Contacts of the helix formed by residues 104 - 125 (chain A) in PDB entry 6O4O
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 GLU 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A LEU* 3.8 18.5 - - + +
38A GLN* 3.8 26.1 + - - +
100A THR 4.6 0.2 - - - +
101A LEU 3.5 7.1 - - - +
102A GLU 3.2 18.5 - - - +
103A PRO* 1.3 86.4 - - + +
105A LEU* 1.3 63.5 + - - +
107A THR* 3.3 8.1 + - - -
108A LEU* 2.9 24.3 + - - +
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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
----------------------------------------------------------
35A LEU* 3.6 23.1 - - + +
87A VAL* 3.8 25.3 - - + +
90A LEU* 4.3 26.0 - - + +
91A ARG* 3.7 27.4 - - + +
98A LEU* 5.3 7.2 - - + +
101A LEU* 2.9 38.8 + - + +
102A GLU* 3.8 8.5 - - + +
103A PRO 3.3 0.6 - - - -
104A GLU* 1.3 75.1 - - - +
106A GLY* 1.3 63.9 + - - +
108A LEU* 3.3 6.3 + - + +
109A GLN* 3.0 21.8 + - - +
157A LEU* 4.3 16.8 - - + -
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Residues in contact with GLY 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ARG* 3.3 34.2 + - - +
102A GLU* 3.0 12.6 + - - -
103A PRO 3.2 2.9 + - - -
105A LEU* 1.3 78.2 - - - +
107A THR* 1.3 60.8 + - - +
109A GLN* 3.3 3.5 + - - +
110A ALA* 3.1 22.2 + - - +
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Residues in contact with THR 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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31A ASP* 5.7 1.6 - - - +
103A PRO* 3.0 18.4 + - - +
104A GLU* 3.3 10.9 + - - -
106A GLY* 1.3 72.8 - - - +
108A LEU* 1.3 65.4 + - - +
110A ALA* 3.2 7.7 + - + +
111A ARG* 3.0 41.4 + - + +
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU* 3.6 21.5 - - + -
31A ASP* 3.9 20.0 - - + -
32A THR* 3.6 23.6 - - - +
35A LEU* 4.1 12.3 - - + -
87A VAL* 4.7 9.2 - - + -
104A GLU 2.9 17.5 + - - +
105A LEU* 3.5 10.5 - - + +
107A THR* 1.3 76.5 - - - +
109A GLN* 1.3 56.1 + - - +
111A ARG* 3.2 6.2 + - - +
112A LEU* 2.8 32.1 + - + +
157A LEU* 3.9 28.3 - - + -
160A LEU* 4.2 17.3 - - + -
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Residues in contact with GLN 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.9 23.2 - - + +
87A VAL* 3.9 12.0 - - + +
88A GLN* 3.4 42.3 + - - +
91A ARG* 2.9 37.7 + - - +
105A LEU 3.0 12.7 + - - +
106A GLY* 3.4 9.9 - - - +
107A THR 3.2 0.2 - - - -
108A LEU* 1.3 76.8 - - - +
110A ALA* 1.3 62.2 + - - +
112A LEU* 3.3 9.2 + - - +
113A ASP* 3.0 27.9 + - - +
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Residues in contact with ALA 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 GLY 3.1 14.0 + - - +
107A THR* 3.2 10.1 + - + +
109A GLN* 1.3 75.5 - - - +
111A ARG* 1.3 63.7 + - + +
113A ASP* 3.3 12.0 + - - +
114A ARG* 3.1 19.9 + - - +
117A ARG* 4.9 2.1 + - - -
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Residues in contact with ARG 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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24A LEU* 4.8 7.4 + - - +
27A SER* 3.2 39.6 + - - -
28A LEU* 3.6 17.1 - - + +
31A ASP* 2.6 30.3 + - - -
107A THR* 3.0 33.8 + - + +
108A LEU* 3.8 3.6 - - - +
110A ALA* 1.3 78.2 - - + +
112A LEU* 1.3 64.1 + - - +
114A ARG* 3.2 25.6 + - + +
115A LEU* 3.0 22.2 + - - +
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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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28A LEU* 3.6 28.6 - - + +
80A LEU* 3.7 41.3 - - + +
83A TYR* 4.1 8.7 - - + +
84A LEU* 3.6 39.3 - - + +
87A VAL* 4.6 7.4 - - + -
108A LEU* 2.8 16.8 + - + +
109A GLN* 3.5 8.1 - - - +
111A ARG* 1.3 76.8 - - - +
113A ASP* 1.3 56.9 + - - +
115A LEU* 3.2 2.8 + - - +
116A LEU* 2.9 34.5 + - + +
160A LEU* 4.4 14.6 - - + -
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Residues in contact with ASP 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.2 26.6 - - - +
109A GLN* 3.0 17.4 + - - +
110A ALA* 3.4 14.3 - - - +
112A LEU* 1.3 75.8 - - - +
114A ARG* 1.3 61.4 + - - +
116A LEU* 3.3 10.3 + - - +
117A ARG* 3.0 41.8 + - - +
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Residues in contact with ARG 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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24A LEU* 3.4 38.9 - - + +
110A ALA 3.1 9.9 + - - +
111A ARG* 3.2 26.8 + - + +
113A ASP* 1.3 78.0 - - - +
115A LEU* 1.3 62.6 + - - +
117A ARG* 3.2 28.7 + - - +
118A ARG* 3.0 29.7 + - + +
202A CL 2.9 34.3 - - - +
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Residues in contact with LEU 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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21A THR* 4.3 18.6 - - + +
24A LEU* 4.2 24.4 - - + +
25A THR* 3.7 32.3 - - + +
28A LEU* 3.7 26.0 - - + -
76A LEU* 6.0 1.1 - - + -
80A LEU* 3.8 24.9 - - + -
111A ARG 3.0 13.3 + - - +
112A LEU* 3.2 8.3 + - - +
114A ARG* 1.3 77.4 - - - +
116A LEU* 1.3 61.6 + - - +
118A ARG* 3.2 4.1 + - + +
119A LEU* 3.0 28.9 + - + +
164A LEU* 4.0 8.7 - - + -
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 3.5 39.0 + - + +
80A LEU* 3.8 23.6 - - + +
81A LEU* 4.0 34.1 - - + +
84A LEU* 4.4 15.9 - - + -
112A LEU* 2.9 18.4 + - + +
113A ASP* 3.6 12.6 - - - +
115A LEU* 1.3 75.3 - - - +
117A ARG* 1.3 62.4 + - - +
119A LEU* 3.2 7.1 + - + +
120A GLN* 3.1 21.7 + - - +
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Residues in contact with ARG 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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110A ALA 4.9 1.8 + - - -
113A ASP* 3.0 32.2 + - - +
114A ARG* 3.2 37.5 + - - +
116A LEU* 1.3 74.9 - - - +
118A ARG* 1.3 62.6 + - - +
120A GLN* 3.4 5.7 + - - +
121A LEU* 3.0 24.5 + - - +
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Residues in contact with ARG 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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17A GLU* 5.9 1.9 + - - -
20A SER* 3.0 28.4 + - - -
21A THR* 3.9 34.1 - - + +
24A LEU* 3.9 26.1 - - + +
114A ARG* 3.0 21.8 + - + +
115A LEU* 3.2 12.3 + - + +
117A ARG* 1.3 77.5 - - - +
119A LEU* 1.3 57.5 + - - +
121A LEU* 3.7 11.5 - - - +
122A LEU* 2.9 27.8 + - + +
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Residues in contact with LEU 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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21A THR* 3.8 27.1 - - + -
73A LEU* 4.0 25.4 - - + -
76A LEU* 3.8 28.0 - - + -
77A ARG* 3.8 27.4 - - + +
80A LEU* 3.9 21.1 - - + -
115A LEU* 3.0 25.9 + - + +
116A LEU* 3.2 6.7 + - - +
118A ARG* 1.3 74.8 - - - +
120A GLN* 1.4 65.1 + - - +
122A LEU* 3.4 6.2 + - + +
123A MET* 3.1 28.2 + - - +
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Residues in contact with GLN 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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77A ARG* 2.6 41.1 + - - +
116A LEU 3.1 12.4 + - - +
117A ARG* 3.4 7.6 + - - +
119A LEU* 1.4 75.9 - - - +
121A LEU* 1.3 58.6 + - - +
123A MET* 3.3 2.8 + - - +
124A SER* 2.9 35.3 + - - +
130A GLN* 3.8 14.0 + - - +
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Residues in contact with LEU 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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117A ARG 3.0 17.3 + - - +
118A ARG* 3.7 11.9 - - - +
120A GLN* 1.3 74.9 - - - +
122A LEU* 1.3 60.0 + - - +
124A SER* 3.1 10.7 + - - -
125A ARG* 2.8 59.8 + - + +
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Residues in contact with LEU 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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17A GLU* 3.3 44.4 - - + +
18A LEU* 4.0 19.7 - - + -
21A THR* 3.7 23.6 - - + +
73A LEU* 4.0 27.1 - - + -
118A ARG* 2.9 18.9 + - + +
119A LEU* 3.6 7.2 - - + +
120A GLN 3.3 0.2 - - - -
121A LEU* 1.3 75.6 - - - +
123A MET* 1.3 63.3 + - - +
125A ARG* 3.9 6.0 - - + +
126A LEU* 3.0 46.2 + - + +
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Residues in contact with MET 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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70A PRO* 4.0 11.7 - - + +
73A LEU* 3.8 29.8 - - + -
74A THR* 3.6 18.6 - - - +
77A ARG* 3.2 35.2 - - - +
119A LEU 3.1 16.1 + - - +
120A GLN 3.7 4.3 - - - +
121A LEU 3.2 0.2 - - - -
122A LEU* 1.3 76.2 - - - +
124A SER* 1.3 58.2 + - - +
126A LEU 3.6 0.2 - - - -
127A ALA 3.0 5.7 + - - -
128A LEU* 2.9 52.6 + - + +
129A PRO 3.4 26.0 - - - +
130A GLN* 3.8 12.3 - - - +
131A PRO* 4.7 0.9 - - + -
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Residues in contact with SER 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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120A GLN* 2.9 15.9 + - - +
121A LEU* 3.1 16.7 + - - -
123A MET* 1.3 77.5 - - - +
125A ARG* 1.3 58.8 + - - +
127A ALA* 2.9 20.4 + - - +
130A GLN* 3.0 20.5 + - - +
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Residues in contact with ARG 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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10A GLY 3.5 19.8 + - - +
12A PRO* 3.4 50.2 - - + +
17A GLU* 2.8 38.7 + - - -
121A LEU* 2.8 49.6 + - + +
122A LEU* 4.0 6.3 - - + +
124A SER* 1.3 73.0 - - - +
126A LEU* 1.3 61.0 + - + +
127A ALA* 3.5 2.6 + - - +
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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
------------------------------------------------------------
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