Contacts of the helix formed by residues 104 - 118 (chain A) in PDB entry 3AG2
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 LEU 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A MET* 2.9 38.4 + - + +
101A SER* 4.7 0.4 - - - -
102A PHE 3.1 0.2 + - - -
103A TRP* 1.3 78.6 - - - +
105A LEU* 1.4 59.0 + - - +
107A PRO* 3.4 5.4 - - - +
108A SER* 3.1 25.5 + - - -
152A LEU* 4.1 19.8 - - + +
155A VAL* 3.8 30.3 - - + -
156A SER* 3.8 28.7 - - - +
159A LEU* 4.8 2.9 - - + -
20C GLY 4.8 0.7 - - - +
21C ALA* 3.9 13.2 - - + +
24C ALA* 3.7 30.7 - - + -
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Residues in contact with LEU 105 (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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19A TYR* 3.6 30.7 - - + -
22A PHE* 3.7 21.4 - - + -
67A PHE 4.8 3.4 - - - +
68A PHE* 4.2 11.1 - - + -
72A PRO* 3.8 26.0 - - + -
101A SER 3.8 11.0 - - - +
102A PHE* 2.9 12.1 + - + +
104A LEU* 1.4 75.7 - - - +
106A PRO* 1.3 68.2 - - + +
108A SER* 3.1 3.0 + - - -
109A PHE* 2.9 24.9 + - - +
153A ALA* 4.1 23.1 - - + +
156A SER* 3.7 22.0 - - - +
157A SER* 6.1 0.7 - - - +
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Residues in contact with PRO 106 (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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22A PHE* 3.7 22.9 - - + -
102A PHE* 3.2 19.5 - - + +
103A TRP* 3.5 30.1 - - + +
105A LEU* 1.3 91.6 - - + +
107A PRO* 1.3 66.5 - - + +
109A PHE* 3.3 3.3 + - + +
110A LEU* 2.8 29.3 + - - +
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Residues in contact with PRO 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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103A TRP* 2.8 30.5 - - + +
104A LEU* 3.4 9.4 - - - +
106A PRO* 1.3 90.6 - - + +
108A SER* 1.3 61.4 + - - +
110A LEU* 3.3 8.2 + - + +
111A LEU* 3.0 27.5 + - - +
152A LEU* 3.9 11.7 - - + -
21C ALA* 4.0 17.0 - - + +
22C LEU* 5.0 7.2 - - + -
25C LEU* 3.8 32.6 - - + +
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Residues in contact with SER 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 3.2 17.2 - - - -
104A LEU 3.1 16.6 + - - -
105A LEU* 3.1 10.3 + - - -
107A PRO* 1.3 75.0 - - - +
109A PHE* 1.3 61.7 + - - +
111A LEU* 3.2 1.8 + - - -
112A LEU 3.1 10.0 + - - -
149A SER* 2.6 56.7 + - - +
152A LEU* 3.9 16.0 - - - +
153A ALA* 3.6 9.0 - - - +
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Residues in contact with PHE 109 (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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22A PHE* 3.7 24.7 - + + -
25A TRP* 3.6 25.8 - + - -
26A ALA* 3.8 19.5 - - + -
29A VAL* 3.8 28.9 - - + -
64A VAL* 3.9 26.5 - - + -
68A PHE* 3.6 23.3 - + + -
105A LEU 2.9 18.4 + - - +
106A PRO* 3.7 4.7 - - + +
108A SER* 1.3 69.5 - - - +
110A LEU* 1.3 60.9 + - - +
112A LEU* 3.2 3.6 + - + +
113A LEU* 2.9 54.5 + - + +
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Residues in contact with LEU 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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106A PRO 2.8 17.6 + - - +
107A PRO* 3.5 6.5 - - + +
109A PHE* 1.3 78.3 - - - +
111A LEU* 1.3 56.8 + - + +
113A LEU* 3.3 12.4 + - + +
114A ALA* 2.8 31.5 + - + +
25C LEU* 4.0 32.3 - - + -
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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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107A PRO 3.0 19.7 + - - +
108A SER* 3.5 6.5 - - - +
109A PHE 3.2 0.2 - - - -
110A LEU* 1.3 77.7 - - + +
112A LEU* 1.3 62.6 + - - +
114A ALA* 3.3 6.9 + - + +
115A SER* 3.0 18.2 + - - -
145A LEU* 3.7 36.7 - - + +
148A PHE* 3.8 23.8 - - + +
149A SER* 3.8 11.2 - - - +
152A LEU* 3.8 18.6 - - + -
25C LEU* 4.0 9.9 - - + -
28C THR* 3.4 23.3 - - - +
29C SER* 3.9 23.1 - - - +
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Residues in contact with LEU 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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60A ALA* 4.4 13.5 - - + +
63A PHE* 3.7 40.4 - - + -
64A VAL* 3.7 30.1 - - + -
68A PHE* 3.8 13.5 - - + -
108A SER 3.1 6.3 + - - +
109A PHE* 3.2 10.3 + - + +
111A LEU* 1.3 77.8 - - - +
113A LEU* 1.3 64.6 + - + +
115A SER* 2.6 31.0 + - - +
116A SER* 3.3 6.8 + - - -
145A LEU 5.1 0.2 - - - -
146A THR* 4.3 16.6 - - + +
149A SER* 3.7 19.4 - - - +
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Residues in contact with LEU 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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25A TRP* 4.5 19.1 - - + -
29A VAL* 4.6 12.6 - - + -
33A LEU* 6.4 0.4 - - + -
60A ALA* 6.5 0.7 - - + -
64A VAL* 5.7 0.9 - - + -
109A PHE* 2.9 48.1 + - + +
110A LEU* 3.8 12.6 - - + +
112A LEU* 1.3 80.5 - - + +
114A ALA* 1.3 62.4 + - - +
116A SER* 2.7 28.4 + - - +
117A MET* 3.2 15.9 + - + +
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Residues in contact with ALA 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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110A LEU* 2.8 21.6 + - + +
111A LEU* 3.4 11.4 - - + +
113A LEU* 1.3 77.2 - - - +
115A SER* 1.3 63.9 + - - +
117A MET* 3.0 17.1 + - - +
118A VAL* 3.0 21.7 + - + +
145A LEU* 3.8 18.8 - - + -
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Residues in contact with SER 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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111A LEU 3.0 9.6 + - - -
112A LEU* 2.6 25.7 + - - +
114A ALA* 1.3 76.4 - - - +
116A SER* 1.3 60.8 + - - +
118A VAL* 3.4 4.0 + - - +
121A GLY* 3.3 7.8 - - - -
122A ALA* 4.8 3.5 + - - +
142A SER* 2.9 51.1 + - - +
145A LEU* 3.6 19.9 - - - +
146A THR* 3.4 16.0 + - - -
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Residues in contact with SER 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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56A VAL* 4.1 20.1 - - - +
60A ALA* 5.7 7.0 - - - -
112A LEU 3.3 5.8 + - - -
113A LEU* 2.7 27.8 + - - +
115A SER* 1.3 81.4 + - - +
117A MET* 1.3 64.2 + - - +
118A VAL 4.3 2.5 - - - +
119A GLU 5.4 0.9 - - - +
120A ALA 5.1 0.9 - - - -
121A GLY* 4.1 14.7 + - - -
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Residues in contact with MET 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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113A LEU* 3.3 18.6 - - + +
114A ALA* 3.0 10.6 + - - +
116A SER* 1.3 83.4 - - - +
118A VAL* 1.3 64.9 + - + +
119A GLU 4.1 3.9 + - - +
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Residues in contact with VAL 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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114A ALA* 3.0 22.0 + - + +
115A SER 3.4 1.6 - - - +
116A SER 4.3 0.2 - - - +
117A MET* 1.3 79.7 - - + +
119A GLU* 1.3 75.0 + - + +
121A GLY 3.1 7.3 + - - -
141A ALA* 4.1 9.9 - - + -
142A SER* 3.0 36.3 + - - +
145A LEU* 3.6 24.0 - - + -
37C PHE* 5.7 9.6 - - + -
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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