Contacts of the helix formed by residues 135 - 150 (chain D) in PDB entry 3RZL
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 ILE 135 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88D GLU* 3.7 44.6 - - + +
89D VAL* 4.9 4.5 - - + +
115D TYR* 4.2 14.8 - - + +
133D PRO 3.4 9.2 + - - +
134D TRP* 1.3 77.6 - - - +
136D PRO* 1.3 79.3 - - + +
137D VAL* 3.4 15.3 - - + -
138D LEU* 2.8 39.3 + - + +
139D GLU* 3.2 11.1 + - - -
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Residues in contact with PRO 136 (chain D).
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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84D GLU* 5.4 4.0 - - - +
134D TRP 4.7 1.1 - - - +
135D ILE* 1.3 87.3 - - + +
137D VAL* 1.3 66.0 + - - +
138D LEU 2.9 0.5 + - - -
139D GLU* 3.1 15.3 + - + +
140D ARG* 2.8 31.3 + - + +
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Residues in contact with VAL 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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81D ILE* 3.8 31.9 - - + +
84D GLU* 3.7 50.6 + - + +
85D LEU* 4.2 18.2 - - + -
88D GLU* 5.2 4.0 - - + -
135D ILE* 4.1 22.0 - - + -
136D PRO* 1.3 76.5 - - - +
138D LEU* 1.3 66.5 + - + +
140D ARG* 3.1 10.3 + - - +
141D ILE* 3.0 26.6 + - + +
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Residues in contact with LEU 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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85D LEU* 4.3 13.9 - - + -
89D VAL* 5.4 0.7 - - + -
115D TYR* 3.4 47.6 - - + -
134D TRP* 3.8 15.9 - - + -
135D ILE* 2.8 39.0 + - + +
137D VAL* 1.3 77.6 - - + +
139D GLU* 1.3 58.6 + - - +
140D ARG 2.9 5.4 + - - -
141D ILE* 3.0 14.4 + - + +
142D ARG* 3.0 13.5 + - - +
156D VAL* 4.3 8.1 - - + -
158D ILE* 4.2 9.6 - - + -
251D LEU* 3.7 30.1 - - + -
253D PHE* 4.3 4.3 - - + -
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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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134D TRP* 3.4 34.0 - - + +
135D ILE 3.7 7.6 - - - +
136D PRO* 3.7 19.3 - - + +
138D LEU* 1.3 77.5 - - - +
140D ARG* 1.3 58.7 + - + +
142D ARG* 3.5 33.6 + - - +
143D ASP* 2.8 35.4 + - - +
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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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73D PHE* 5.8 1.0 - - - -
77D GLU* 5.9 2.0 + - - +
80D GLU* 3.9 15.1 + - - -
81D ILE* 3.4 30.2 - - - +
84D GLU* 3.5 19.0 + - - -
136D PRO* 2.8 21.1 + - + +
137D VAL* 3.2 14.2 - - - +
138D LEU 2.9 0.2 - - - -
139D GLU* 1.3 80.3 - - + +
141D ILE* 1.3 65.3 + - + +
143D ASP* 3.5 4.0 + - - +
144D HIS* 3.3 42.7 + - - +
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Residues in contact with ILE 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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73D PHE* 4.1 20.9 - - + -
81D ILE* 3.7 42.8 - - + -
85D LEU* 4.9 2.0 - - + -
137D VAL* 3.0 17.5 + - + +
138D LEU* 3.8 4.9 - - + +
140D ARG* 1.3 71.5 - - - +
142D ARG* 1.3 68.2 + - - +
144D HIS* 2.9 10.5 + - - +
145D VAL* 2.9 31.5 + - + +
187D VAL* 4.3 7.6 - - + -
189D PHE* 3.7 7.9 - - + -
251D LEU* 3.7 23.6 - - + -
253D PHE* 3.9 20.2 - - + -
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Residues in contact with ARG 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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117D ASP* 4.7 4.2 + - - -
134D TRP* 3.7 38.1 - - - +
138D LEU 3.0 11.8 + - - +
139D GLU* 3.5 35.4 + - - +
141D ILE* 1.3 76.3 - - - +
143D ASP* 1.3 70.6 + - - +
145D VAL* 2.7 28.1 + - - +
146D SER* 2.9 15.7 + - - +
153D PHE* 3.4 39.9 + - + +
154D ASN* 5.7 0.2 - - - +
253D PHE* 3.7 27.9 - - + -
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Residues in contact with ASP 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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139D GLU* 2.8 21.2 - - - +
140D ARG* 3.5 4.4 + - - +
141D ILE 3.3 0.6 - - - -
142D ARG* 1.3 98.7 + - - +
144D HIS* 1.3 54.3 + - - +
146D SER* 3.8 8.8 + - - +
147D GLY* 2.8 31.0 + - - -
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Residues in contact with HIS 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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72D LEU* 4.2 13.4 - - + +
73D PHE* 3.3 37.6 - + + -
77D GLU* 4.7 11.8 + - - -
140D ARG* 3.3 31.5 + - - +
141D ILE* 2.9 13.2 + - - +
143D ASP* 1.3 77.1 - - - +
145D VAL* 1.3 57.4 + - - +
147D GLY* 3.8 1.6 + - - -
148D VAL* 3.0 32.2 + - + +
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Residues in contact with VAL 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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72D LEU* 4.5 10.8 - - + -
141D ILE* 2.9 34.2 + - + +
142D ARG* 2.7 13.5 + - - +
144D HIS* 1.3 76.9 - - - +
146D SER* 1.3 49.7 + - - -
148D VAL* 3.5 2.1 + - - +
149D THR* 2.6 48.3 + - + +
153D PHE* 3.9 13.7 - - + -
185D ALA* 3.7 28.0 - - + -
187D VAL* 4.1 16.2 - - + -
223D LEU* 4.1 13.9 - - + -
253D PHE* 4.4 5.2 - - + -
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Residues in contact with SER 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 ARG* 2.9 18.5 + - - +
143D ASP* 3.9 10.2 + - - -
145D VAL* 1.3 67.9 - - - +
147D GLY* 1.3 56.9 + - - +
148D VAL 2.7 16.2 + - - -
149D THR* 3.5 0.7 - - - -
150D GLY* 2.9 24.3 + - - -
151D GLN 2.7 27.8 + - - -
152D THR* 3.9 10.1 - - - -
153D PHE* 4.2 5.0 + - - -
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Residues in contact with GLY 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 ASP 2.8 22.6 + - - -
144D HIS* 4.0 2.7 - - - -
145D VAL 3.5 0.2 - - - -
146D SER* 1.3 71.3 - - - +
148D VAL* 1.3 62.7 + - - +
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Residues in contact with VAL 148 (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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55D HIS* 5.4 8.1 - - + -
57D TRP* 3.8 30.1 - - + +
72D LEU* 4.0 23.1 - - + -
144D HIS* 3.0 21.5 - - + +
145D VAL* 3.5 3.9 + - - +
146D SER 2.7 4.6 + - - -
147D GLY* 1.3 80.2 - - - +
149D THR* 1.3 68.2 + - + +
150D GLY 3.5 0.4 - - - -
223D LEU* 5.7 1.6 - - + -
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Residues in contact with THR 149 (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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57D TRP* 4.8 6.7 - - + -
145D VAL* 2.6 30.7 + - + +
148D VAL* 1.3 85.1 - - + +
150D GLY* 1.3 64.9 + - - +
151D GLN* 3.0 31.1 + - - +
153D PHE* 4.3 1.8 - - + -
223D LEU* 4.2 9.4 - - + -
225D MET* 3.9 37.0 - - + -
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Residues in contact with GLY 150 (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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146D SER* 2.9 15.7 + - - -
148D VAL 3.5 0.6 - - - -
149D THR* 1.3 78.8 + - - +
151D GLN* 1.3 64.9 + - - +
152D THR* 3.7 11.1 + - - +
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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
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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