Contacts of the helix formed by residues 124 - 142 (chain A) in PDB entry 2FQ4
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 TYR 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A MSE 4.3 16.2 - - + -
64A PHE* 4.5 1.8 - + - -
65A LEU* 4.0 10.1 - - + -
70A ALA* 4.2 1.1 - - + -
91A LEU* 3.4 23.8 - - + +
94A PHE* 3.5 31.9 - + - -
95A LEU* 3.7 4.0 - - - +
103A ILE* 3.9 25.6 - - + -
120A TYR* 3.0 13.7 + - + +
123A ARG* 1.3 80.0 - - - +
125A PHE* 1.3 99.6 + + + +
126A GLN 3.5 0.4 - - - -
127A PRO* 3.2 4.3 - - - +
128A ARG* 2.9 72.1 + - + +
163A PHE* 4.4 8.1 - + - -
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Residues in contact with PHE 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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103A ILE* 4.3 5.6 - - + -
107A VAL* 4.0 21.1 - - + -
120A TYR* 3.0 58.8 + + + -
121A ARG* 3.8 12.6 - - + +
124A TYR* 1.3 89.2 - + - +
126A GLN* 1.3 66.7 + - - +
128A ARG* 3.2 6.5 + - - +
129A ARG* 2.9 35.3 + - - +
159A TYR* 4.9 7.1 - + - -
163A PHE* 3.5 48.0 - + - -
167A LEU* 6.5 0.2 - - + -
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Residues in contact with GLN 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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121A ARG 2.8 21.9 + - - +
122A VAL* 3.1 28.5 + - - +
125A PHE* 1.3 72.5 - - - +
127A PRO* 1.3 80.2 - - + +
129A ARG* 3.2 8.8 + - - +
130A LEU* 2.8 43.2 + - + +
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Residues in contact with PRO 127 (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 VAL 3.3 18.2 - - - +
123A ARG 3.5 16.4 - - - +
124A TYR 3.2 14.1 - - - +
126A GLN* 1.3 103.5 - - + +
128A ARG* 1.3 72.8 + - - +
130A LEU* 3.5 7.7 - - + +
131A GLN* 3.2 26.0 + - - +
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Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A LEU* 3.9 6.1 - - - +
70A ALA* 2.9 55.2 + - - +
71A ARG* 4.1 2.7 - - - +
72A LEU* 4.4 10.9 - - + +
87A HIS* 3.5 2.6 + - - +
91A LEU* 4.8 5.1 - - + +
123A ARG 4.0 4.4 + - - -
124A TYR* 2.9 67.3 + - + +
125A PHE* 3.2 5.5 + - - +
127A PRO* 1.3 89.9 - - - +
129A ARG* 1.3 65.3 + - - +
131A GLN* 3.2 23.9 + - - +
132A ALA 3.2 15.8 + - - -
159A TYR* 3.0 30.9 + - + +
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Residues in contact with ARG 129 (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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125A PHE* 2.9 30.6 + - + +
126A GLN* 3.7 6.5 - - - +
128A ARG* 1.3 75.1 - - - +
130A LEU* 1.3 66.4 + - - +
132A ALA* 3.1 8.4 + - - +
133A LYS* 2.9 20.4 + - - +
152A GLU* 3.0 54.6 + - - +
155A ILE* 3.4 31.1 - - + +
156A ASP* 2.8 24.1 + - - +
159A TYR* 3.8 27.8 - - + +
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Residues in contact with LEU 130 (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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126A GLN* 2.8 32.1 + - + +
127A PRO* 3.5 12.6 - - + +
129A ARG* 1.3 72.3 - - - +
131A GLN* 1.3 61.4 + - + +
133A LYS* 3.2 28.2 + - + +
134A GLN* 3.1 48.8 + - + +
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Residues in contact with GLN 131 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ARG* 5.2 5.8 - - - +
72A LEU* 3.0 47.4 + - - +
73A PRO 5.4 0.4 - - - -
74A VAL* 3.7 22.6 - - + +
87A HIS* 3.8 14.4 + - + +
127A PRO 3.2 12.7 + - - +
128A ARG* 3.2 23.6 + - - +
130A LEU* 1.3 76.4 - - + +
132A ALA* 1.3 62.2 + - - +
134A GLN* 3.3 18.4 + - - +
135A LEU* 3.3 27.6 + - + +
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Residues in contact with ALA 132 (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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84A ILE* 4.0 10.8 - - + +
87A HIS* 4.0 19.0 + - + +
128A ARG 3.2 8.3 + - - +
129A ARG* 3.1 10.2 + - - +
131A GLN* 1.3 77.1 - - - +
133A LYS* 1.3 63.6 + - - +
135A LEU* 3.3 9.8 + - - +
136A LEU* 3.1 26.4 + - - +
155A ILE* 4.0 24.9 - - + -
158A ILE* 6.4 1.1 - - + -
159A TYR* 4.4 4.3 - - + -
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Residues in contact with LYS 133 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ARG 2.9 12.0 + - - +
130A LEU* 3.2 28.5 + - + +
132A ALA* 1.3 75.2 - - - +
134A GLN* 1.3 59.0 + - + +
136A LEU* 3.3 2.4 + - - +
137A GLU* 2.9 63.2 + - - +
151A ILE* 3.9 28.4 - - + +
152A GLU* 3.9 17.6 + - - +
155A ILE* 3.7 10.0 - - + +
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Residues in contact with GLN 134 (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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130A LEU* 3.1 36.6 + - + +
131A GLN* 3.5 21.1 - - - +
133A LYS* 1.3 77.7 - - + +
135A LEU* 1.3 63.2 + - + +
137A GLU* 3.5 14.5 + - - +
138A LYS* 3.2 31.4 + - - +
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Residues in contact with LEU 135 (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 VAL* 5.2 4.9 - - + -
75A PRO* 3.5 36.8 - - + +
80A ALA* 4.6 8.9 - - - +
83A ASP* 3.6 29.8 - - + +
84A ILE* 3.9 15.7 - - + -
87A HIS* 3.6 36.6 - - + -
131A GLN 3.3 14.6 + - - +
132A ALA* 3.7 5.2 - - - +
133A LYS 3.3 0.4 - - - -
134A GLN* 1.3 73.5 - - + +
136A LEU* 1.3 66.4 + - - +
138A LYS* 3.3 22.4 + - - +
139A GLY* 3.3 15.4 + - - -
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Residues in contact with LEU 136 (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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80A ALA* 5.3 1.6 - - + -
84A ILE* 4.0 25.4 - - + -
132A ALA 3.1 17.0 + - - +
133A LYS* 3.7 4.3 - - - +
135A LEU* 1.3 76.3 - - - +
137A GLU* 1.3 58.0 + - - +
139A GLY* 2.9 5.0 + - - -
140A ILE* 2.9 28.8 + - - +
145A LEU* 3.5 26.6 - - + +
149A LEU* 4.6 8.5 - - + -
151A ILE* 4.1 14.1 - - + +
154A SER* 4.0 22.7 - - - -
155A ILE* 3.7 31.2 - - + +
158A ILE* 5.3 5.6 - - + -
186A PHE* 4.6 10.5 - - + -
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A LYS* 2.9 59.8 + - - +
134A GLN* 3.8 12.6 - - - +
135A LEU 3.3 0.4 - - - -
136A LEU* 1.3 71.6 - - - +
138A LYS* 1.3 64.4 + - - +
140A ILE* 3.9 11.8 - - + +
141A LYS* 3.3 23.9 + - - +
151A ILE* 3.6 20.7 - - + +
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Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A VAL* 5.6 4.4 - - - +
75A PRO 3.4 23.4 + - - -
76A ASP* 3.7 27.3 + - - +
83A ASP* 4.1 11.9 - - - +
134A GLN* 3.2 23.8 + - - +
135A LEU* 3.5 18.1 - - - +
136A LEU 3.2 0.6 - - - -
137A GLU* 1.3 75.5 - - - +
139A GLY* 1.3 58.4 + - - +
141A LYS* 3.3 12.0 + - + +
142A ARG* 2.8 51.3 + - - +
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Residues in contact with GLY 139 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ALA* 3.9 13.2 - - - -
135A LEU 3.3 4.2 + - - -
136A LEU 2.9 8.8 + - - -
138A LYS* 1.3 76.6 - - - +
140A ILE* 1.3 63.5 + - - +
142A ARG* 3.3 3.4 + - - +
143A GLY 3.1 4.3 + - - -
144A GLU* 3.1 47.5 + - - +
145A LEU* 3.7 7.5 + - - -
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Residues in contact with ILE 140 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A LEU 2.9 16.9 + - - +
137A GLU* 3.9 10.5 - - + +
138A LYS 3.3 0.2 - - - -
139A GLY* 1.3 76.6 - - - +
141A LYS* 1.3 59.8 + - + +
143A GLY* 2.9 20.8 + - - -
145A LEU* 4.3 12.8 - - + +
146A LYS 5.3 2.7 - - - +
149A LEU* 3.9 39.0 - - + +
151A ILE* 4.0 24.5 - - + -
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Residues in contact with LYS 141 (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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137A GLU 3.3 12.2 + - - +
138A LYS* 3.3 18.2 - - + +
140A ILE* 1.3 81.5 - - + +
142A ARG* 1.3 58.3 + - + +
143A GLY 3.2 0.6 + - - -
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Residues in contact with ARG 142 (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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76A ASP* 4.5 4.9 + - - -
78A GLY* 3.4 38.2 + - - +
79A SER 3.8 2.8 - - - +
80A ALA* 3.6 13.9 - - - +
83A ASP* 4.7 2.4 + - - -
138A LYS* 2.8 42.4 + - - +
139A GLY 3.5 22.8 - - - +
140A ILE 3.1 0.2 - - - -
141A LYS* 1.3 76.9 - - + +
143A GLY* 1.3 61.3 + - - +
144A GLU* 2.8 41.1 + - + +
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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