Contacts of the helix formed by residues 129 - 147 (chain A) in PDB entry 1F16
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 VAL 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A ALA 3.4 14.5 + - - +
125A LEU 4.8 0.2 + - - -
127A THR* 3.7 22.0 - - + +
128A LYS* 1.3 80.9 - - - +
130A PRO* 1.3 62.7 - - - +
131A GLU* 3.1 11.2 - - + +
132A LEU* 2.9 47.3 + - + +
133A ILE* 3.6 2.8 + - - +
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Residues in contact with PRO 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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44A GLU* 4.6 14.5 - - + +
124A ALA 4.8 0.2 - - - -
125A LEU* 6.1 0.2 - - - -
128A LYS* 3.4 10.8 - - - +
129A VAL* 1.3 83.9 - - - +
131A GLU* 1.3 66.2 + - + +
132A LEU 2.9 6.1 - - - -
133A ILE* 3.0 40.3 + - + +
134A ARG* 3.6 9.8 + - - +
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Residues in contact with GLU 131 (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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129A VAL* 3.1 10.8 - - + +
130A PRO* 1.3 81.8 - - + +
132A LEU* 1.3 59.4 + - - +
134A ARG* 3.9 11.2 + - - +
135A THR* 2.9 24.5 + - - -
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Residues in contact with LEU 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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88A PRO* 5.7 9.4 - - + -
124A ALA* 3.9 20.6 - - + -
129A VAL* 2.9 28.8 + - + +
131A GLU* 1.3 79.1 - - - +
133A ILE* 1.3 65.4 + - - +
134A ARG 3.2 0.4 - - - -
135A THR* 3.0 17.2 + - + +
136A ILE* 2.9 35.6 + - + +
139A TRP* 4.7 13.5 - - + -
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Residues in contact with ILE 133 (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 ILE* 6.3 0.2 - - + -
44A GLU* 3.0 49.6 - - + +
45A LEU* 4.6 10.1 - - + -
121A VAL* 4.3 21.3 - - + +
124A ALA* 4.4 4.2 - - + +
125A LEU* 4.0 37.5 - - + +
129A VAL 4.3 2.7 - - - +
130A PRO* 3.0 26.7 + - + +
132A LEU* 1.3 80.4 - - - +
134A ARG* 1.3 64.3 + - + +
136A ILE* 3.3 10.0 + - - +
137A MET* 3.3 26.0 + - + +
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Residues in contact with ARG 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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43A PRO 5.6 1.2 + - - -
44A GLU* 4.7 20.3 + - + +
45A LEU* 4.8 17.3 - - + -
46A ALA* 6.4 0.4 - - - +
130A PRO 3.6 11.3 + - - +
131A GLU* 4.1 10.1 - - - +
132A LEU 3.2 0.2 - - - -
133A ILE* 1.3 79.4 - - + +
135A THR* 1.3 63.2 + - - +
137A MET* 3.6 7.1 + - - +
138A GLY* 3.2 18.5 + - - -
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Residues in contact with THR 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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131A GLU 2.9 16.2 + - - -
132A LEU* 3.0 20.4 + - + +
134A ARG* 1.3 79.5 - - - +
136A ILE* 1.3 64.3 + - - +
138A GLY* 3.4 3.8 + - - -
139A TRP* 3.3 49.8 + - + +
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Residues in contact with ILE 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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92A PHE* 6.2 1.6 - - + -
117A ALA* 4.7 2.7 - - + +
120A LEU* 3.2 46.9 - - + +
121A VAL* 3.4 27.8 - - + -
124A ALA* 3.9 13.2 - - + -
132A LEU* 2.9 32.1 + - + +
133A ILE* 3.5 6.1 - - - +
135A THR* 1.3 72.5 - - - +
137A MET* 1.3 56.5 + - - +
138A GLY 2.4 17.6 + - - -
139A TRP* 2.4 42.1 + - + +
140A THR* 3.1 16.2 + - + -
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Residues in contact with MET 137 (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 ALA 5.4 1.3 - - - +
27A LEU* 4.6 11.0 - - - -
28A GLN* 3.8 36.3 - - + +
31A ILE* 3.6 29.8 - - - -
45A LEU* 4.5 16.8 - - + -
121A VAL* 4.7 8.7 - - + -
133A ILE* 3.3 22.6 + - + +
134A ARG* 4.1 7.4 - - - +
136A ILE* 1.3 75.1 - - - +
138A GLY* 1.3 58.9 + - - +
140A THR* 2.3 32.3 + - - +
141A LEU* 3.1 25.1 + - + +
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Residues in contact with GLY 138 (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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134A ARG 3.2 12.4 + - - -
135A THR* 3.6 6.3 - - - -
136A ILE 2.4 12.9 + - - -
137A MET* 1.3 71.0 - - - +
139A TRP* 1.3 56.5 + - - -
141A LEU* 4.3 3.0 - - - +
142A ASP* 2.4 43.8 + - - +
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Residues in contact with TRP 139 (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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88A PRO* 4.5 21.3 - - + -
89A ARG* 3.3 43.0 - - + +
92A PHE* 3.7 46.9 - + + -
120A LEU* 5.9 3.4 - - + -
132A LEU* 4.7 13.2 - - + -
135A THR* 3.3 38.4 + - + +
136A ILE* 2.4 41.5 + - + +
138A GLY* 1.3 74.8 - - - -
140A THR* 1.3 63.9 + - + +
142A ASP* 3.6 13.9 - - - +
143A PHE* 3.3 13.2 + - - +
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Residues in contact with THR 140 (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* 3.8 28.9 - - + +
92A PHE* 4.5 11.0 - - + -
113A LEU* 5.9 4.8 - - + +
117A ALA* 4.0 23.3 - - + -
121A VAL* 5.6 0.7 - - + -
136A ILE* 3.7 17.0 - - + +
137A MET* 2.3 35.9 + - - +
139A TRP* 1.3 75.0 - - + +
141A LEU* 1.3 73.3 + - - +
142A ASP 3.0 1.5 + - - -
143A PHE* 3.0 6.3 + - - +
144A LEU* 2.9 21.9 + - - +
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Residues in contact with LEU 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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20A MET* 3.5 25.8 - - + -
23A GLY 4.5 3.4 - - - +
24A ALA* 3.8 42.6 - - + +
27A LEU* 6.1 1.8 - - + -
137A MET* 3.1 25.2 + - + +
138A GLY* 4.4 3.4 - - - +
140A THR* 1.3 84.7 + - - +
142A ASP* 1.3 57.8 + - - +
144A LEU* 3.6 11.4 - - + -
145A ARG* 2.6 37.4 + - + +
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Residues in contact with ASP 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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138A GLY* 2.4 30.7 - - - +
139A TRP* 3.6 15.7 - - - +
140A THR 3.0 0.6 + - - -
141A LEU* 1.3 79.4 - - - +
143A PHE* 1.3 58.5 + - - +
145A ARG* 4.8 2.2 - - - -
146A GLU* 2.9 40.1 + - + +
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Residues in contact with PHE 143 (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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92A PHE* 4.8 13.9 - + + -
93A PHE* 5.2 17.5 - + - -
96A ALA* 4.4 20.0 - - + -
97A ALA* 5.1 5.8 - - - -
100A PHE* 3.9 44.2 - + + -
113A LEU* 4.2 13.9 - - + -
139A TRP 3.3 9.1 + - - +
140A THR* 3.0 7.9 + - - +
142A ASP* 1.3 79.7 - - - +
144A LEU* 1.3 59.2 + - - +
146A GLU* 4.7 3.6 - - - -
147A ARG* 2.9 63.5 + - + +
148A LEU* 3.5 16.7 + - + -
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Residues in contact with LEU 144 (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 ILE* 4.9 7.2 - - + -
20A MET* 4.3 12.8 - - + -
23A GLY* 4.4 20.0 - - - +
113A LEU* 6.4 0.4 - - + -
114A PHE* 4.9 12.8 - - + -
140A THR 2.9 15.9 + - - +
141A LEU* 3.8 12.8 - - + +
143A PHE* 1.3 76.2 - - - +
145A ARG* 1.3 67.9 + - - +
148A LEU* 3.1 60.7 + - + +
149A LEU* 3.4 1.7 + - + +
152A ILE* 4.0 9.6 - - + -
158A TRP* 4.2 21.5 - - + -
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Residues in contact with ARG 145 (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 MET* 3.6 34.5 - - + +
141A LEU 2.6 23.8 + - - +
142A ASP* 4.2 2.9 - - - +
144A LEU* 1.3 75.3 - - - +
146A GLU* 1.3 72.9 + - + +
149A LEU* 3.4 27.0 - - + +
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Residues in contact with GLU 146 (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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142A ASP* 2.9 29.0 + - + +
143A PHE* 4.3 2.0 - - - +
145A ARG* 1.3 97.9 + - + +
147A ARG* 1.3 66.1 - - + +
149A LEU* 5.0 1.5 + - - +
151A TRP* 5.6 1.2 - - - -
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Residues in contact with ARG 147 (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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93A PHE* 6.2 2.8 - - - -
100A PHE* 6.1 5.3 - - + +
143A PHE* 2.9 62.6 + - + +
146A GLU* 1.3 82.8 - - + +
148A LEU* 1.3 63.2 + - + +
149A LEU 3.0 10.3 + - - -
150A GLY 4.2 0.5 + - - -
151A TRP* 3.1 42.0 - - - -
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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