Contacts of the helix formed by residues 113 - 127 (chain B) in PDB entry 2RHM
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 SER 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B ALA* 1.3 77.6 - - - +
114B GLY* 1.3 60.3 + - - +
115B ASP* 3.9 7.3 + - - +
116B VAL* 3.3 27.9 + - - +
117B LEU* 2.9 26.3 + - - +
167B THR* 3.0 21.3 + - - +
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Residues in contact with GLY 114 (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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112B ALA 3.7 1.6 + - - -
113B SER* 1.3 72.5 - - - +
115B ASP* 1.3 56.2 + - - +
117B LEU* 3.2 6.4 + - - +
118B VAL* 2.9 34.1 + - - +
146B VAL 4.2 5.8 - - - -
147B ARG* 3.7 36.3 + - - -
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Residues in contact with ASP 115 (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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113B SER* 3.3 7.5 + - - +
114B GLY* 1.3 75.2 - - - +
116B VAL* 1.3 64.4 + - + +
118B VAL* 3.4 6.0 + - - +
119B GLU* 3.1 21.7 + - - +
147B ARG* 3.8 22.7 - - - +
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Residues in contact with VAL 116 (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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112B ALA* 4.3 8.1 - - + -
113B SER* 3.2 23.7 + - - +
115B ASP* 1.3 78.1 - - + +
117B LEU* 1.3 66.4 + - - +
119B GLU* 3.3 8.0 + - - +
120B ARG* 3.1 61.7 + - + +
167B THR* 3.7 24.9 - - + +
168B PHE* 5.9 1.6 - - + -
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Residues in contact with LEU 117 (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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12B HIS* 4.9 9.6 - - + -
13B PRO 3.8 9.9 - - - +
14B ALA* 3.4 34.1 - - - +
15B THR* 3.7 22.7 - - + -
112B ALA* 3.6 28.0 - - + +
113B SER 2.9 20.0 + - - +
114B GLY* 3.6 7.0 - - - +
116B VAL* 1.3 75.3 - - - +
118B VAL* 1.3 62.9 + - - +
120B ARG* 3.3 5.5 + - - +
121B ILE* 3.0 31.1 + - + +
146B VAL* 3.8 24.5 - - + +
149B ARG* 5.7 2.2 - - - +
150B GLY 6.1 0.4 - - - +
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Residues in contact with VAL 118 (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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114B GLY 2.9 20.4 + - - +
115B ASP* 3.8 5.4 - - - +
116B VAL 3.3 0.2 - - - -
117B LEU* 1.3 75.6 - - - +
119B GLU* 1.3 63.3 + - - +
121B ILE* 3.4 4.2 + - - +
122B LEU* 3.1 43.5 + - + +
143B LEU* 3.5 44.6 - - + +
146B VAL* 3.8 12.8 - - + -
147B ARG* 4.2 13.0 - - + -
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Residues in contact with GLU 119 (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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115B ASP 3.1 13.8 + - - +
116B VAL* 3.3 11.4 + - + +
118B VAL* 1.3 78.0 - - - +
120B ARG* 1.3 56.9 + - + +
122B LEU* 3.5 6.6 + - - +
123B SER* 3.0 31.3 + - - -
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Residues in contact with ARG 120 (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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14B ALA* 2.9 36.8 + - + -
15B THR 3.9 3.6 - - - -
16B GLY* 4.3 2.4 - - - +
112B ALA* 4.1 4.4 - - - +
116B VAL* 3.1 38.9 + - + +
117B LEU* 3.7 6.1 - - - +
119B GLU* 1.3 74.1 - - + +
121B ILE* 1.3 68.2 + - - +
123B SER* 3.2 7.4 + - - -
124B ARG* 2.9 53.9 + - - +
166B THR* 2.7 46.9 + - - -
167B THR 4.3 0.2 + - - -
169B PRO* 3.8 18.8 - - - +
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Residues in contact with ILE 121 (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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13B PRO* 4.7 8.7 - - + +
14B ALA* 4.0 15.7 - - + -
117B LEU 3.0 20.6 + - - +
118B VAL* 3.8 3.6 - - - +
120B ARG* 1.3 76.0 - - - +
122B LEU* 1.3 65.5 + - - +
125B ILE* 3.2 35.8 + - + +
137B ASP 5.0 9.2 - - - +
138B ARG* 5.1 2.7 - - + -
143B LEU* 4.2 17.0 - - + -
146B VAL* 3.8 36.8 - - + -
149B ARG* 5.7 0.7 - - - +
194B BEZ 3.7 37.0 - - + -
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Residues in contact with LEU 122 (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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118B VAL* 3.1 37.5 + - + +
119B GLU* 3.8 5.6 - - - +
121B ILE* 1.3 81.3 - - + +
123B SER* 1.3 57.8 + - - +
125B ILE* 3.3 6.0 + - + +
126B ALA* 2.9 30.0 + - - +
138B ARG* 4.9 9.9 - - + +
143B LEU* 3.8 27.4 - - + -
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Residues in contact with SER 123 (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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119B GLU 3.0 19.3 + - - -
120B ARG* 3.2 9.7 + - - -
122B LEU* 1.3 76.2 - - - +
124B ARG* 1.3 57.9 + - - +
126B ALA* 4.3 5.8 - - - -
127B GLN* 2.7 46.7 + - - +
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Residues in contact with ARG 124 (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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14B ALA* 3.5 11.7 + - - +
16B GLY* 5.4 3.0 - - - +
19B THR* 5.6 4.2 + - - -
120B ARG* 2.9 53.9 + - - +
121B ILE 3.9 2.9 - - - +
123B SER* 1.3 80.7 + - - +
125B ILE* 1.3 58.0 + - - +
127B GLN* 5.0 0.7 - - - -
128B GLY 3.1 5.2 + - - -
129B ALA* 3.0 45.7 + - + -
130B ARG* 3.3 10.1 + - + +
193B CL 3.4 23.8 - - - +
194B BEZ 3.0 42.4 + - + -
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Residues in contact with ILE 125 (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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121B ILE* 3.2 33.4 + - + +
122B LEU* 3.8 5.6 - - + +
124B ARG* 1.3 75.0 - - - +
126B ALA* 1.3 67.7 + - - +
128B GLY* 3.5 9.4 + - - -
130B ARG* 4.4 10.5 - - + +
136B ASP* 3.9 32.5 - - + +
138B ARG* 4.1 19.1 - - + -
194B BEZ 4.1 9.0 - - + -
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Residues in contact with ALA 126 (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 LEU 2.9 18.3 + - - +
123B SER* 3.8 6.5 - - - +
125B ILE* 1.3 79.6 - - - +
127B GLN* 1.3 67.9 + - - +
128B GLY* 3.2 3.9 + - - -
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Residues in contact with GLN 127 (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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123B SER* 2.7 30.6 + - - +
124B ARG* 4.6 2.2 - - - +
126B ALA* 1.3 81.0 + - + +
128B GLY* 1.3 61.5 + - - +
129B ALA* 3.2 6.9 + - + +
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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