Contacts of the helix formed by residues 121 - 135 (chain A) in PDB entry 3U9O
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 HIS 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.5 0.6 - - - +
38A LEU* 4.1 3.6 - - - -
75A GLU* 3.0 20.5 + - - -
91A TYR* 3.0 42.3 + + + -
93A TYR* 3.7 4.3 + - - -
98A MET* 3.2 31.2 - - + +
120A THR* 1.3 92.3 + - + +
122A GLU* 1.3 63.7 + - - +
123A GLN 3.3 2.9 + - - -
124A HIS* 3.4 16.3 + - + +
125A LEU* 2.9 29.4 + - + +
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Residues in contact with GLU 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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38A LEU* 3.6 23.0 - - + +
111A VAL* 4.7 4.2 - - + +
112A ALA 5.2 1.6 - - - +
113A TYR* 5.8 0.5 - - - -
114A VAL* 3.4 30.3 + - + +
119A ASN* 3.1 25.2 + - - +
120A THR 3.4 0.2 - - - -
121A HIS* 1.3 77.2 - - - +
123A GLN* 1.3 71.1 + - + +
125A LEU* 3.4 4.5 + - - +
126A ARG* 3.0 47.3 + - + +
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Residues in contact with GLN 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 ASN 4.8 0.4 + - - -
120A THR 4.9 2.6 + - - +
121A HIS 3.3 0.8 - - - -
122A GLU* 1.3 94.5 - - + +
124A HIS* 1.3 65.2 + - - +
126A ARG* 3.1 14.5 + - - +
127A LYS* 3.1 43.3 + - - +
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Residues in contact with HIS 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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101A GLU* 2.7 43.8 + - - -
121A HIS* 3.4 22.1 + - + +
123A GLN* 1.3 80.3 - - - +
125A LEU* 1.3 61.6 + - + +
127A LYS* 3.5 17.8 + - + +
128A ALA* 3.3 17.7 + - - +
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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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37A LEU 4.4 5.8 - - - +
38A LEU* 3.7 37.7 - - + +
39A VAL* 5.2 1.3 - - + -
91A TYR* 4.7 4.5 - - + -
100A GLY 4.1 1.6 - - - -
101A GLU* 3.5 41.5 - - + +
104A VAL* 3.6 21.9 - - + +
111A VAL* 3.5 14.9 - - + +
121A HIS* 2.9 29.6 + - + +
122A GLU 3.8 4.3 - - - +
124A HIS* 1.3 75.4 - - + +
126A ARG* 1.3 59.6 + - - +
128A ALA* 3.3 4.9 + - - +
129A GLU* 2.9 28.1 + - - +
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Residues in contact with ARG 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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111A VAL* 3.7 35.7 + - + +
112A ALA 4.1 11.3 + - - -
113A TYR* 4.8 14.1 - - - +
122A GLU* 3.0 35.8 + - + +
123A GLN* 3.1 18.6 + - - +
125A LEU* 1.3 76.1 - - - +
127A LYS* 1.3 58.6 + - + +
129A GLU* 3.0 31.9 + - - +
130A ALA* 2.9 28.8 + - - +
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Residues in contact with LYS 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 GLN* 3.1 34.2 + - - +
124A HIS* 3.6 17.7 - - + +
126A ARG* 1.3 73.8 - - + +
128A ALA* 1.3 65.6 + - - +
130A ALA* 3.2 8.0 + - - +
131A GLN* 3.0 24.1 + - - +
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Residues in contact with ALA 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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101A GLU* 4.3 20.4 - - + +
104A VAL* 4.0 11.4 - - + -
105A ARG* 3.9 31.5 - - + +
124A HIS 3.3 10.5 + - - +
125A LEU* 3.3 8.9 + - - +
127A LYS* 1.3 78.6 - - - +
129A GLU* 1.3 62.9 + - - +
131A GLN* 3.3 4.6 + - - +
132A ALA* 3.1 21.8 + - - +
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Residues in contact with GLU 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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104A VAL* 3.4 20.4 - - + +
109A ALA 5.3 0.4 - - - +
110A LYS* 3.6 12.6 - - - +
111A VAL* 3.0 29.9 + - + +
125A LEU 2.9 13.9 + - - +
126A ARG* 3.0 39.8 + - - +
128A ALA* 1.3 76.1 - - - +
130A ALA* 1.3 59.6 + - - +
132A ALA* 3.4 3.8 + - - +
133A LYS* 2.9 32.2 + - + +
140A TRP* 3.9 26.3 + - + +
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Residues in contact with ALA 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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126A ARG 2.9 13.5 + - - +
127A LYS* 3.2 11.2 + - - +
129A GLU* 1.3 75.4 - - - +
131A GLN* 1.3 59.6 + - - +
133A LYS* 3.1 19.1 - - - +
134A LYS* 2.8 29.2 + - - +
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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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105A ARG* 3.4 31.2 - - - +
127A LYS 3.0 12.1 + - - +
128A ALA* 3.6 8.5 - - - +
130A ALA* 1.3 75.7 - - - +
132A ALA* 1.3 64.8 + - - +
134A LYS* 3.1 29.3 + - - +
135A GLU* 3.0 51.7 + - - +
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Residues in contact with ALA 132 (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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104A VAL 3.4 17.9 - - - +
105A ARG* 3.4 30.3 - - - +
107A GLY* 3.7 10.1 - - - +
128A ALA 3.1 7.5 + - - +
129A GLU 3.6 7.4 - - - +
131A GLN* 1.3 73.3 - - - +
133A LYS* 1.4 60.5 + - - +
135A GLU* 3.3 2.1 + - - -
136A LYS 3.2 3.3 + - - -
137A LEU* 3.1 32.6 + - + +
140A TRP* 3.7 12.8 - - + +
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Residues in contact with LYS 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 GLU* 2.9 17.4 + - - +
130A ALA* 3.1 21.1 - - - +
132A ALA* 1.4 73.6 - - - +
134A LYS* 1.3 66.1 + - - +
136A LYS* 3.0 24.9 + - - +
140A TRP* 3.7 45.7 - - + +
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Residues in contact with LYS 134 (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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130A ALA 2.8 16.6 + - - +
131A GLN* 3.1 33.2 + - - +
133A LYS* 1.3 73.0 - - - +
135A GLU* 1.3 57.9 + - + +
136A LYS* 3.1 29.5 + - - +
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Residues in contact with GLU 135 (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 ARG* 2.6 45.4 + - - -
131A GLN* 3.0 31.5 + - - +
132A ALA 3.7 4.7 - - - +
133A LYS 3.1 0.4 - - - -
134A LYS* 1.3 77.3 - - + +
136A LYS* 1.3 67.6 + - - +
137A LEU* 3.1 22.7 + - + +
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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