Contacts of the helix formed by residues 128 - 136 (chain B) in PDB entry 3RIE
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 GLY 128 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125B GLY 3.0 14.8 + - - -
126B GLY 3.0 1.0 - - - -
127B ASP* 1.3 78.7 + - - +
129B GLY* 1.3 59.4 + - - +
130B ILE 3.3 2.7 - - - -
131B ILE* 3.1 12.8 + - - +
132B ARG* 2.9 25.8 + - - +
163B ILE 3.2 12.5 - - - +
164B SER* 4.6 0.4 - - - -
166B GLY 5.4 1.0 + - - -
167B TYR* 3.8 19.7 - - - -
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Residues in contact with GLY 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B HIS* 3.8 20.3 - - - +
125B GLY 4.7 0.2 + - - -
127B ASP* 2.8 22.9 + - - -
128B GLY* 1.3 72.5 - - - +
130B ILE* 1.3 62.6 + - - +
132B ARG* 3.3 9.1 + - - +
133B GLU* 3.2 24.6 + - - +
163B ILE* 3.6 19.4 - - - +
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Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B TYR* 4.7 1.6 - - + -
103B HIS* 3.7 22.0 - - + +
106B MET* 3.6 27.6 - - + -
107B THR* 3.4 19.3 - - - +
122B VAL* 3.7 27.6 - - + -
125B GLY* 5.5 2.4 + - - +
127B ASP* 4.5 0.4 + - - -
128B GLY 3.3 0.2 - - - -
129B GLY* 1.3 75.4 - - - +
131B ILE* 1.3 53.5 + - + +
133B GLU* 3.0 4.2 + - - +
134B LEU* 2.7 36.0 + - + +
194B ILE* 3.7 34.5 - - + -
196B ASP* 3.8 31.0 - - + +
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B VAL* 4.4 8.3 - - + -
125B GLY 5.2 0.6 + - - +
128B GLY* 3.1 13.1 + - - +
130B ILE* 1.3 75.7 - - + +
132B ARG* 1.3 63.7 + - - +
134B LEU* 3.1 8.5 + - - +
135B CYS* 2.9 25.5 + - - -
143B ILE* 4.2 13.5 - - + -
145B ILE* 3.4 42.4 - - + -
166B GLY* 3.9 18.6 - - - +
167B TYR* 3.7 26.0 - - + +
172B VAL* 3.8 30.3 - - + -
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLU* 2.9 42.1 + - - -
100B PHE* 4.4 8.9 - - - +
103B HIS* 4.1 11.1 + - - +
128B GLY 2.9 12.0 + - - +
129B GLY* 3.4 10.3 - - - +
131B ILE* 1.3 78.0 - - - +
133B GLU* 1.3 90.5 + - - +
135B CYS* 3.5 11.6 + - - +
136B LYS* 3.7 21.4 - - - +
162B ASN* 3.0 29.9 + - - +
163B ILE* 3.6 19.0 - - - +
165B CYS* 3.8 19.7 - - - -
166B GLY* 4.5 10.5 - - - +
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Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B HIS* 3.7 23.8 - - + +
104B GLU* 3.8 13.6 - - - +
107B THR* 3.5 24.9 - - + +
108B HIS* 2.8 28.8 + - - +
129B GLY 3.2 10.7 + - - +
130B ILE 3.0 3.2 + - - +
132B ARG* 1.3 110.3 + - - +
134B LEU* 1.3 64.1 + - - +
136B LYS* 2.9 44.6 + - - +
137B TYR* 3.7 8.5 - - - -
296B LEU* 3.5 4.2 - - - +
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B THR* 3.5 20.4 - - + -
111B MET* 3.7 31.9 - - + -
120B VAL* 3.8 23.8 - - + -
122B VAL* 3.5 32.1 - - + -
130B ILE* 2.7 28.3 + - + +
131B ILE* 3.1 4.5 + - - +
133B GLU* 1.3 76.5 - - - +
135B CYS* 1.3 55.8 + - - +
136B LYS 3.0 0.7 - - - -
137B TYR* 3.0 32.1 + - - +
140B VAL* 4.7 2.4 - - + +
143B ILE* 3.9 29.3 - - + +
194B ILE* 4.1 4.7 - - + -
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Residues in contact with CYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ILE* 2.9 29.5 + - - +
132B ARG* 3.7 8.7 - - - +
133B GLU 3.3 0.4 - - - -
134B LEU* 1.3 75.5 - - - +
136B LYS* 1.3 59.7 + - + +
137B TYR 3.0 3.5 + - - +
138B LYS* 4.4 1.4 + - - +
143B ILE* 4.1 11.0 - - - -
166B GLY* 3.8 17.5 - - - -
169B ASP* 3.5 38.8 - - + +
171B ARG* 2.9 24.3 + - - +
172B VAL* 4.2 0.7 - - - -
292B GLU* 5.3 1.2 - - - +
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Residues in contact with LYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLU* 5.2 1.2 + - - -
108B HIS* 4.7 0.2 - - - +
132B ARG* 3.7 25.7 - - - +
133B GLU* 2.9 47.0 + - - +
134B LEU 3.0 0.6 - - - -
135B CYS* 1.3 76.8 - - + +
137B TYR* 1.4 55.6 + - - +
138B LYS* 3.5 6.7 + - - +
292B GLU* 3.4 55.0 + - + +
293B PHE* 3.4 37.1 - - + -
295B ASP* 4.7 9.8 + - - -
296B LEU* 3.6 14.6 - - - +
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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