Contacts of the helix formed by residues 133 - 143 (chain A) in PDB entry 2RD0
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 ASP 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A VAL* 4.0 10.6 - - + +
132A LYS* 1.3 75.8 - - - +
134A PRO* 1.3 74.1 - - - +
135A GLU* 3.1 29.6 + - - +
136A VAL* 3.3 33.8 + - + +
137A GLN* 3.5 3.8 + - - +
432A TYR* 5.4 0.5 - - - -
645A LEU* 5.9 0.2 - - - +
682A GLN* 5.2 3.0 + - - +
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Residues in contact with PRO 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LYS 3.0 8.5 - - - +
133A ASP* 1.3 90.5 - - - +
135A GLU* 1.3 51.2 + - - +
137A GLN* 3.7 6.6 - - + +
138A ASP* 2.8 41.7 + - - +
141A ARG* 4.9 1.5 + - - +
432A TYR* 3.7 14.6 - - + +
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Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A ASP* 3.1 19.6 + - - +
134A PRO* 1.3 77.5 - - - +
136A VAL* 1.3 52.4 + - - +
138A ASP* 3.5 2.1 - - - +
139A PHE* 2.8 34.1 + - - +
432A TYR* 3.6 50.2 + - + +
643A GLN 5.3 0.6 - - - +
644A TYR* 3.1 22.2 - - - +
645A LEU* 2.8 45.7 + - + -
646A ASP* 4.5 3.2 + - + +
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Residues in contact with VAL 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PHE* 4.9 2.2 - - + +
131A VAL* 4.0 17.5 - - + -
133A ASP* 3.4 26.9 - - + +
135A GLU* 1.3 75.5 - - - +
137A GLN* 1.3 81.0 + - - +
138A ASP 2.9 1.4 + - - -
139A PHE* 2.9 13.7 + - - +
140A ARG* 3.1 16.2 + - - +
645A LEU* 3.9 16.2 - - + -
682A GLN* 3.4 34.1 - - - +
686A LEU* 3.8 22.2 - - + -
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Residues in contact with GLN 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PHE 3.3 13.2 + - - +
129A ASP* 4.6 2.9 + - - +
130A MET 5.1 1.1 - - - -
131A VAL 2.9 26.8 + - - +
132A LYS 5.4 1.1 - - - +
133A ASP 3.5 5.8 + - - +
134A PRO* 3.3 9.4 + - + +
136A VAL* 1.3 84.7 - - - +
138A ASP* 1.3 60.1 + - - +
140A ARG* 2.9 48.5 + - - +
141A ARG* 3.4 49.1 + - + +
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Residues in contact with ASP 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A PRO* 2.8 22.0 + - - +
135A GLU* 3.5 4.3 - - - +
137A GLN* 1.3 70.5 - - - +
139A PHE* 1.3 56.2 + - - +
141A ARG* 2.7 34.5 + - - +
142A ASN* 2.6 56.5 + - - +
432A TYR* 2.7 31.8 + - + +
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Residues in contact with PHE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLU 2.8 16.3 + - - +
136A VAL 2.9 9.2 + - - +
138A ASP* 1.3 71.5 - - - +
140A ARG* 1.3 67.4 + - - +
142A ASN* 4.3 4.2 - - - +
143A ILE* 2.9 70.9 + - + +
645A LEU* 3.7 33.2 - - + -
646A ASP* 3.5 31.3 - - + +
650A VAL* 4.7 16.2 - - + -
683A ARG 5.9 0.4 - - - -
686A LEU* 4.0 39.5 - - + -
687A LEU* 4.7 10.5 - - + -
690A SER* 4.5 2.5 - - - -
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ARG* 5.1 2.6 - - - +
125A VAL* 4.2 6.5 - - - +
128A PHE* 3.5 14.9 - - - +
129A ASP* 3.3 43.9 + - - +
136A VAL* 3.1 10.4 + - - +
137A GLN* 2.9 38.2 - - - +
139A PHE* 1.3 81.1 - - - +
141A ARG* 1.3 59.5 + - + +
143A ILE* 3.8 4.3 - - - +
144A LEU* 3.3 29.6 - - - +
306A SER* 5.5 10.0 + - - +
686A LEU* 3.5 29.6 - - + -
689A GLU* 2.9 37.7 + - - +
693A ARG* 4.7 2.2 - - - +
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Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A PRO* 4.9 1.8 + - - +
137A GLN* 3.4 35.7 + - - +
138A ASP* 2.7 37.4 + - - +
140A ARG* 1.3 81.8 - - + +
142A ASN* 1.3 67.3 + - - +
143A ILE 3.2 1.8 + - - -
144A LEU* 3.4 25.4 + - - +
145A ASN* 4.8 1.6 - - - +
306A SER* 4.5 25.1 - - - +
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Residues in contact with ASN 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ASP* 2.6 48.2 + - - +
139A PHE* 4.2 1.1 - - - +
141A ARG* 1.3 73.7 + - - +
143A ILE* 1.3 52.1 + - - +
144A LEU 3.4 0.4 - - - -
145A ASN* 2.5 40.4 + - - +
432A TYR* 6.1 0.6 - - - -
646A ASP* 3.7 19.5 + - - +
651A ARG* 3.0 7.3 + - - +
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A PHE* 2.9 55.2 + - + +
140A ARG* 3.8 12.1 - - - +
142A ASN* 1.3 75.5 - - - +
144A LEU* 1.3 66.1 + - + +
145A ASN* 2.8 14.1 + - - +
146A VAL* 3.1 19.2 + - + +
147A CYS* 3.7 2.9 + - - -
646A ASP* 4.7 2.0 - - - +
650A VAL* 5.3 3.6 - - + -
651A ARG* 3.8 39.3 - - + +
654A LEU* 3.7 20.6 - - + -
687A LEU* 6.2 0.2 - - + -
690A SER* 3.7 25.8 - - - -
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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