Contacts of the helix formed by residues 129 - 137 (chain D) in PDB entry 2RHB
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 129 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D VAL 3.4 0.8 + - - -
128D GLU* 1.3 79.6 - - - +
130D GLN* 1.3 56.8 + - - +
131D VAL* 3.5 2.5 - - - -
132D ASP* 3.5 14.1 + - - +
133D LEU* 2.9 33.6 + - - +
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Residues in contact with GLN 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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81D ALA* 3.5 26.4 + - - +
82D ASN* 4.5 7.8 - - - +
111D PRO* 5.7 0.7 - - - +
122D LEU 4.2 0.6 + - - -
123D PHE* 3.3 28.2 - - - +
124D ASP* 3.0 41.3 - - - +
127D VAL* 3.3 36.6 + - + +
128D GLU 3.1 5.7 + - - +
129D GLY* 1.3 75.8 - - - +
131D VAL* 1.3 56.1 + - - +
133D LEU* 3.2 16.1 + - + +
134D PHE* 2.8 34.0 + - - +
142D LEU* 4.9 0.2 - - - -
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Residues in contact with VAL 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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125D GLY* 3.6 27.6 - - - +
127D VAL 4.7 0.6 + - - -
129D GLY 5.0 0.2 - - - +
130D GLN* 1.3 75.9 - - - +
132D ASP* 1.3 64.2 + - - +
134D PHE* 3.2 17.8 + - - +
135D ARG* 3.3 37.3 + - + +
142D LEU* 3.9 28.9 - - + +
144D THR* 4.0 9.0 - - + -
148D VAL* 4.4 13.9 - - + -
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Residues in contact with ASP 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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129D GLY* 3.5 16.2 + - - +
130D GLN 3.2 0.2 - - - -
131D VAL* 1.3 81.0 - - - +
133D LEU* 1.3 62.2 + - - +
135D ARG* 3.3 38.3 + - - +
136D ASN* 3.6 18.5 + - - -
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Residues in contact with LEU 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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111D PRO* 3.8 28.5 - - + +
112D THR* 4.4 23.8 - - - +
123D PHE* 3.9 11.7 - - + -
128D GLU 5.8 0.4 - - - +
129D GLY 2.9 19.8 + - - +
130D GLN* 3.2 22.4 + - + +
132D ASP* 1.3 74.6 - - - +
134D PHE* 1.3 63.2 - - - +
136D ASN* 3.3 8.9 + - + +
137D ALA* 3.1 24.1 + - - +
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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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123D PHE* 3.5 34.7 - + + -
130D GLN 2.8 16.3 + - - +
131D VAL 3.2 9.6 - - - +
133D LEU* 1.3 73.4 - - - +
135D ARG* 1.3 72.3 + - + +
136D ASN 3.3 0.2 + - - -
137D ALA* 3.0 19.8 + - - +
140D GLY* 3.2 29.2 - - - -
142D LEU* 3.5 37.2 - - + -
151D LEU* 4.7 12.8 - - + -
179D PHE* 3.8 27.6 - - + -
180D LYS 4.1 2.0 - - - -
181D LYS* 3.8 31.2 - - + +
186D ILE* 5.2 4.0 - - + -
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Residues in contact with ARG 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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131D VAL* 3.3 26.4 + - + +
132D ASP* 3.5 28.3 + - - +
134D PHE* 1.3 86.4 - - + +
136D ASN* 1.3 59.6 + - - +
148D VAL* 3.9 23.8 - - - +
149D LYS* 3.4 28.1 + - - +
151D LEU* 4.4 14.1 - - + +
181D LYS* 2.5 34.3 + - - +
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Residues in contact with ASN 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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132D ASP* 3.6 20.6 + - - -
133D LEU* 3.3 10.5 + - + +
134D PHE 3.3 0.4 - - - -
135D ARG* 1.3 80.6 - - - +
137D ALA* 1.3 65.0 + - - +
138D ARG* 3.5 7.8 + - - +
181D LYS* 4.4 1.6 + - - -
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Residues in contact with ALA 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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111D PRO 4.5 12.8 - - - +
121D VAL* 6.0 1.8 - - + -
123D PHE* 3.9 24.9 - - + -
133D LEU 3.1 17.0 + - - +
134D PHE* 3.0 16.6 + - - +
136D ASN* 1.3 75.3 - - - +
138D ARG* 1.3 65.2 + - - +
139D ASN 4.8 7.0 - - - +
140D GLY* 5.8 0.2 - - - -
181D LYS* 3.5 11.3 + - - +
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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