Contacts of the helix formed by residues 139 - 148 (chain A) in PDB entry 3F7G
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 ASP 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A LEU* 5.6 4.5 - - - +
137A GLY 3.3 5.9 + - - +
138A ASP* 1.3 71.8 - - - +
140A PRO* 1.4 70.8 - - - +
141A TRP* 3.9 15.0 + - - +
142A THR* 2.7 35.8 + - - +
143A GLU* 2.9 34.0 + - - +
162A PHE* 4.8 3.3 - - - -
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Residues in contact with PRO 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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103A VAL* 4.3 6.7 - - + -
107A LEU* 3.8 39.3 - - + +
108A LEU* 3.9 24.2 - - + +
111A ALA* 3.7 20.9 - - + -
113A PHE* 3.7 8.1 - - + -
134A TRP* 4.0 13.4 - - + -
138A ASP 3.5 8.7 - - - +
139A ASP* 1.4 92.0 - - - +
141A TRP* 1.3 57.2 + - + +
143A GLU 3.9 0.2 - - - -
144A HIS* 2.9 30.7 + - - +
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Residues in contact with TRP 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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107A LEU* 5.6 1.1 - - + -
110A ALA* 3.5 23.0 - - - +
111A ALA* 3.6 29.1 - - + +
139A ASP* 3.3 14.5 - - - +
140A PRO* 1.3 81.5 - - + +
142A THR* 1.3 57.9 + - - +
144A HIS* 3.5 6.9 - - - +
145A ALA* 3.1 27.5 + - - +
153A PHE* 3.6 16.4 - + - -
154A LEU* 3.5 31.7 - - + +
157A SER* 3.3 33.2 - - - -
158A LYS* 3.4 36.4 - - + +
162A PHE* 3.6 18.7 - - + -
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Residues in contact with THR 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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139A ASP* 2.7 37.2 + - - +
141A TRP* 1.3 75.5 - - - +
143A GLU* 1.3 66.8 + - - +
145A ALA* 3.2 2.8 + - - -
146A LYS* 2.8 30.2 + - + +
162A PHE* 4.2 12.5 - - - -
166A VAL* 3.5 23.8 - - + +
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Residues in contact with GLU 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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131A LEU* 3.8 19.2 - - + +
134A TRP* 3.9 11.7 - - + -
138A ASP* 4.6 7.6 - - + -
139A ASP 2.9 22.7 + - - +
140A PRO 3.9 3.1 - - - +
142A THR* 1.3 79.9 - - - +
144A HIS* 1.3 65.9 + - - +
146A LYS* 3.3 16.2 + - - +
147A TRP* 3.0 52.8 + - + +
71D ALA* 3.9 19.8 + - - -
72D GLY 4.3 1.0 + - - -
73D ALA* 3.7 33.1 + - + +
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Residues in contact with HIS 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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111A ALA 2.8 29.5 + - - -
113A PHE* 3.7 16.1 - + + -
124A CYS* 3.6 16.1 - - + +
140A PRO 2.9 18.4 + - - +
141A TRP* 3.5 11.6 - + - +
143A GLU* 1.3 77.2 - - - +
145A ALA* 1.3 57.5 + - - +
148A PHE* 2.9 44.0 + + + +
151A CYS* 3.5 6.5 - - + -
153A PHE* 4.3 8.1 - + - -
154A LEU* 3.7 23.5 - - + +
1001A ZN 2.3 36.8 - - - -
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Residues in contact with ALA 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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141A TRP 3.1 15.0 + - - +
142A THR 3.7 3.8 - - - +
144A HIS* 1.3 77.3 - - - +
146A LYS* 1.3 62.1 + - - +
149A PRO* 3.7 12.8 - - - +
154A LEU* 3.5 16.6 - - + -
162A PHE* 4.1 9.2 - - + -
163A VAL* 4.2 12.5 - - - +
166A VAL* 3.8 25.1 - - + -
167A GLN* 2.9 21.8 - - - +
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Residues in contact with LYS 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 THR* 2.8 19.1 + - + +
143A GLU* 3.5 18.7 + - - +
145A ALA* 1.3 76.7 - - - +
147A TRP* 1.3 96.9 + - + +
149A PRO* 4.3 0.7 - - - +
166A VAL* 3.5 15.8 - - + +
167A GLN* 2.9 17.9 + - - +
71D ALA* 3.3 31.9 - - - +
72D GLY 5.0 1.0 - - - +
73D ALA 5.3 1.0 + - - -
150D SER* 5.7 0.3 - - - -
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Residues in contact with TRP 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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131A LEU* 3.5 22.0 - - + +
143A GLU* 3.0 45.9 + - - +
146A LYS* 1.3 103.9 - - + +
148A PHE* 1.3 83.1 + - + +
149A PRO* 3.3 11.7 - - - +
73D ALA 3.8 17.2 + - - -
74D THR* 5.0 1.1 - - - -
75D LEU* 3.6 42.0 - - + -
149D PRO* 5.2 1.2 - - - +
150D SER* 2.6 37.6 + - - -
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Residues in contact with PHE 148 (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 PHE* 4.5 3.4 - + - -
127A CYS* 3.7 19.1 - - + -
129A GLY* 3.3 42.4 - - - -
130A GLY 3.5 6.7 - - - -
131A LEU* 3.7 22.0 - - + -
144A HIS* 2.9 31.8 + + + +
147A TRP* 1.3 96.6 - - + +
149A PRO* 1.3 64.2 - - - +
150A SER* 3.3 3.6 - - - -
151A CYS* 3.1 18.7 + - + +
154A LEU* 3.4 6.2 - - - +
75D LEU* 3.5 31.4 - - + -
150D SER* 4.0 6.3 - - - -
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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