0.2 - - - -
104A ASN 3.4 1.3 - - - -
105A LEU* 1.3 81.0 - - - +
107A ALA* 1.3 59.7 + - - -
108A ASN* 3.2 12.8 - - - -
109A ALA 3.0 15.8 + - - -
110A THR* 3.1 12.1 + - - +
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 4.8 0.9 - - - +
48A ALA* 3.9 20.6 - - + -
49A LEU 2.9 21.7 + - - +
50A GLU* 4.5 1.6 - - + +
102A TYR* 3.7 8.3 - - + +
106A GLY* 1.3 72.5 - - - -
108A ASN* 1.3 58.5 + - - +
109A ALA 3.3 0.2 - - - -
110A THR* 3.4 9.6 + - - -
111A LEU* 3.0 32.6 + - - +
334A ASN* 3.8 22.6 - - - +
337A GLY* 4.1 6.9 - - - +
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Residues in contact with ASN 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A THR* 5.1 4.4 + - - +
21A VAL* 3.8 18.5 - - + +
37A VAL* 3.3 42.2 - - + +
50A GLU* 3.5 26.3 + - + +
51A LEU 3.0 41.6 + - - +
63A VAL* 3.7 16.0 - - - +
66A ALA* 3.6 17.4 - - - +
106A GLY* 3.6 5.4 - - - -
107A ALA* 1.3 73.6 - - - +
109A ALA* 1.3 63.8 + - - +
112A GLY 3.8 1.0 + - - -
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 5.0 1.5 - - - +
66A ALA* 3.6 24.7 - - - +
69A ASN* 4.2 2.0 - - + -
70A VAL* 3.8 16.3 - - + +
74A ILE* 3.9 12.9 - - + +
105A LEU 3.3 26.9 - - - +
106A GLY 3.0 2.7 + - - +
108A ASN* 1.3 80.7 + - - +
110A THR* 1.3 64.6 + - - +
112A GLY* 4.3 0.3 - - - -
113A VAL* 3.5 25.8 + - - +
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Residues in contact with THR 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ILE* 4.3 7.4 - - + -
93A LEU* 3.8 20.6 - - + +
102A TYR* 3.7 30.1 - - + -
105A LEU* 3.7 27.6 - - + -
106A GLY 3.1 11.1 + - - +
107A ALA* 3.4 13.5 + - - -
109A ALA* 1.3 76.3 - - - +
111A LEU* 1.3 65.5 + - - +
112A GLY 3.3 0.2 + - - -
113A VAL* 3.3 1.6 + - - -
114A SER* 3.0 23.0 + - - -
337A GLY* 2.7 24.5 + - - -
338A THR* 4.4 1.1 - - - -
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 4.3 9.6 - - + -
38A PRO* 4.5 5.4 - - + -
107A ALA 3.0 19.0 + - - +
110A THR* 1.3 76.1 - - - +
112A GLY* 1.3 57.9 + - - +
114A SER* 3.2 1.7 + - - -
115A MET* 2.8 54.6 + - + +
333A PRO* 4.0 19.7 - - + +
334A ASN* 3.7 32.5 - - + +
337A GLY* 3.0 14.0 + - - +
338A THR* 3.8 30.5 - - - +
339A ILE* 4.1 11.2 - - + +
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Residues in contact with GLY 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 5.7 0.2 - - - -
23A ALA* 3.5 17.5 - - - +
35A ALA* 4.0 5.0 - - - +
37A VAL* 3.5 25.7 - - - +
108A ASN 4.4 0.7 - - - -
109A ALA 3.8 4.2 + - - -
110A THR 3.2 0.8 - - - -
111A LEU* 1.3 79.4 - - - +
113A VAL* 1.3 57.4 + - - +
115A MET* 3.5 7.4 + - - +
116A ALA* 2.9 32.1 + - - +
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 4.0 9.4 - - + -
23A ALA* 4.3 6.7 - - + -
25A VAL* 4.2 2.2 - - + +
70A VAL* 3.6 31.0 - - + -
74A ILE* 4.2 14.1 - - + -
78A ILE* 3.5 31.0 - - + -
89A LEU* 4.5 2.0 - - + -
93A LEU* 4.4 11.4 - - + -
109A ALA 3.5 14.9 + - - +
110A THR* 3.3 6.0 + - - +
111A LEU 3.3 0.4 - - - -
112A GLY* 1.3 74.0 - - - +
114A SER* 1.3 58.2 + - - +
116A ALA* 3.8 3.3 - - - +
117A THR* 2.8 44.0 + - - +
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLN* 3.1 21.9 + - - +
89A LEU* 4.1 4.9 - - - -
90A ASP* 2.6 32.2 + - - -
93A LEU* 4.3 2.2 - - - +
110A THR 3.0 18.0 + - - -
111A LEU 3.4 4.0 - - - -
113A VAL* 1.3 77.6 - - - +
115A MET* 1.3 61.4 + - - +
117A THR* 4.0 0.5 - - - -
118A ALA* 3.4 13.5 + - - +
338A THR* 4.0 7.0 - - - -
339A ILE* 2.9 29.2 + - - +
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Residues in contact with MET 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA* 3.4 21.3 - - + -
36A ILE 3.7 22.9 - - - +
37A VAL* 4.0 5.6 - - + -
38A PRO* 4.9 2.5 - - + -
111A LEU* 2.8 51.3 + - + +
112A GLY* 4.0 8.3 - - - -
114A SER* 1.3 73.5 - - - +
116A ALA* 1.3 60.0 + - - +
118A ALA 3.4 1.6 + - - -
119A ARG* 3.0 31.2 + - - +
333A PRO* 5.9 1.6 - - - -
339A ILE* 3.6 16.4 - - + -
367A ASP* 5.1 0.4 - - - +
369A PHE* 3.5 48.5 - - + -
370A ILE* 6.5 0.2 - - - -
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Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA 3.8 18.6 - - - +
25A VAL* 3.7 22.4 - - + -
33A GLY* 3.6 23.3 - - - +
34A ALA* 4.0 3.4 - - - +
35A ALA* 4.1 5.4 - - - +
112A GLY 2.9 22.6 + - - +
113A VAL 3.4 0.2 + - - -
115A MET* 1.3 71.4 - - - +
117A THR* 1.3 60.7 + - - +
119A ARG* 3.4 1.5 + - - +
120A ALA* 2.9 28.8 + - - +
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Residues in contact with THR 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE* 4.1 23.3 - - + +
25A VAL* 3.7 23.4 - - + +
27A LEU* 5.1 2.9 - - + +
82A ASP 5.7 0.4 - - - +
83A ALA* 3.8 20.9 - - - +
86A GLN* 4.4 4.9 - - - +
89A LEU* 3.4 29.2 - - + +
113A VAL* 2.8 24.0 + - - +
114A SER 4.0 0.7 - - - -
115A MET 3.3 0.2 - - - -
116A ALA* 1.3 77.3 - - - +
118A ALA* 1.3 57.4 + - - +
120A ALA* 3.1 2.3 + - - +
121A ALA* 2.9 27.9 + - - +
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Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLN* 3.6 20.5 + - - +
114A SER 3.4 9.5 + - - +
115A MET 3.6 8.5 - - - +
116A ALA 3.3 0.2 - - - -
117A THR* 1.3 79.7 - - - +
119A ARG* 1.3 55.0 + - - +
121A ALA 3.5 0.2 + - - -
122A ALA* 3.0 29.5 + - - +
129A LEU* 4.0 15.9 - - + +
132A TYR* 3.7 14.5 - - + -
133A LEU* 4.2 17.9 - - + -
339A ILE* 5.1 0.9 - - + -
369A PHE* 4.6 5.8 - - + -
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Residues in contact with ARG 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A GLY* 3.9 11.2 - - - -
34A ALA 3.0 25.0 + - - +
35A ALA* 3.6 7.9 - - - +
115A MET 3.0 19.7 + - - +
116A ALA 3.8 4.5 - - - +
118A ALA* 1.3 75.2 - - - +
120A ALA* 1.3 61.8 + - - +
122A ALA* 3.9 3.2 - - - +
123A ALA* 3.0 24.9 + - - +
129A LEU* 3.9 27.0 - - + +
367A ASP* 2.8 43.4 + - - -
368A ALA* 4.0 6.1 - - - +
369A PHE* 3.3 28.7 - - + +
372A ASP* 5.4 2.2 + - - -
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL 3.6 12.3 - - - +
27A LEU* 3.4 29.8 - - + +
31A SER* 3.7 3.4 - - - +
32A VAL 4.0 5.2 - - - -
33A GLY* 3.4 24.8 - - - +
116A ALA 2.9 14.9 + - - +
117A THR* 3.1 6.3 + - - +
119A ARG* 1.3 76.3 - - - +
121A ALA* 1.3 57.7 + - - +
123A ALA* 3.4 3.1 + - - +
124A ALA* 2.9 23.6 + - - +
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 3.7 11.3 - - + +
83A ALA 3.7 11.0 - - - +
84A PHE* 3.7 16.1 - - + -
117A THR 2.9 15.7 + - - +
118A ALA 3.8 1.6 - - - +
120A ALA* 1.3 73.9 - - - +
122A ALA* 1.3 64.9 + - - +
124A ALA* 3.2 3.3 + - - +
125A LEU* 3.2 25.5 + - - +
132A TYR* 3.5 34.8 - - + +
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ALA 3.0 18.2 + - - +
119A ARG* 3.9 5.6 - - - +
121A ALA* 1.3 74.3 - - - +
123A ALA* 1.3 61.7 + - - +
125A LEU* 3.2 4.8 + - - -
126A GLY 3.1 3.8 + - - -
127A MET* 2.8 47.8 + - - +
129A LEU* 4.1 13.5 - - + +
132A TYR* 3.6 27.7 - - + -
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A SER* 4.2 8.2 + - - -
32A VAL 4.1 16.4 - - - +
119A ARG 3.0 18.5 + - - +
120A ALA 3.6 4.3 - - - +
122A ALA* 1.3 73.4 - - - +
124A ALA* 1.3 67.3 + - - +
126A GLY* 2.9 15.1 + - - +
127A MET 4.9 0.9 - - - -
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LEU* 3.4 31.9 - - + -
27A LEU* 4.1 2.7 - - + -
29A ASP* 3.5 5.7 - - - +
31A SER* 3.2 22.8 + - - +
84A PHE* 4.4 5.2 - - + -
120A ALA 2.9 13.2 + - - +
121A ALA 3.2 7.6 + - - +
123A ALA* 1.3 77.5 - - - +
125A LEU* 1.3 60.5 + - - +
126A GLY 3.5 0.3 + - - -
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Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.9 27.8 - - + -
84A PHE* 3.6 26.0 - - + -
121A ALA 3.2 8.7 + - - +
122A ALA 3.2 7.3 + - - +
123A ALA 3.1 0.8 - - - -
124A ALA* 1.3 78.3 - - - +
126A GLY* 1.3 61.7 + - - +
127A MET* 3.3 26.9 + - + +
132A TYR* 4.0 21.5 - - + -
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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