Contacts of the helix formed by residues 126 - 144 (chain A) in PDB entry 3KJO
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 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ASN* 3.4 25.5 + - - +
125A PHE* 1.3 77.3 - - - +
127A THR* 1.3 60.2 + - - +
128A GLU* 3.0 34.2 + - - +
129A ASP* 2.7 32.7 + - - +
130A HIS* 3.1 19.1 + - - -
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Residues in contact with THR 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A THR* 1.3 75.8 - - - +
128A GLU* 1.3 88.6 + - - +
129A ASP 3.2 0.2 - - - -
130A HIS* 3.3 14.0 + - - +
131A LYS* 3.1 33.9 + - + +
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Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 6.1 4.9 - - + -
126A THR* 3.0 22.0 + - - +
127A THR* 1.3 103.9 - - - +
129A ASP* 1.3 56.8 + - - +
131A LYS* 3.5 20.4 + - + +
132A MET* 3.0 34.9 + - + +
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Residues in contact with ASP 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.6 8.4 + - - -
26A TYR* 2.6 31.4 + - - +
80A ARG* 2.7 36.1 + - - -
106A PHE* 5.3 0.2 - - + -
124A ASN* 4.1 1.7 - - - +
125A PHE* 3.3 18.1 - - + -
126A THR* 2.7 35.9 + - - +
128A GLU* 1.3 76.2 - - - +
130A HIS* 1.3 58.8 + - - +
132A MET* 3.1 4.8 + - - +
133A VAL* 2.8 36.1 + - - +
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Residues in contact with HIS 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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114A ILE* 4.0 31.4 + - + +
125A PHE* 3.4 36.6 - + - -
126A THR 3.1 21.2 + - - -
127A THR* 3.3 13.6 + - - +
129A ASP* 1.3 76.7 - - - +
131A LYS* 1.3 58.9 + - + +
133A VAL* 3.3 6.8 + - - +
134A GLU* 2.9 47.6 + - - +
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Residues in contact with LYS 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 THR* 3.1 31.3 + - + +
128A GLU* 3.6 21.5 - - - +
130A HIS* 1.3 79.4 - - + +
132A MET* 1.3 57.0 + - + +
134A GLU* 3.9 7.5 - - - +
135A ALA* 2.9 31.1 + - - +
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Residues in contact with MET 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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11A TYR* 4.0 27.8 - - + -
26A TYR* 3.6 53.6 - - + -
52A GLN* 6.4 0.4 - - - -
128A GLU* 3.0 26.0 + - + +
129A ASP 3.1 7.4 + - - +
131A LYS* 1.3 75.5 - - + +
133A VAL* 1.3 65.7 + - - +
135A ALA* 3.3 8.6 + - - +
136A LEU* 3.1 28.3 + - + +
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Residues in contact with VAL 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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26A TYR* 4.1 8.1 - - + -
78A ILE* 3.5 20.4 - - + +
106A PHE* 3.8 47.6 - - + -
114A ILE* 4.4 13.0 - - + -
129A ASP 2.8 23.9 + - - +
130A HIS* 3.6 5.8 - - - +
132A MET* 1.3 73.2 - - - +
134A GLU* 1.3 63.6 + - - +
136A LEU 3.0 2.9 + - - -
137A ARG* 2.9 51.4 + - - +
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Residues in contact with GLU 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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110A LEU* 4.7 1.0 - - - +
114A ILE* 3.9 24.7 - - + +
130A HIS* 2.9 36.0 + - - +
131A LYS* 3.9 6.8 - - - +
133A VAL* 1.3 74.3 - - - +
135A ALA* 1.3 56.2 + - - +
137A ARG* 3.2 13.1 + - - +
138A VAL* 3.0 37.1 + - + +
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Residues in contact with ALA 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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52A GLN* 3.9 19.8 + - - +
131A LYS 2.9 19.7 + - - +
132A MET* 3.5 10.8 - - - +
134A GLU* 1.3 76.8 - - - +
136A LEU* 1.3 62.5 + - - +
138A VAL* 3.5 7.4 + - - +
139A TRP* 3.2 21.7 + - - +
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Residues in contact with LEU 136 (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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26A TYR* 4.0 17.3 - - + -
27A GLY* 3.6 31.6 - - - +
28A VAL* 4.2 15.6 - - + +
51A ASP* 4.2 16.2 - - + -
52A GLN* 3.1 31.0 - - + +
78A ILE* 3.7 29.4 - - + -
132A MET* 3.1 11.8 + - + +
133A VAL 3.0 8.1 + - - +
135A ALA* 1.3 73.7 - - - +
137A ARG* 1.3 61.5 + - - +
139A TRP* 3.4 6.6 + - + +
140A ALA* 2.9 31.7 + - - +
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Residues in contact with ARG 137 (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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78A ILE* 3.4 17.9 - - + -
106A PHE* 4.6 0.6 - - - +
107A GLU* 2.9 32.3 + - - +
108A GLY 3.5 19.2 - - - +
109A THR 3.4 19.5 + - - -
110A LEU* 3.7 20.9 - - + +
111A GLY* 4.4 3.6 - - - +
112A ALA* 2.7 29.6 + - - +
113A PRO 3.0 24.9 + - - -
114A ILE* 3.4 25.0 - - - +
133A VAL* 2.9 22.1 + - - +
134A GLU* 3.2 13.9 + - - +
136A LEU* 1.3 73.9 - - - +
138A VAL* 1.3 66.4 + - - +
140A ALA* 3.9 1.8 - - - +
141A SER* 3.0 24.9 + - - -
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Residues in contact with VAL 138 (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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110A LEU* 3.9 19.3 - - + -
134A GLU* 3.0 24.3 + - + +
135A ALA* 3.7 8.3 - - - +
137A ARG* 1.3 76.5 - - - +
139A TRP* 1.3 63.1 + - - +
141A SER* 2.6 24.9 + - - +
142A THR* 4.0 5.2 + - - +
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Residues in contact with TRP 139 (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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28A VAL* 4.0 24.2 - - + -
30A LYS* 6.2 0.2 - - - -
50A VAL* 3.8 32.5 - - + -
51A ASP 3.4 21.3 - - - -
52A GLN* 3.8 38.3 + - + +
54A ASN* 3.9 19.8 + - - +
135A ALA 3.2 13.5 + - - +
136A LEU* 3.7 6.3 - - + +
137A ARG 3.3 0.2 - - - -
138A VAL* 1.3 80.8 - - - +
140A ALA* 1.3 88.0 - - + +
142A THR* 3.1 10.1 - - - +
143A HIS* 2.9 68.1 + + + -
144A MET* 4.3 10.5 - - + -
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Residues in contact with ALA 140 (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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28A VAL* 4.2 14.1 - - + -
76A GLY* 5.8 1.3 - - - +
78A ILE* 6.2 0.4 - - + -
108A GLY 4.9 8.3 - - - +
136A LEU 2.9 18.4 + - - +
137A ARG* 4.0 4.5 - - - +
139A TRP* 1.3 88.3 - - + +
141A SER* 1.3 61.7 + - - +
142A THR 3.0 3.1 - - - -
143A HIS 4.2 1.6 - - - +
144A MET* 2.9 47.6 + - + +
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Residues in contact with SER 141 (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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110A LEU* 3.4 33.2 - - - +
137A ARG 3.0 10.5 + - - -
138A VAL* 2.6 21.1 + - - +
140A ALA* 1.3 75.3 - - - +
142A THR* 1.3 59.1 + - - +
144A MET 4.0 7.9 - - - +
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Residues in contact with THR 142 (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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138A VAL 4.1 5.6 - - - +
139A TRP* 3.1 18.8 - - - +
141A SER* 1.3 81.5 + - - +
143A HIS* 1.3 80.3 + - + +
144A MET 3.4 3.7 + - - +
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Residues in contact with HIS 143 (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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30A LYS* 5.6 1.6 + - - -
54A ASN* 4.7 9.0 - - - -
139A TRP* 2.9 74.8 + + + +
140A ALA 3.2 0.2 + - - -
142A THR* 1.3 98.9 - - + +
144A MET* 1.3 68.8 + - - +
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Residues in contact with MET 144 (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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28A VAL* 3.5 29.4 - - + -
29A VAL 3.9 19.7 - - - +
30A LYS* 4.5 23.3 - - - +
50A VAL* 4.9 6.1 - - - -
75A ASN* 5.1 4.9 - - + -
76A GLY* 4.3 11.4 - - - +
139A TRP* 4.3 12.1 - - + -
140A ALA* 2.9 27.2 + - + +
141A SER* 4.0 9.5 - - - +
142A THR 3.4 2.2 - - - -
143A HIS* 1.3 90.6 - - - +
145A SER* 1.3 67.1 + - - +
146A PRO* 4.1 3.8 - - - +
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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