Contacts of the helix formed by residues 121 - 133 (chain A) in PDB entry 3KHE
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 SER 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLN 5.1 2.5 - - - -
118A LEU 4.2 9.5 + - - -
119A LEU 2.9 10.0 + - - -
120A LEU* 1.3 77.7 - - - +
122A ARG* 1.3 59.4 - - - +
123A GLU* 3.9 13.7 + - - +
124A ARG* 3.1 34.2 + - - +
125A LEU* 2.9 28.6 + - - +
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Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A LEU 3.9 0.2 + - - -
121A SER* 1.3 73.6 - - - +
123A GLU* 1.3 66.6 + - - +
125A LEU* 3.5 6.4 + - - +
126A LEU* 2.9 32.2 + - - +
176A PHE* 4.6 5.8 - - + -
191A VAL* 2.9 54.5 + - + +
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A SER* 4.1 11.1 - - - +
122A ARG* 1.3 87.6 + - - +
124A ARG* 1.3 58.6 + - + +
126A LEU* 3.3 4.5 + - - +
127A ALA* 2.9 30.2 + - - +
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Residues in contact with ARG 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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29A MET* 3.9 11.9 - - + +
33A LEU* 3.2 50.0 + - + +
34A THR* 3.7 7.4 - - - +
35A THR* 5.6 0.2 - - - +
38A GLU* 2.8 43.6 + - - -
114A MET* 3.8 5.1 - - - +
118A LEU 2.8 27.3 + - - -
119A LEU* 2.7 39.2 + - - +
121A SER* 3.1 19.6 + - - +
123A GLU* 1.3 77.5 - - + +
125A LEU* 1.3 61.5 + - - +
127A ALA* 3.4 0.6 + - - -
128A ALA* 2.9 30.7 + - - +
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Residues in contact with LEU 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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29A MET* 4.0 20.0 - - + -
120A LEU* 3.6 22.7 - - + +
121A SER 2.9 20.4 + - - +
122A ARG* 3.7 5.8 - - - +
124A ARG* 1.3 75.4 - - - +
126A LEU* 1.3 57.4 + - - +
128A ALA* 3.6 0.2 - - - +
129A PHE* 2.9 29.8 + - - +
176A PHE* 4.0 14.1 - - + -
179A PHE* 3.6 20.6 - - + -
180A VAL* 4.8 9.4 - - + -
183A MET* 3.9 31.6 - - + -
191A VAL* 3.8 30.1 - - + -
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Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ARG 2.9 18.4 + - - +
123A GLU* 3.9 4.9 - - - +
125A LEU* 1.3 74.4 - - - +
127A ALA* 1.3 66.7 + - - +
129A PHE* 4.2 4.3 - - + -
130A GLN* 3.1 54.7 + - + +
176A PHE* 3.7 37.0 - - + -
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.8 25.4 - - + -
123A GLU 2.9 17.7 + - - +
124A ARG* 4.5 0.2 - - - -
126A LEU* 1.3 74.7 - - - +
128A ALA* 1.3 66.7 + - - +
130A GLN* 3.2 11.6 + - - +
131A GLN* 3.0 31.5 + - + +
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ALA 4.7 2.5 - - - +
28A PHE* 3.9 22.4 - - + -
29A MET* 4.1 18.2 - - + -
33A LEU* 4.0 1.8 - - - +
124A ARG 2.9 21.9 + - - +
125A LEU 3.6 4.3 - - - +
127A ALA* 1.3 71.6 - - - +
129A PHE* 1.3 66.6 + - - +
131A GLN* 3.0 2.9 + - - -
132A PHE* 3.0 37.2 + - + -
179A PHE* 4.2 15.5 - - + -
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Residues in contact with PHE 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 LEU 2.9 17.2 + - - +
126A LEU* 3.6 7.9 - - + +
127A ALA 3.2 0.2 - - - -
128A ALA* 1.3 79.6 - - - +
130A GLN* 1.3 68.4 + - + +
132A PHE* 3.2 2.4 + - - +
133A ASP* 2.8 44.8 + - + +
138A GLY* 3.4 32.1 - - - -
139A LYS* 4.1 0.2 - - - -
140A ILE* 3.6 32.0 - - + +
174A VAL 3.6 7.4 - - - -
175A ASP 3.6 6.1 - - - -
176A PHE* 3.5 53.4 - + + -
179A PHE* 3.8 17.9 - + + -
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Residues in contact with GLN 130 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A LEU* 3.1 49.9 + - + +
127A ALA* 3.9 7.9 - - - +
129A PHE* 1.3 81.8 - - + +
131A GLN* 1.3 72.9 + - - +
133A ASP* 3.4 22.0 - - - +
134A SER* 4.7 1.2 - - - -
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Residues in contact with GLN 131 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A PHE* 3.9 32.3 - - + -
33A LEU* 6.3 0.2 - - + -
127A ALA* 3.0 23.7 + - + +
128A ALA 3.6 3.8 - - - +
130A GLN* 1.3 87.7 + - - +
132A PHE* 1.3 65.3 + - + +
134A SER* 4.0 7.3 + - - -
147A ARG* 2.9 21.0 + - - -
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Residues in contact with PHE 132 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.9 17.3 - - + -
24A ALA* 3.6 23.8 - - + -
25A ALA* 3.7 28.9 - - + -
28A PHE* 4.1 25.8 - + + -
128A ALA* 3.0 22.6 + - + +
129A PHE 3.8 3.1 - - - +
131A GLN* 1.3 79.6 - - + +
133A ASP* 1.3 57.3 + - - +
134A SER* 2.9 14.4 + - - -
140A ILE* 4.0 20.4 - - + -
144A GLU* 3.4 23.7 - - - +
147A ARG* 4.2 5.6 + - - +
148A LEU* 3.6 43.1 - - + -
179A PHE* 4.5 6.7 - + - -
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Residues in contact with ASP 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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129A PHE* 2.8 31.7 + - + +
130A GLN* 3.4 15.1 - - - +
132A PHE* 1.3 71.2 - - - +
134A SER* 1.3 63.4 + - - +
135A ASP* 3.0 7.6 - - - +
136A GLY* 3.0 14.0 + - - -
137A SER* 3.3 6.6 + - - -
138A GLY* 2.8 29.4 + - - -
139A LYS 3.2 6.6 - - - +
140A ILE* 4.1 7.0 - - + +
144A GLU* 4.0 5.4 - - - -
193A CA 2.2 32.4 - - - -
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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