Contacts of the helix formed by residues 134 - 147 (chain E) in PDB entry 2RCY
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 ASN 134 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132E ASN 3.7 7.2 + - - +
133E VAL* 1.3 74.7 - - - +
135E SER* 1.3 59.6 + - - +
136E THR* 2.5 35.0 + - + +
137E ASP* 2.8 18.6 + - - +
138E LYS* 3.1 33.6 + - - +
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Residues in contact with SER 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E ASN* 1.3 75.8 - - - +
136E THR* 1.3 65.3 + - - +
138E LYS* 3.7 15.2 - - - +
139E LYS* 3.0 26.3 + - - +
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Residues in contact with THR 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E ASN* 2.5 24.2 + - - +
135E SER* 1.3 81.5 - - - +
137E ASP* 1.3 67.7 + - - +
139E LYS* 3.6 7.3 + - - +
140E TYR* 3.4 26.9 + - - +
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Residues in contact with ASP 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E LEU* 3.4 42.2 - - + +
132E ASN 4.9 2.1 - - - +
133E VAL* 3.7 24.7 - - + -
134E ASN* 2.8 33.6 + - - +
136E THR* 1.3 82.6 + - - +
138E LYS* 1.3 60.1 + - - +
140E TYR* 3.4 7.6 + - - +
141E VAL* 2.9 27.1 + - - +
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Residues in contact with LYS 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E TYR* 4.0 15.7 - - + +
129E SER* 3.4 22.1 + - - -
133E VAL* 4.0 22.4 + - + -
134E ASN 3.1 18.6 + - - +
135E SER* 3.7 14.1 - - - +
136E THR 3.3 0.2 - - - -
137E ASP* 1.3 75.5 - - - +
139E LYS* 1.3 58.7 + - - +
141E VAL* 3.4 8.2 - - - +
142E ASN* 2.8 34.7 + - - +
153E GLU* 3.2 31.1 + - - +
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Residues in contact with LYS 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E SER 3.0 17.7 + - - +
136E THR* 3.6 10.3 - - - +
137E ASP 3.3 0.4 - - - -
138E LYS* 1.3 77.5 - - - +
140E TYR* 1.3 55.8 + - + +
142E ASN* 3.5 5.2 + - - +
143E ASP* 3.1 38.6 + - - +
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Residues in contact with TYR 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ILE* 4.4 24.9 - - + -
86E LEU* 5.0 5.8 - - + -
136E THR 3.4 15.3 + - - +
137E ASP* 3.7 9.9 - - - +
138E LYS 3.3 0.2 - - - -
139E LYS* 1.3 75.0 - - - +
141E VAL* 1.3 64.9 + - - +
143E ASP* 4.0 8.5 - - + +
144E ILE* 3.1 41.7 + - + +
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Residues in contact with VAL 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E LEU* 5.4 4.2 - - + +
88E ILE* 6.4 1.1 - - + -
110E VAL* 5.2 13.2 - - + -
127E TYR* 4.7 17.3 - - + -
137E ASP 2.9 14.5 + - - +
138E LYS* 3.4 12.8 - - - +
140E TYR* 1.3 77.9 - - - +
142E ASN* 1.3 64.6 + - - +
144E ILE* 4.9 2.0 - - - -
145E PHE* 3.0 43.9 + - + +
151E ILE* 4.2 2.0 - - - +
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Residues in contact with ASN 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E TYR* 3.1 36.7 + - - -
138E LYS 2.8 16.6 + - - +
139E LYS* 3.9 6.3 - - - +
140E TYR 3.4 0.2 - - - -
141E VAL* 1.3 76.4 - - - +
143E ASP* 1.3 61.9 + - - +
146E ASN* 3.0 47.5 + - - +
151E ILE* 4.0 15.3 + - - +
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Residues in contact with ASP 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E LYS* 3.1 22.6 + - - +
140E TYR* 3.5 10.2 + - + +
141E VAL 3.3 0.2 - - - -
142E ASN* 1.3 80.2 - - - +
144E ILE* 1.3 66.4 + - + +
146E ASN* 4.2 3.3 + - - +
147E SER* 3.4 23.2 + - - -
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Residues in contact with ILE 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E LEU* 4.5 15.5 - - + -
23E ILE* 3.8 32.7 - - + +
61E ILE* 3.7 40.4 - - + -
86E LEU* 6.3 1.1 - - + -
140E TYR* 3.1 32.7 + - + +
141E VAL* 4.2 5.2 - - - +
143E ASP* 1.3 76.3 - - + +
145E PHE* 1.3 77.1 + - + +
147E SER* 2.7 21.6 + - - -
148E CYS* 4.0 7.6 - - - -
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Residues in contact with PHE 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E LEU* 3.7 29.2 - - + -
23E ILE* 5.0 1.1 - - + -
63E VAL* 5.8 1.6 - - + -
88E ILE* 3.7 30.7 - - + -
112E VAL* 3.9 25.8 - - + -
114E PRO* 5.5 0.2 - - + -
125E PHE* 3.2 42.4 - + + -
141E VAL* 3.0 30.8 + - + +
143E ASP 3.3 0.2 - - - -
144E ILE* 1.3 95.1 - - + +
146E ASN* 1.3 58.6 + - - +
147E SER 3.2 5.4 - - - -
148E CYS* 3.4 4.6 + - - -
149E GLY 3.1 22.0 + - - -
151E ILE* 3.6 28.7 - - + -
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Residues in contact with ASN 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E ASN* 3.0 36.7 + - - +
143E ASP* 4.2 4.0 + - - +
145E PHE* 1.3 73.3 - - - +
147E SER* 1.3 61.5 + - - +
148E CYS 3.3 0.4 - - - -
149E GLY 3.2 18.7 + - - +
150E ILE* 3.5 4.2 - - - +
151E ILE* 3.2 37.0 + - - +
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Residues in contact with SER 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E ILE* 4.8 5.5 - - - +
26E ALA* 3.7 31.4 - - - +
121E GLY* 5.1 2.3 - - - +
143E ASP 3.4 14.4 + - - -
144E ILE* 2.7 24.3 + - - -
146E ASN* 1.3 79.5 - - - +
148E CYS* 1.3 58.8 + - - +
149E GLY 3.7 0.4 - - - -
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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