Contacts of the helix formed by residues 128 - 147 (chain D) in PDB entry 3U53
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 128 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D LEU* 4.9 1.6 - - + -
82D TYR* 3.0 60.3 - + + -
83D VAL 5.4 3.1 - - - -
126D ALA 2.7 13.5 + - - +
127D GLN* 1.3 79.5 - - - +
129D LYS* 1.3 67.5 + - - +
130D GLU* 3.1 32.8 - - + -
131D MET* 2.9 35.8 + - + +
132D LYS* 3.0 12.5 + - - +
160D SO4 6.1 1.1 - - - -
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Residues in contact with LYS 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 4.0 16.0 - - - +
81A ASN* 3.7 23.1 + - - +
90A THR* 4.4 9.6 + - + +
127D GLN 4.1 1.8 + - - -
128D PHE* 1.3 76.9 - - + +
130D GLU* 1.3 67.2 + - - +
132D LYS* 3.3 15.3 + - + +
133D ALA* 3.0 27.6 + - - +
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Residues in contact with GLU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASN* 3.4 33.7 - - - +
130A GLU* 4.9 0.9 - - - +
80D LEU* 3.8 24.4 - - + +
81D ASN 3.2 21.7 + - - +
82D TYR* 4.1 6.1 - - + +
128D PHE* 3.1 41.5 - - + -
129D LYS* 1.3 83.1 - - - +
131D MET* 1.3 56.5 + - - +
133D ALA* 3.4 7.6 + - - +
134D ALA* 3.0 27.9 + - - +
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Residues in contact with MET 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ILE* 5.9 0.9 - - - -
28D LEU* 6.1 0.4 - - + -
38D TRP 5.0 4.7 - - - +
39D THR* 4.3 11.2 - - + -
40D PRO* 3.9 26.5 - - + -
42D LYS* 5.5 0.9 - - + +
80D LEU* 3.8 13.8 - - + +
82D TYR* 5.6 4.9 - - + +
93D TYR* 3.2 39.5 - - + +
126D ALA* 3.6 21.8 - - + -
128D PHE* 2.9 26.5 + - + +
130D GLU* 1.3 79.2 - - - +
132D LYS* 1.3 64.2 + - - +
134D ALA* 3.3 7.3 + - - +
135D LEU* 3.0 37.9 + - + +
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Residues in contact with LYS 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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123D CYS* 3.6 39.8 + - + +
124D GLN* 5.6 1.6 + - - +
126D ALA* 4.2 2.2 - - + -
127D GLN* 3.2 39.4 + - - +
128D PHE 3.0 14.7 + - - +
129D LYS* 3.6 13.8 - - + +
131D MET* 1.3 72.3 - - - +
133D ALA* 1.3 61.4 + - - +
135D LEU* 3.3 5.3 + - - +
136D GLN* 2.9 40.6 + - + +
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Residues in contact with ALA 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 4.0 28.9 - - + +
129D LYS 3.0 13.0 + - - +
130D GLU* 3.5 11.9 - - - +
132D LYS* 1.3 74.9 - - - +
134D ALA* 1.3 64.3 + - - +
136D GLN* 3.2 10.6 + - - +
137D GLU* 2.8 45.2 + - - +
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Residues in contact with ALA 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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9D ILE* 4.3 16.5 - - + +
76D PHE* 3.9 6.4 - - - -
78D ARG* 4.5 11.2 - - + -
80D LEU* 4.2 18.8 - - + -
93D TYR* 5.2 1.8 - - + -
130D GLU 3.0 17.9 + - - +
131D MET* 3.4 14.6 - - - +
132D LYS 3.2 0.2 - - - -
133D ALA* 1.3 78.3 - - - +
135D LEU* 1.3 56.1 + - - +
137D GLU* 3.7 9.9 - - - +
138D GLY* 2.9 25.8 + - - -
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Residues in contact with LEU 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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9D ILE* 3.9 34.3 - - + -
26D PHE* 4.1 21.9 - - + -
28D LEU* 4.9 9.4 - - + -
40D PRO* 4.8 11.0 - - + -
119D LEU* 3.6 19.6 - - + +
122D ALA* 4.0 33.0 - - + +
123D CYS* 4.3 5.8 - - - -
126D ALA* 4.4 4.7 - - + -
131D MET* 3.0 36.1 + - + +
132D LYS 3.7 3.1 - - - +
134D ALA* 1.3 73.4 - - - +
136D GLN* 1.3 65.9 + - - +
138D GLY* 3.2 2.2 + - - -
139D HIS* 3.0 19.6 + - - +
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Residues in contact with GLN 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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77A LYS* 5.6 10.4 + - + +
79A GLU* 5.8 0.2 - - - +
119D LEU* 3.7 20.7 - - + +
123D CYS* 3.9 21.6 - - - +
132D LYS* 2.9 28.5 + - - +
133D ALA* 3.6 8.8 - - - +
135D LEU* 1.3 75.7 - - - +
137D GLU* 1.3 65.4 + - + +
139D HIS* 3.4 3.1 + - - +
140D GLN* 3.0 23.3 + - - +
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Residues in contact with GLU 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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75A GLY 5.0 1.2 - - - +
77A LYS* 3.1 40.3 - - + +
78A ARG* 3.5 6.8 + - - -
79A GLU* 3.1 24.0 + - - +
76D PHE* 3.8 5.2 - - + -
78D ARG* 2.9 39.9 + - - +
133D ALA* 2.8 33.6 + - - +
134D ALA* 3.7 3.3 - - - +
136D GLN* 1.3 80.0 - - + +
138D GLY* 1.3 56.6 + - - +
140D GLN* 3.3 8.5 + - - +
141D PHE* 2.9 28.2 + - - +
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Residues in contact with GLY 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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9D ILE* 5.7 1.1 - - - -
26D PHE* 4.9 1.3 - - - -
76D PHE* 3.6 21.9 - - - -
95D LEU* 4.0 15.5 - - - +
134D ALA 2.9 13.1 + - - -
135D LEU* 3.2 3.5 + - - -
137D GLU* 1.3 73.9 - - - +
139D HIS* 1.3 65.7 + - - +
141D PHE* 3.3 2.5 + - - +
142D LEU* 3.0 31.4 + - - +
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Residues in contact with HIS 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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24D ILE* 3.9 24.7 - - + +
26D PHE* 4.2 16.6 - + + -
119D LEU* 4.1 30.3 - - + +
135D LEU 3.0 13.3 + - - +
136D GLN 3.6 8.3 - - - +
138D GLY* 1.3 76.4 - - - +
140D GLN* 1.3 59.5 + - - +
142D LEU* 3.2 6.6 + - - +
143D CYS* 2.9 48.5 + - - -
157D SO4 2.8 48.4 + - - -
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Residues in contact with GLN 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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74A GLU* 5.3 4.2 + - - +
75A GLY* 3.5 38.6 - - - +
76A PHE 3.8 3.7 + - - +
77A LYS* 3.6 40.2 + - - +
94A TRP* 5.0 5.1 - - - +
136D GLN 3.0 16.7 + - - +
137D GLU* 3.5 7.4 - - - +
138D GLY 3.2 0.2 - - - -
139D HIS* 1.3 78.6 - - - +
141D PHE* 1.3 63.5 + - - +
143D CYS* 3.4 6.9 + - + +
144D SER* 3.1 24.1 + - - -
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Residues in contact with PHE 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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75A GLY 3.8 10.7 + - - +
76A PHE* 6.3 0.2 - + - -
141A PHE* 3.7 37.0 - + - -
144A SER* 4.2 7.9 - - - -
73D ILE* 3.6 26.7 - - + -
74D GLU 3.5 19.5 - - - -
75D GLY* 3.8 16.8 - - - -
76D PHE* 3.6 23.1 - + + -
78D ARG* 6.3 0.2 - - - +
95D LEU* 3.7 17.3 - - + -
137D GLU 2.9 16.0 + - - +
138D GLY 3.6 3.6 - - - +
139D HIS 3.2 0.2 - - - -
140D GLN* 1.3 78.0 - - - +
142D LEU* 1.3 59.9 - - - +
144D SER* 3.3 3.0 + - - -
145D ILE* 3.0 47.5 + - + +
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Residues in contact with LEU 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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11D PHE* 3.5 50.9 - - + -
13D ARG* 3.5 20.4 + - - +
24D ILE* 3.7 28.3 - - + -
26D PHE* 4.9 1.6 - - + -
73D ILE* 4.5 14.4 - - + -
95D LEU* 4.1 18.4 - - + -
138D GLY 3.0 20.6 + - - +
139D HIS* 3.4 7.9 - - - +
141D PHE* 1.3 74.3 - - + +
143D CYS* 1.3 65.7 + - - +
145D ILE* 3.4 8.9 + - + +
146D GLU* 3.0 25.1 + - - +
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Residues in contact with CYS 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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13D ARG* 5.7 0.4 - - - +
23D ALA* 6.4 1.1 - - - -
24D ILE* 4.7 9.4 - - - -
139D HIS* 2.9 47.9 + - - +
140D GLN* 3.9 7.0 - - + +
142D LEU* 1.3 77.7 - - - +
144D SER* 1.3 61.2 + - - +
146D GLU* 3.4 7.2 + - - +
147D ALA* 3.2 22.0 + - - +
157D SO4 4.4 4.5 - - - -
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Residues in contact with SER 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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74A GLU* 3.9 9.6 + - - +
75A GLY* 3.7 25.0 - - - -
141A PHE* 4.7 5.9 - - - -
145A ILE* 4.9 3.1 - - - +
140D GLN 3.1 15.4 + - - -
141D PHE* 3.6 4.1 + - - -
143D CYS* 1.3 79.9 - - - +
145D ILE* 1.3 65.0 + - - +
146D GLU 3.4 0.5 + - - -
147D ALA* 3.4 21.3 + - - +
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Residues in contact with ILE 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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144A SER* 5.2 1.8 - - - +
145A ILE* 3.8 28.9 - - + -
13D ARG* 4.8 9.4 - - - +
73D ILE* 5.0 11.2 - - + -
141D PHE* 3.0 42.8 + - + +
142D LEU* 3.4 15.7 + - + +
144D SER* 1.3 78.7 - - - +
146D GLU* 1.3 63.2 + - - +
147D ALA 3.7 6.7 - - - +
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Residues in contact with GLU 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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13D ARG* 3.8 25.1 - - - +
142D LEU 3.0 17.4 + - - +
143D CYS* 3.6 7.6 - - - +
144D SER 3.2 0.2 - - - -
145D ILE* 1.3 75.2 - - - +
147D ALA* 1.3 67.2 + - - +
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Residues in contact with ALA 147 (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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143D CYS 3.2 10.8 + - - +
144D SER* 3.6 18.6 - - - +
145D ILE 3.4 6.6 - - - +
146D GLU* 1.3 82.0 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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