Contacts of the helix formed by residues 131 - 139 (chain D) in PDB entry 1EFP
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 THR 131 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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400C AMP 3.1 46.0 + - - +
98D PRO* 3.0 34.4 - - - +
101D VAL* 3.9 23.7 - - + +
102D ALA* 4.2 3.3 - - - +
105D LEU* 4.1 12.3 - - + -
119D ALA* 5.5 1.1 - - + -
130D ALA* 1.3 73.8 - - - +
132D GLY* 1.3 67.0 + - - +
134D MET* 3.3 5.3 + - - +
135D LEU* 2.9 22.1 + - + +
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Residues in contact with GLY 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400C AMP 4.6 4.6 + - - -
119D ALA* 4.6 6.7 - - - +
120D GLY 5.6 0.2 + - - -
130D ALA 3.5 0.6 - - - -
131D THR* 1.3 78.6 - - - +
133D GLN* 1.3 63.0 + - - +
135D LEU* 3.1 8.2 + - - +
136D ALA* 2.9 25.0 + - - +
143D GLN* 5.9 0.9 - - - -
145D THR* 6.1 0.2 - - - -
177D VAL* 3.4 24.8 - - - +
179D THR* 3.9 16.9 - - - +
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Residues in contact with GLN 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C LYS 2.9 26.7 + - - -
97C ASN* 3.6 8.0 - - - +
100C PRO* 3.6 13.8 - - + +
101C ARG* 4.0 10.8 - - - +
121D LYS 5.2 0.9 - - - +
129D ASN* 3.1 31.4 + - - +
130D ALA* 3.4 18.4 + - - +
131D THR 3.3 0.2 - - - -
132D GLY* 1.3 75.1 + - - +
134D MET* 1.3 66.8 + - - +
136D ALA* 3.3 3.1 + - - +
137D ALA* 2.9 24.6 + - - +
143D GLN* 3.2 32.8 + - - +
145D THR* 3.8 18.4 - - + +
146D PHE* 5.1 0.4 - - - -
179D THR* 4.5 4.5 - - - +
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Residues in contact with MET 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C PRO* 3.7 21.1 - - + +
103C ALA* 4.1 6.7 - - + -
104C ALA* 3.7 16.2 - - + +
108C VAL 3.8 22.9 - - - +
109C MET* 4.2 4.0 - - - -
110C VAL* 4.1 22.7 - - + +
98D PRO* 3.9 13.7 - - - -
99D LEU* 3.8 37.2 - - + -
102D ALA* 3.9 12.1 - - + -
130D ALA* 3.0 24.1 + - - +
131D THR 3.8 4.5 - - - +
133D GLN* 1.3 75.5 - - - +
135D LEU* 1.3 57.2 + - - +
137D ALA* 3.5 0.9 - - - +
138D ILE* 3.0 35.5 + - - +
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D PRO* 5.2 0.4 - - + -
102D ALA* 3.4 28.9 - - + +
105D LEU* 3.8 29.4 - - + +
106D ALA* 3.5 24.7 - - + +
117D ILE* 3.8 29.6 - - + -
119D ALA* 5.9 1.6 - - + -
131D THR 2.9 12.4 + - - +
132D GLY* 3.2 10.5 - - - +
134D MET* 1.3 73.7 - - - +
136D ALA* 1.3 67.7 + - - +
137D ALA 3.0 1.2 + - - -
138D ILE* 3.0 3.5 + - - +
139D LEU* 2.9 44.5 + - + +
177D VAL* 4.0 9.0 - - + -
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Residues in contact with ALA 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ARG* 3.4 19.0 + - - +
132D GLY 2.9 11.9 + - - +
133D GLN 3.7 5.4 - - - +
135D LEU* 1.3 73.9 - - - +
137D ALA* 1.3 51.6 + - - +
139D LEU* 4.7 0.2 - - - -
140D GLY* 2.7 30.1 + - - -
141D TRP* 2.7 16.1 + - - +
142D ALA 3.6 21.3 - - - +
143D GLN* 3.7 13.9 - - + +
177D VAL* 3.8 14.6 - - + +
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Residues in contact with ALA 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ARG* 3.6 33.7 + - + +
104C ALA* 3.6 19.7 - - + -
105C LEU* 4.5 19.3 - - + +
133D GLN 2.9 17.6 + - - +
134D MET 3.5 4.9 - - - +
136D ALA* 1.3 77.5 - - - +
138D ILE* 1.3 62.4 + - - +
140D GLY* 3.1 13.2 + - - -
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Residues in contact with ILE 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ALA* 4.2 15.9 - - + +
99D LEU* 4.5 14.1 - - + -
102D ALA* 4.0 17.0 - - + -
103D LYS* 3.8 33.4 - - + +
106D ALA* 4.4 18.2 - - + -
110D ARG* 3.9 15.6 + - - +
134D MET 3.0 19.0 + - - +
135D LEU* 3.9 3.1 - - - +
137D ALA* 1.3 76.3 - - - +
139D LEU* 1.3 61.4 + - - +
140D GLY* 4.7 0.2 - - - -
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Residues in contact with LEU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D ALA* 3.9 28.7 - - + +
109D ALA* 4.7 2.7 - - + -
110D ARG* 4.0 27.9 + - + +
117D ILE* 3.8 11.2 - - + -
135D LEU* 2.9 43.8 + - + +
136D ALA 4.0 0.4 - - - +
138D ILE* 1.3 77.3 - - - +
140D GLY* 1.3 61.9 + - - +
141D TRP* 3.6 57.7 + - + +
177D VAL* 4.2 2.5 - - + -
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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