Contacts of the helix formed by residues 98 - 111 (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 PRO 98 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109C MET* 3.8 13.7 - - + -
400C AMP 3.9 9.2 - - + +
96D ILE 3.7 1.5 - - - +
97D GLU* 1.3 87.1 - - + +
99D LEU* 1.3 55.5 + - - +
101D VAL* 3.7 7.0 - - + +
102D ALA* 2.8 31.9 + - - +
126D ASN* 4.4 6.1 - - - +
128D MET* 3.6 37.5 - - + -
130D ALA* 4.5 2.2 - - + -
131D THR* 3.0 31.3 + - - +
134D MET* 3.9 16.6 - - - +
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Residues in contact with LEU 99 (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* 4.5 13.5 - - - +
107C ASP* 4.2 7.6 - - - +
108C VAL 4.0 7.2 - - - +
109C MET* 3.7 36.2 - - + +
97D GLU* 2.9 4.1 + - + +
98D PRO* 1.3 78.9 - - - +
100D ALA* 1.3 63.1 + - - +
102D ALA* 3.7 1.4 + - - +
103D LYS* 3.2 43.8 + - - +
134D MET* 3.8 22.8 - - + -
138D ILE* 4.5 11.0 - - + -
218D ARG* 3.7 41.1 - - + +
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Residues in contact with ALA 100 (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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96D ILE* 4.2 2.7 - - + -
97D GLU* 2.8 16.3 + - + +
99D LEU* 1.3 75.3 - - - +
101D VAL* 1.3 67.6 + - - +
103D LYS* 3.1 8.2 + - - +
104D ILE* 3.0 28.1 + - - +
213D VAL* 4.1 9.4 - - + +
214D ASP 5.1 1.3 - - - +
215D VAL* 3.5 40.8 - - + -
216D ALA 5.8 2.2 - - - +
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Residues in contact with VAL 101 (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 3.8 36.6 - - + +
63D ILE* 3.9 17.5 - - + -
96D ILE* 3.6 32.3 - - + +
97D GLU 3.0 12.9 + - - +
98D PRO* 3.7 10.5 - - + +
100D ALA* 1.3 76.2 - - - +
102D ALA* 1.3 58.2 + - - +
104D ILE* 3.2 1.4 + - - +
105D LEU* 2.8 40.5 + - + +
131D THR* 3.9 17.5 - - + -
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Residues in contact with ALA 102 (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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98D PRO 2.8 22.5 + - - +
99D LEU 3.9 4.7 - - - +
101D VAL* 1.3 73.0 - - - +
103D LYS* 1.3 60.6 + - - +
105D LEU* 4.5 1.8 - - - -
106D ALA* 2.9 30.1 + - - +
131D THR* 4.2 6.7 - - + +
134D MET* 3.9 24.0 - - + -
135D LEU* 3.4 24.0 - - - +
138D ILE* 4.0 10.4 - - + +
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Residues in contact with LYS 103 (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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107C ASP* 3.1 30.8 + - - -
99D LEU* 3.2 27.7 + - + +
100D ALA* 3.1 9.2 + - - +
102D ALA* 1.3 77.4 - - - +
104D ILE* 1.3 61.2 + - - +
106D ALA* 3.5 7.0 - - - +
107D ALA* 3.3 19.8 + - - +
138D ILE* 3.8 20.6 - - + -
213D VAL* 4.1 28.0 - - + +
218D ARG* 3.7 14.6 - - - +
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Residues in contact with ILE 104 (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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63D ILE* 3.8 33.2 - - + -
86D VAL* 4.1 29.2 - - + -
88D ALA* 5.3 0.2 - - + -
96D ILE* 4.6 4.7 - - + -
100D ALA 3.0 16.4 + - - +
101D VAL 3.6 5.6 - - - +
102D ALA 3.2 0.2 - - - -
103D LYS* 1.3 73.6 - - - +
105D LEU* 1.3 66.1 + - + +
106D ALA 3.0 1.6 - - - -
107D ALA* 2.9 15.7 + - - +
108D VAL* 2.9 20.2 + - + +
208D ALA* 4.2 24.0 - - + -
211D TYR* 4.3 8.7 - - + -
213D VAL* 3.7 26.0 - - + -
215D VAL* 5.2 3.4 - - + -
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Residues in contact with LEU 105 (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 4.9 1.8 - - + -
4D LEU* 4.0 4.3 - - + +
6D PRO* 3.6 35.7 - - + -
61D VAL* 4.3 21.8 - - + -
63D ILE* 3.6 24.9 - - + -
101D VAL* 2.8 38.6 + - + +
102D ALA* 4.9 0.2 - - - -
104D ILE* 1.3 73.1 - - - +
106D ALA* 1.3 56.9 + - - +
108D VAL* 3.2 7.2 - - - +
109D ALA* 2.8 32.9 + - - +
131D THR* 4.1 10.8 - - + -
135D LEU* 3.8 30.1 - - + -
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Residues in contact with ALA 106 (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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102D ALA 2.9 19.9 + - - +
103D LYS* 3.5 10.1 - - - +
104D ILE 3.0 0.2 - - - -
105D LEU* 1.3 78.4 - - - +
107D ALA* 1.3 57.5 + - - +
109D ALA* 3.6 1.9 - - - +
110D ARG* 3.0 41.0 + - - +
135D LEU* 3.5 13.9 - - + +
138D ILE* 4.4 16.6 - - + -
139D LEU* 3.9 17.3 - - + +
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Residues in contact with ALA 107 (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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103D LYS 3.3 9.0 + - - +
104D ILE 2.9 8.5 + - - +
106D ALA* 1.3 77.2 - - - +
108D VAL* 1.3 59.9 + - - +
110D ARG* 3.0 11.5 + - - +
111D ALA* 2.7 31.2 + - - +
211D TYR* 3.6 36.6 - - + +
213D VAL* 5.6 0.4 - - + -
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Residues in contact with VAL 108 (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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4D LEU* 3.6 23.6 - - + -
61D VAL* 4.7 13.2 - - + -
84D ILE* 5.0 7.0 - - + -
86D VAL* 4.7 6.5 - - + -
104D ILE* 2.9 20.0 + - + +
105D LEU* 3.2 18.4 - - - +
107D ALA* 1.3 74.6 - - - +
109D ALA* 1.3 59.1 + - - +
111D ALA* 3.1 2.6 + - - -
112D GLU* 2.8 45.7 + - + +
211D TYR* 3.4 41.3 - - + +
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Residues in contact with ALA 109 (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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4D LEU* 3.8 5.8 - - + -
105D LEU 2.8 19.8 + - - +
106D ALA* 3.6 6.3 - - - +
108D VAL* 1.3 77.9 - - - +
110D ARG* 1.3 61.3 + - - +
113D GLY* 3.2 2.8 + - - -
114D THR* 2.9 48.4 + - - +
117D ILE* 3.7 25.1 - - + -
139D LEU* 4.7 7.0 - - + -
141D TRP* 4.8 2.9 - - + -
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Residues in contact with ARG 110 (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* 3.0 24.3 + - - +
107D ALA* 3.5 9.4 - - - +
109D ALA* 1.3 76.3 - - - +
111D ALA* 1.3 64.1 + - - +
113D GLY* 3.5 10.4 + - - -
138D ILE* 3.9 23.6 + - - +
139D LEU* 4.0 25.5 + - + +
141D TRP* 6.2 1.8 - - + -
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Residues in contact with ALA 111 (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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107D ALA 2.7 20.7 + - - +
108D VAL* 3.5 8.5 - - - +
110D ARG* 1.3 76.0 - - - +
112D GLU* 1.3 69.8 + - - +
113D GLY 3.5 0.5 + - - -
211D TYR* 4.8 10.3 - - + -
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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