Contacts of the helix formed by residues 120 - 131 (chain A) in PDB entry 2ETK
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 PHE 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A PHE* 3.7 29.8 - + - -
105A LYS* 5.6 2.5 - - - -
107A LEU* 4.8 12.3 - - + -
112A MET* 4.1 25.8 - - + -
116A SER* 4.0 18.6 - - - -
118A SER* 3.1 28.2 - - - +
119A ALA* 1.3 76.3 - - - +
121A PHE* 1.3 73.5 + + + +
122A TRP 3.2 0.4 - - - -
123A GLU* 3.1 27.8 + - - +
124A GLU* 3.5 16.7 + - - +
216A ASP* 6.0 0.2 - - - -
218A GLY* 3.0 41.3 - - - +
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Residues in contact with PHE 121 (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* 4.2 17.7 - - + -
112A MET* 3.7 27.1 - - + -
119A ALA* 3.8 22.9 - - + -
120A PHE* 1.3 89.9 - + + +
122A TRP* 1.3 102.7 + + - +
123A GLU 3.3 0.2 - - - -
124A GLU* 3.8 8.2 - - - +
125A ARG* 2.9 32.8 + - - +
149A LEU* 4.1 4.5 - - + -
151A MET* 5.1 1.6 - - + +
393A PRO* 4.0 5.6 - - + -
394A PHE* 3.5 37.2 - + - -
397A PHE* 3.8 27.6 - + + -
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Residues in contact with TRP 122 (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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119A ALA* 3.3 30.3 - - + +
120A PHE 3.1 0.8 + - - -
121A PHE* 1.3 97.9 - + - +
123A GLU* 1.3 62.5 + - + +
125A ARG* 3.5 17.0 + - - +
126A ASP* 3.0 30.7 + - - +
393A PRO 3.6 14.7 + - - -
394A PHE* 4.5 1.1 - - - -
395A VAL 3.4 22.2 - - - -
396A GLY* 3.7 8.3 - - - -
397A PHE* 3.6 36.8 - + + -
58B ARG* 3.4 28.9 - - - +
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Residues in contact with GLU 123 (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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119A ALA 5.2 1.1 - - - +
120A PHE* 3.1 16.7 + - - +
122A TRP* 1.3 80.8 - - + +
124A GLU* 1.3 56.6 + - - +
126A ASP* 3.4 4.7 + - - +
127A ILE* 3.1 37.9 + - + +
194A PHE* 3.5 24.5 - - - -
217A PHE 4.3 7.2 - - - +
218A GLY 5.4 1.1 - - - +
220A CYS* 3.4 30.8 - - + +
221A MET* 4.9 3.8 - - - -
222A LYS* 4.4 7.4 + - - +
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Residues in contact with GLU 124 (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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105A LYS* 3.1 28.0 + - - +
107A LEU* 5.1 0.3 - - - +
120A PHE* 3.5 17.5 + - - +
121A PHE* 3.4 8.7 + - - +
122A TRP 3.3 0.4 - - - -
123A GLU* 1.3 77.9 - - - +
125A ARG* 1.3 63.5 + - - +
127A ILE* 4.3 0.4 - - - +
128A MET* 3.2 49.0 + - + +
151A MET* 3.6 22.5 - - - +
153A MET* 5.4 0.7 - - - +
216A ASP* 3.4 20.1 - - - +
217A PHE* 3.5 36.7 + - + +
218A GLY* 4.2 6.6 + - - +
416A HFS 5.5 0.2 + - - -
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Residues in contact with ARG 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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21A PRO 4.5 13.7 + - - -
22A LYS* 6.0 1.0 - - - +
121A PHE 2.9 18.0 + - - +
122A TRP* 3.8 16.4 + - - +
124A GLU* 1.3 76.3 - - - +
126A ASP* 1.3 66.3 + - - +
129A ALA* 3.2 29.2 + - + +
130A PHE* 4.6 14.1 - - - -
139A LEU* 3.8 23.3 - - + +
142A ALA* 4.5 3.8 - - + -
151A MET* 4.8 2.9 - - - -
396A GLY 3.7 12.5 + - - -
397A PHE* 3.2 54.1 + - + +
398A THR 3.4 17.2 + - - -
399A TYR* 3.4 23.6 - - + +
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Residues in contact with ASP 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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22A LYS* 5.4 3.5 - - - +
122A TRP 3.0 18.9 + - - +
123A GLU* 3.8 6.7 - - - +
125A ARG* 1.3 81.9 + - - +
127A ILE* 1.3 64.5 + - + +
130A PHE* 3.2 54.8 + - - +
192A MET* 4.9 2.1 - - - +
194A PHE* 4.5 15.6 - - + -
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Residues in contact with ILE 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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123A GLU 3.1 18.4 + - - +
124A GLU 4.3 2.5 - - - +
126A ASP* 1.3 73.7 - - - +
128A MET* 1.3 61.8 + - - +
131A ALA* 2.8 35.0 + - - +
136A VAL* 4.0 5.6 - - + -
189A ILE* 3.8 26.2 - - + -
192A MET* 3.9 22.7 - - + -
194A PHE* 4.0 28.7 - - + -
217A PHE* 3.9 24.2 - - + -
220A CYS* 3.8 36.3 - - + -
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Residues in contact with MET 128 (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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124A GLU* 3.2 33.8 + - + +
127A ILE* 1.3 75.8 - - - +
129A ALA* 1.3 55.8 + - - +
131A ALA* 4.8 1.6 + - - +
132A ASN 5.6 0.9 + - - -
136A VAL* 4.3 3.8 - - - +
137A VAL* 3.4 28.0 - - - +
138A GLN* 3.4 10.7 - - - +
139A LEU* 2.7 37.8 + - + -
151A MET* 3.7 30.3 - - - -
153A MET* 3.7 37.2 - - + +
216A ASP 4.9 4.7 - - - -
217A PHE* 3.7 23.6 - - + -
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Residues in contact with ALA 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 ARG* 3.2 21.5 + - + +
127A ILE 3.2 0.8 - - - -
128A MET* 1.3 77.2 - - - +
130A PHE* 1.3 74.2 + - + +
132A ASN 5.3 0.8 + - - -
138A GLN* 5.7 1.8 - - - +
139A LEU* 3.9 20.1 - - + +
399A TYR* 3.6 41.5 + - + -
404A ARG* 3.9 7.6 + - - +
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Residues in contact with PHE 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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21A PRO* 3.8 28.0 - - + -
22A LYS* 4.0 32.5 - - + +
125A ARG* 4.6 11.4 - - - -
126A ASP* 3.2 46.7 + - - +
127A ILE 3.3 1.8 + - - -
129A ALA* 1.3 90.2 - - + +
131A ALA* 1.3 66.0 + - - +
132A ASN* 3.1 4.4 - - - +
192A MET* 4.9 3.8 - - + -
399A TYR* 3.7 33.9 - + - -
404A ARG* 3.0 46.7 + - + +
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Residues in contact with ALA 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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127A ILE* 2.8 24.6 + - + +
128A MET* 4.7 1.5 - - - -
130A PHE* 1.3 73.1 - - - +
132A ASN* 1.3 67.5 + - - +
133A SER* 3.1 6.2 + - - -
136A VAL* 3.7 32.8 - - + -
192A MET* 3.7 34.6 - - + +
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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