Contacts of the helix formed by residues 128 - 140 (chain D) in PDB entry 3DZU
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 CYS 128 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111D CYS* 3.2 10.4 - - + +
114D CYS* 3.2 10.8 - - - -
116D ASP* 3.6 18.6 - - - +
117D LYS 3.9 18.6 - - - +
118D ALA* 4.0 0.4 - - - +
119D SER* 4.4 0.2 - - - -
127D ALA* 1.3 78.3 - - - +
129D GLU* 1.3 66.3 + - - +
130D GLY* 3.6 7.0 - - - +
131D CYS* 2.9 29.0 + - - -
132D LYS* 2.9 22.1 + - - +
159D ARG* 4.1 6.1 - - - -
7121D ZN 2.4 31.4 - - - -
4011F A 6.0 0.4 - - - +
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Residues in contact with GLU 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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3008C G 4.5 0.5 - - - +
117D LYS 5.0 1.2 + - - -
119D SER* 2.4 43.1 + - - +
122D HIS* 4.1 1.2 - - - -
127D ALA 4.0 0.4 + - - -
128D CYS* 1.3 72.3 - - - +
130D GLY* 1.3 62.6 + - - +
132D LYS* 3.1 25.6 + - + +
133D GLY* 3.1 20.1 + - - -
4010F G 4.1 3.5 - - - +
4011F A 3.2 49.7 + - + +
4012F C 2.5 35.3 + - + +
4013F C 4.5 1.6 + - - -
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Residues in contact with GLY 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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128D CYS* 3.1 8.2 - - - -
129D GLU* 1.3 78.1 - - - +
131D CYS* 1.3 65.4 + - - +
132D LYS 2.9 1.2 + - - -
133D GLY* 3.2 1.2 + - - -
134D PHE* 3.0 21.1 + - - +
137D ARG* 4.9 0.9 + - - -
159D ARG* 4.6 2.5 - - - -
166D ARG* 3.3 6.2 + - - -
4010F G 3.4 40.8 + - - +
4011F A 4.6 1.2 + - - -
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Residues in contact with CYS 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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111D CYS* 4.3 0.4 - - - -
113D VAL* 3.5 24.7 - - + -
114D CYS* 3.5 12.8 - - - -
127D ALA* 4.3 11.7 - - + -
128D CYS* 2.9 17.0 - - - +
130D GLY* 1.3 70.7 - - - +
132D LYS* 1.3 64.2 + - - +
134D PHE* 3.5 2.9 - - - +
135D PHE 3.1 13.9 + - - -
166D ARG* 3.1 24.9 - - - +
170D CYS* 4.6 1.4 - - - -
175D MET* 3.2 15.4 - - + +
7121D ZN 2.4 35.4 - - - -
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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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3007C A 3.7 18.8 + - - +
3008C G 2.9 46.2 + - - -
3009C G 4.4 2.2 + - - +
122D HIS* 3.1 42.9 - - + +
123D TYR* 4.1 17.9 - - + -
127D ALA* 4.9 2.2 - - + +
128D CYS 2.9 14.1 + - - +
129D GLU* 3.1 31.1 + - - +
130D GLY 2.9 0.8 + - - -
131D CYS* 1.3 74.2 - - - +
133D GLY* 1.3 67.8 + - - +
135D PHE* 2.8 18.6 + - - +
136D ARG* 3.2 12.3 + - + +
175D MET* 4.6 6.1 - - - -
4012F C 4.2 2.7 - - - +
4013F C 4.9 0.4 - - - +
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Residues in contact with GLY 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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129D GLU 3.1 8.9 + - - -
130D GLY 3.8 2.2 - - - -
132D LYS* 1.3 83.1 - - - +
134D PHE* 1.3 61.9 + - - +
136D ARG* 3.9 15.8 + - - +
137D ARG* 3.0 37.7 + - - +
4010F G 5.0 11.4 - - - -
4011F A 6.1 1.6 - - - -
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Residues in contact with PHE 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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130D GLY 3.0 12.8 + - - +
131D CYS 3.5 8.3 - - - +
132D LYS 2.8 1.4 + - - -
133D GLY* 1.3 77.9 - - - +
135D PHE* 1.3 66.5 + - - +
137D ARG* 3.5 19.5 + - - +
138D THR* 2.9 28.6 + - - -
145D TYR* 3.7 33.4 - + - -
163D GLN* 4.0 15.5 - - + -
166D ARG* 3.5 45.3 - - + +
167D PHE* 3.6 31.2 - + + -
170D CYS* 4.3 11.2 - - - -
4009F T 3.4 26.7 - - - -
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Residues in contact with PHE 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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123D TYR* 3.4 52.5 - + + -
131D CYS 3.1 1.0 + - - -
132D LYS* 2.8 11.0 + - - +
134D PHE* 1.3 79.3 - - - +
136D ARG* 1.3 63.0 + - - +
138D THR* 3.3 5.8 - - - -
139D ILE* 3.2 41.8 + - + +
167D PHE* 4.1 16.6 - + - -
170D CYS* 4.5 3.8 - - - -
171D LEU* 3.9 16.8 - - + -
175D MET* 3.0 62.1 - - + -
176D SER* 3.4 13.9 - - - -
177D HIS 4.2 1.1 - - - -
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Residues in contact with ARG 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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3008C G 3.7 51.6 + - - +
3009C G 3.6 31.4 + - - -
3010C T 4.2 14.6 + - - +
123D TYR* 3.2 30.9 - - + +
132D LYS* 3.2 9.2 + - + +
133D GLY* 4.0 14.6 + - - +
135D PHE* 1.3 75.9 - - - +
137D ARG* 1.3 93.5 + - - +
138D THR 2.9 2.2 + - - -
139D ILE* 3.0 6.9 + - + -
140D ARG* 2.8 43.5 + - + +
177D HIS* 5.4 0.4 - - - +
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Residues in contact with ARG 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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130D GLY 4.9 0.6 + - - -
133D GLY* 3.0 17.1 + - - +
134D PHE* 3.5 34.4 + - - +
136D ARG* 1.3 95.1 - - - +
138D THR* 1.3 63.7 + - - +
140D ARG* 5.0 1.1 - - - -
141D LEU* 3.3 33.0 - - + +
143D LEU* 3.8 9.5 - - + +
145D TYR* 5.0 3.2 + - - -
4008F T 4.8 1.7 - - - -
4009F T 2.6 83.8 + - - +
4010F G 4.1 10.7 + - - -
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Residues in contact with THR 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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134D PHE* 2.9 23.1 + - - -
135D PHE 3.3 9.9 - - - -
136D ARG 2.9 0.8 + - - -
137D ARG* 1.3 80.0 - - - +
139D ILE* 1.3 62.6 + - + +
141D LEU 3.2 0.2 + - - -
142D LYS 2.8 21.1 + - - -
143D LEU* 3.1 25.4 + - - +
145D TYR* 2.9 31.6 + - + +
167D PHE* 3.1 45.8 - - + -
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Residues in contact with ILE 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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123D TYR* 4.9 0.9 - - + -
135D PHE* 3.2 41.1 - - + +
136D ARG* 3.0 5.2 + - - +
138D THR* 1.3 85.0 - - + +
140D ARG* 1.3 62.4 + - + +
141D LEU 2.9 10.0 + - - -
142D LYS* 3.2 26.5 + - + +
167D PHE* 4.1 16.6 - - + -
171D LEU* 6.0 0.2 - - + -
177D HIS* 3.3 39.3 - - + -
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Residues in contact with ARG 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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3008C G 3.0 47.1 + - - -
3009C G 3.9 18.0 + - - -
136D ARG* 2.8 41.0 + - + +
137D ARG* 4.3 0.9 - - - +
139D ILE* 1.3 77.2 - - + +
141D LEU* 1.3 72.7 + - + +
177D HIS* 4.2 9.7 + - - -
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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