Contacts of the helix formed by residues 107 - 126 (chain A) in PDB entry 2FC3
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 ALA 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ALA* 3.4 34.8 - - - +
25A ARG* 3.8 11.9 - - + +
26A ALA* 3.7 9.0 - - + +
104A PRO* 2.8 23.2 + - + +
106A ASP* 1.3 76.1 - - - +
108A GLU* 1.3 65.3 + - - +
109A THR 3.3 2.5 - - - -
110A LEU* 3.2 8.1 + - - -
111A VAL* 2.9 26.7 + - + +
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Residues in contact with GLU 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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104A PRO* 3.4 32.7 - - - +
105A GLY 3.1 15.9 + - - +
106A ASP* 3.1 2.7 - - - -
107A ALA* 1.3 77.9 - - - +
109A THR* 1.3 65.1 + - - +
111A VAL* 3.3 4.3 + - - +
112A ARG* 2.9 76.8 + - - +
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Residues in contact with THR 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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106A ASP 4.7 3.4 + - - -
107A ALA 3.3 0.6 - - - -
108A GLU* 1.3 76.1 - - - +
110A LEU* 1.3 68.8 + - + +
112A ARG* 3.2 11.0 + - + +
113A GLU* 2.9 45.3 + - + +
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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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18A LYS* 4.1 36.3 - - + +
21A GLU* 3.6 32.5 - - + -
22A ALA* 3.7 25.6 - - + +
25A ARG* 4.0 17.7 - - - +
106A ASP 5.4 1.3 + - - +
107A ALA* 3.2 8.7 + - - +
109A THR* 1.3 78.9 - - + +
111A VAL* 1.3 59.2 + - - +
113A GLU* 3.2 11.5 + - - +
114A ILE* 2.8 36.8 + - + +
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Residues in contact with VAL 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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22A ALA* 4.2 7.0 - - + -
49A LYS* 4.8 10.5 - - + +
50A LEU* 4.3 15.9 - - + -
101A ILE* 4.0 27.6 - - + -
104A PRO* 4.1 26.0 - - + -
107A ALA* 2.9 22.1 + - + +
108A GLU* 3.7 5.4 - - - +
110A LEU* 1.3 76.2 - - - +
112A ARG* 1.3 59.9 + - + +
114A ILE* 3.2 7.7 + - - +
115A VAL* 2.9 47.4 + - + +
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Residues in contact with ARG 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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108A GLU* 2.9 57.7 + - - +
109A THR* 3.7 10.7 + - + +
111A VAL* 1.3 78.9 - - + +
113A GLU* 1.3 63.2 + - + +
115A VAL* 3.4 6.4 + - - +
116A GLU* 3.0 25.3 + - - +
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Residues in contact with GLU 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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15A LEU* 5.0 1.6 - - - -
18A LYS* 2.8 38.6 + - + +
109A THR* 2.9 39.2 + - + +
110A LEU* 3.6 13.6 - - - +
112A ARG* 1.3 77.0 - - + +
114A ILE* 1.3 57.0 + - - +
116A GLU* 3.4 5.3 + - - +
117A LYS* 3.0 30.0 + - - +
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Residues in contact with ILE 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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15A LEU* 4.0 24.2 - - + +
18A LYS* 3.7 20.4 - - + +
19A ALA* 3.6 29.8 - - + +
22A ALA* 3.7 14.6 - - + -
50A LEU* 3.9 26.9 - - + -
78A VAL* 4.1 14.6 - - + -
110A LEU 2.8 25.5 + - - +
111A VAL 3.6 3.1 - - - +
113A GLU* 1.3 70.6 - - - +
115A VAL* 1.3 60.9 + - - +
117A LYS* 3.2 1.0 + - - +
118A VAL* 2.8 44.7 + - + +
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Residues in contact with VAL 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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49A LYS 4.6 2.9 - - - +
50A LEU* 4.3 9.4 - - + -
76A PRO* 3.8 36.2 - - + +
111A VAL* 2.9 35.5 + - + +
112A ARG* 3.8 6.3 - - - +
114A ILE* 1.3 76.9 - - - +
116A GLU* 1.3 65.1 + - - +
118A VAL* 3.5 4.8 + - - +
119A LYS* 3.1 28.5 + - + +
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Residues in contact with GLU 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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112A ARG 3.0 17.6 + - - +
113A GLU* 3.9 4.9 - - - +
115A VAL* 1.3 76.4 - - - +
117A LYS* 1.3 62.6 + - - +
119A LYS* 2.7 41.7 + - - +
120A GLU* 3.1 19.8 + - - +
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Residues in contact with LYS 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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12A PRO* 4.8 9.6 - - - -
15A LEU* 3.7 34.5 - - + -
113A GLU 3.0 17.5 + - - +
114A ILE 3.8 0.2 - - - +
116A GLU* 1.3 77.4 - - - +
118A VAL* 1.3 57.7 + - - +
120A GLU* 3.0 44.4 + - - +
121A LEU* 2.9 40.1 + - + +
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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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9A PHE* 4.0 7.9 - - + -
15A LEU* 4.0 9.2 - - + -
50A LEU* 5.8 0.7 - - + -
76A PRO* 5.6 6.1 - - + -
77A TYR 3.5 21.3 - - - +
78A VAL* 3.8 35.0 - - + -
114A ILE* 2.8 25.5 + - + +
115A VAL* 4.0 5.4 - - - +
117A LYS* 1.3 73.6 - - - +
119A LYS* 1.3 60.5 + - - +
121A LEU* 3.1 9.3 + - + +
122A ARG* 2.8 51.7 + - + +
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Residues in contact with LYS 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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115A VAL* 3.1 17.1 + - + +
116A GLU* 2.7 50.2 + - - +
118A VAL* 1.3 76.8 - - - +
120A GLU* 1.3 58.3 + - - +
122A ARG* 4.0 4.7 - - - +
123A ALA* 3.0 31.2 + - + +
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Residues in contact with GLU 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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116A GLU* 3.1 11.2 + - - +
117A LYS* 3.0 49.1 + - - +
119A LYS* 1.3 74.3 - - - +
121A LEU* 1.3 72.2 + - + +
123A ALA* 3.3 5.3 + - - +
124A LYS* 3.1 23.0 + - + +
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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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9A PHE* 4.6 9.1 - - + +
10A GLU 3.7 23.3 - - - +
11A VAL* 4.2 9.0 - - + -
12A PRO* 3.7 24.0 - - + -
15A LEU* 3.7 26.0 - - + -
117A LYS* 2.9 30.5 + - - +
118A VAL* 3.6 12.6 - - + +
120A GLU* 1.3 82.6 - - + +
122A ARG* 1.3 59.8 + - + +
124A LYS* 3.3 5.7 + - - +
125A ALA* 3.0 30.0 + - - +
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Residues in contact with ARG 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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9A PHE* 3.6 32.0 - - + -
71A ASP* 3.0 39.2 + - - -
75A ILE 5.6 0.2 + - - -
76A PRO* 5.6 3.2 - - - +
77A TYR* 3.4 27.7 + - - +
118A VAL* 2.8 37.3 + - + +
119A LYS* 4.1 4.7 - - - +
121A LEU* 1.3 71.6 - - - +
123A ALA* 1.3 61.4 + - - +
125A ALA* 4.4 4.3 - - - +
126A GLY* 2.8 25.6 + - - -
127A VAL* 2.7 48.4 + - + +
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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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119A LYS* 3.0 20.5 + - + +
120A GLU* 3.8 6.1 - - - +
122A ARG* 1.3 77.5 - - - +
124A LYS* 1.3 63.3 + - - +
126A GLY* 3.6 7.3 + - - -
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Residues in contact with LYS 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 GLU* 3.1 14.3 + - + +
121A LEU* 3.7 9.4 - - - +
123A ALA* 1.3 79.0 - - - +
125A ALA* 1.3 62.1 + - - +
126A GLY* 3.4 0.7 + - - -
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Residues in contact with ALA 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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8A ARG 5.6 0.2 - - - +
9A PHE* 4.6 10.8 - - + -
121A LEU 3.0 17.8 + - - +
122A ARG* 4.2 1.3 - - - +
124A LYS* 1.3 78.0 - - - +
126A GLY* 1.3 61.4 + - - +
127A VAL* 3.6 29.0 + - + +
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Residues in contact with GLY 126 (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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122A ARG 2.8 10.7 + - - -
123A ALA* 4.1 6.7 - - - -
124A LYS 3.2 3.6 - - - -
125A ALA* 1.3 79.5 - - - +
127A VAL* 1.3 62.5 + - - +
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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