Contacts of the helix formed by residues 126 - 146 (chain D) in PDB entry 6CAJ
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 TYR 126 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D ARG* 5.9 8.7 - - - +
51D TRP* 3.9 25.7 + + - +
52D SER* 3.6 37.3 + - - -
125D HIS* 1.3 113.8 + + - +
127D ALA* 1.3 65.5 + - + +
128D GLN 3.6 0.2 - - - -
129D LEU* 4.4 0.8 - - - +
130D GLN* 3.4 24.0 + - - +
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Residues in contact with ALA 127 (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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126D TYR* 1.3 78.6 - - + +
128D GLN* 1.3 61.6 + - - +
129D LEU 3.4 0.4 - - - -
130D GLN* 3.4 9.4 + - - +
131D SER* 2.9 29.8 + - - -
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Residues in contact with GLN 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LEU* 4.1 23.6 - - + +
125D HIS* 5.1 11.2 + - - +
126D TYR 3.6 1.0 - - - +
127D ALA* 1.3 77.8 - - - +
129D LEU* 1.3 60.4 + - - +
131D SER* 2.8 22.1 + - - +
132D ASN* 2.8 33.3 + - - +
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Residues in contact with LEU 129 (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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51D TRP* 4.9 12.1 - - + +
54D ALA* 4.1 27.4 - - + +
89D ILE* 4.9 4.5 - - + +
92D GLU* 3.8 30.1 - - + -
93D TYR* 4.2 10.5 - - + +
96D LEU* 3.8 24.8 - - + +
125D HIS* 3.5 30.0 + - + +
126D TYR 4.3 1.3 + - - +
128D GLN* 1.3 78.0 - - - +
130D GLN* 1.3 57.8 + - - +
132D ASN* 3.3 7.6 + - - +
133D ILE* 2.9 48.9 + - + +
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Residues in contact with GLN 130 (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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46D ILE* 3.7 26.4 + - + -
47D THR* 3.9 20.8 + - - +
49D HIS 5.5 1.2 + - - -
50D ARG* 5.9 1.2 + - - -
51D TRP* 3.9 25.0 - - + -
126D TYR 3.4 20.7 + - - +
127D ALA* 3.4 9.1 + - - +
128D GLN 3.3 0.6 - - - -
129D LEU* 1.3 79.4 - - - +
131D SER* 1.3 56.6 + - - +
133D ILE* 3.3 11.3 + - - +
134D ILE* 2.9 35.9 + - + +
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Residues in contact with SER 131 (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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127D ALA 2.9 16.0 + - - -
128D GLN* 2.8 25.5 + - - +
130D GLN* 1.3 73.2 - - - +
132D ASN* 1.3 62.0 + - - +
134D ILE* 3.5 9.8 - - - +
135D GLU* 2.9 31.6 + - - +
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Residues in contact with ASN 132 (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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92D GLU* 3.3 28.5 + - + +
96D LEU* 3.7 23.8 - - - +
128D GLN* 2.8 39.1 + - - +
129D LEU* 3.6 6.1 - - - +
130D GLN 3.3 0.2 - - - -
131D SER* 1.3 78.4 + - - +
133D ILE* 1.3 59.4 + - - +
135D GLU* 3.3 18.2 - - - +
136D ALA* 2.9 31.4 + - - +
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Residues in contact with ILE 133 (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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46D ILE* 3.9 20.9 - - + -
51D TRP* 5.3 4.5 - - + -
57D LEU* 5.0 13.7 - - + -
88D ILE* 5.7 1.8 - - + -
89D ILE* 3.8 49.6 - - + -
92D GLU* 5.0 4.3 - - + -
129D LEU* 2.9 38.4 + - + +
130D GLN* 3.3 8.9 + - - +
132D ASN* 1.3 75.0 - - - +
134D ILE* 1.3 57.3 + - - +
136D ALA* 3.8 4.4 - - - +
137D ILE* 2.9 52.3 + - + +
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Residues in contact with ILE 134 (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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43D ARG* 4.8 14.2 - - + +
46D ILE* 3.7 14.8 - - + -
47D THR* 3.7 29.6 - - + -
130D GLN* 2.9 23.7 + - + +
131D SER* 3.5 11.7 - - - +
132D ASN 3.3 0.2 - - - -
133D ILE* 1.3 76.8 - - - +
135D GLU* 1.3 58.2 + - + +
137D ILE* 3.9 3.2 - - + +
138D ASN* 2.8 49.1 + - - +
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Residues in contact with GLU 135 (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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92D GLU* 4.3 10.7 - - - +
131D SER 2.9 17.5 + - - +
132D ASN* 3.3 30.6 - - - +
134D ILE* 1.3 77.4 - - + +
136D ALA* 1.3 61.5 + - - +
138D ASN* 3.5 9.8 + - - +
139D GLU* 2.9 40.1 + - - +
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Residues in contact with ALA 136 (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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88D ILE* 3.7 33.0 - - + +
92D GLU* 4.7 7.2 - - + +
132D ASN 2.9 19.9 + - - +
133D ILE* 3.8 3.8 - - - +
135D GLU* 1.3 83.9 - - - +
137D ILE* 1.3 59.8 + - - +
139D GLU* 3.3 10.4 + - - +
140D LEU* 2.9 26.9 + - - +
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Residues in contact with ILE 137 (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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39D LEU* 3.5 28.0 - - + +
42D LEU* 5.0 3.1 - - + -
43D ARG* 3.2 51.3 + - + +
46D ILE* 4.9 4.3 - - + -
85D VAL* 4.2 30.7 - - + -
88D ILE* 5.5 6.1 - - + -
133D ILE* 2.9 39.6 + - + +
134D ILE* 4.1 3.1 - - - +
136D ALA* 1.3 74.9 - - + +
138D ASN* 1.3 60.8 + - - +
140D LEU* 3.2 7.7 + - + +
141D LEU 2.9 23.2 + - - -
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Residues in contact with ASN 138 (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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43D ARG* 2.6 35.2 + - - +
134D ILE* 2.8 42.7 + - - +
135D GLU* 3.7 8.6 - - - +
137D ILE* 1.3 77.3 - - - +
139D GLU* 1.3 55.6 + - - +
141D LEU* 3.2 6.5 + - - +
142D VAL* 3.0 33.2 + - + +
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Residues in contact with GLU 139 (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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135D GLU* 2.9 29.6 + - - +
136D ALA* 3.3 9.9 + - - +
138D ASN* 1.3 74.8 - - - +
140D LEU* 1.3 58.3 + - - +
142D VAL* 3.3 11.4 + - + +
143D GLU* 2.9 29.2 + - + +
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Residues in contact with LEU 140 (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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39D LEU* 3.7 21.5 - - + -
81D MET* 3.8 25.1 - - + -
84D ARG* 3.4 32.8 - - + +
85D VAL* 4.3 9.9 - - + -
88D ILE* 4.2 24.7 - - + -
136D ALA 2.9 14.3 + - - +
137D ILE* 3.2 12.1 + - - +
139D GLU* 1.3 74.9 - - - +
141D LEU* 1.3 60.5 + - - +
143D GLU* 3.4 11.3 + - + +
144D LEU* 2.9 32.2 + - + +
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Residues in contact with LEU 141 (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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36D ARG* 4.0 34.1 - - + +
39D LEU* 3.7 30.5 - - + +
40D GLY* 6.0 1.1 - - - +
43D ARG* 3.3 31.2 - - - +
137D ILE 2.9 6.8 + - - +
138D ASN* 3.2 8.7 + - - +
140D LEU* 1.3 73.5 - - - +
142D VAL* 1.3 61.4 + - + +
144D LEU* 3.8 6.2 - - + -
145D GLU* 2.9 46.5 + - + +
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Residues in contact with VAL 142 (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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138D ASN* 3.0 21.8 + - + +
139D GLU* 3.3 14.1 + - + +
141D LEU* 1.3 76.4 - - + +
143D GLU* 1.3 62.4 + - - +
145D GLU* 3.7 14.4 + - - +
146D GLY* 3.8 8.1 + - - -
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Residues in contact with GLU 143 (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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84D ARG* 4.0 21.3 + - - -
139D GLU* 2.9 18.3 + - + +
140D LEU* 3.8 11.8 - - + +
142D VAL* 1.3 79.5 - - - +
144D LEU* 1.3 62.8 + - - +
146D GLY* 3.7 7.6 + - - -
147D THR* 3.2 12.8 + - - -
150D ASN* 5.5 0.7 + - - -
271D MET* 4.7 10.6 - - - +
327D ASN* 2.7 34.3 + - - +
328D ILE* 5.0 3.6 - - - +
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Residues in contact with LEU 144 (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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32D GLU* 3.3 36.5 - - + +
35D ALA* 3.9 14.4 - - + -
36D ARG* 3.8 29.6 - - + -
39D LEU* 4.2 12.8 - - + -
81D MET* 3.8 28.5 - - + -
84D ARG* 5.5 2.0 - - - +
140D LEU* 2.9 19.8 + - + +
141D LEU* 3.3 7.1 + - + +
143D GLU* 1.3 79.7 + - - +
145D GLU* 1.3 65.9 + - + +
146D GLY 3.3 0.4 - - - -
147D THR* 3.3 17.6 + - - +
272D PHE* 4.4 16.2 - - + -
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Residues in contact with GLU 145 (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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32D GLU* 4.0 13.0 - - - +
36D ARG* 4.8 20.2 - - + -
141D LEU* 2.9 34.2 + - + +
142D VAL* 4.3 8.1 - - - +
143D GLU 3.5 0.4 - - - -
144D LEU* 1.3 77.2 - - - +
146D GLY* 1.3 57.6 + - - +
147D THR 3.4 2.0 + - - -
148D MET* 5.0 2.1 + - - +
149D GLU* 4.3 13.3 - - - +
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Residues in contact with GLY 146 (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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142D VAL 3.8 7.2 + - - -
143D GLU 3.7 7.5 + - - -
144D LEU 3.3 0.8 - - - -
145D GLU* 1.3 80.1 - - - +
147D THR* 1.3 56.5 + - - +
148D MET 3.7 0.9 - - - -
149D GLU* 3.9 22.2 - - - +
150D ASN* 2.6 40.1 + - - -
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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
------------------------------------------------------------
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