Contacts of the helix formed by residues 139 - 151 (chain A) in PDB entry 5MR9
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 ARG 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ALA 3.3 5.1 + - - +
138A ALA* 1.3 74.9 - - - +
140A VAL* 1.4 59.0 + - - +
141A TYR* 3.2 5.0 - - + +
142A ASP* 3.1 29.6 + - - +
143A LEU* 3.0 27.6 + - - +
163A PRO* 6.2 2.9 - - + -
197A VAL 5.5 1.6 - - - -
166B ARG* 4.7 4.5 - - - +
170B TYR* 3.3 53.3 - - - -
188B GLU* 2.7 44.1 + - - +
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Residues in contact with VAL 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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138A ALA 3.9 1.2 + - - -
139A ARG* 1.4 70.2 - - - +
141A TYR* 1.4 58.7 + - - +
143A LEU* 3.5 9.3 + - + +
144A GLY* 3.1 27.2 + - - -
117B LEU* 3.7 32.9 - - + +
119B TYR* 5.8 2.7 - - + +
186B VAL* 3.8 21.5 - - + -
187B HIS 3.3 26.2 - - - +
188B GLU* 3.8 2.7 + - + +
189B LEU* 3.8 17.4 - - + +
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Residues in contact with TYR 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ARG* 4.7 5.2 - - + +
140A VAL* 1.4 80.7 - - - +
142A ASP* 1.4 74.5 + - - +
145A LEU* 3.0 50.6 + - + +
160A ARG 4.9 1.0 + - - -
127B PHE* 3.8 12.5 - + - -
128B ARG 3.6 20.2 - - - -
129B TYR* 3.4 11.9 - - + +
130B CYS* 3.0 29.3 + - - +
166B ARG* 3.8 8.3 - - - -
167B PRO* 3.6 20.4 - - + +
170B TYR* 3.6 26.7 - + + -
188B GLU 3.6 12.5 + - - +
189B LEU 3.3 28.3 - - - +
191B ALA* 4.0 9.9 - - + -
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Residues in contact with ASP 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ALA* 5.3 0.8 - - + -
139A ARG* 3.1 28.4 + - - +
141A TYR* 1.4 85.7 - - - +
143A LEU* 1.3 56.7 + - - +
145A LEU* 3.4 4.5 + - - +
146A ARG* 3.0 46.3 + - - +
161A ALA* 3.3 22.1 - - - +
163A PRO* 3.6 17.7 - - - +
166B ARG* 2.7 44.5 + - - -
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Residues in contact with LEU 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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138A ALA* 3.5 26.7 - - + +
139A ARG 3.0 13.8 + - - +
140A VAL* 3.7 8.3 - - + +
142A ASP* 1.3 72.0 - - - +
144A GLY* 1.3 64.0 + - - +
146A ARG* 3.3 36.5 + - + +
147A ARG* 3.2 23.9 + - - +
115B LEU 3.9 3.7 - - - +
116B GLY 5.8 2.5 - - - +
117B LEU* 4.0 18.4 - - + -
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Residues in contact with GLY 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A VAL 3.1 15.7 + - - -
141A TYR 3.9 1.8 - - - -
143A LEU* 1.3 75.1 - - - +
145A LEU* 1.3 55.6 + - - +
147A ARG* 3.6 2.4 + - - +
148A LEU* 3.2 39.5 + - - +
115B LEU* 3.8 31.4 + - - +
117B LEU* 4.4 2.6 - - - +
127B PHE* 4.6 3.8 - - - -
189B LEU* 5.4 0.4 - - - -
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Residues in contact with LEU 145 (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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141A TYR* 3.0 51.6 + - + +
142A ASP 3.6 5.6 - - - +
143A LEU 3.3 0.2 - - - -
144A GLY* 1.3 73.3 - - - +
146A ARG* 1.4 53.4 + - - +
148A LEU* 3.5 2.0 + - - -
149A ARG* 2.9 34.7 + - + +
154A LEU* 3.6 26.5 - - + +
159A VAL* 3.7 22.9 - - + -
160A ARG 4.1 4.7 - - - +
161A ALA* 4.1 16.4 - - + -
127B PHE* 3.6 25.0 - - + -
129B TYR* 3.7 17.0 - - + -
130B CYS 4.9 0.4 - - - +
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Residues in contact with ARG 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ALA* 3.4 18.2 - - - +
142A ASP* 3.0 28.1 + - - +
143A LEU* 3.3 35.1 + - + +
145A LEU* 1.4 73.1 - - - +
147A ARG* 1.4 57.4 + - - +
149A ARG* 3.3 23.1 + - - +
150A GLN* 3.1 34.6 + - - +
161A ALA* 2.6 44.8 + - + -
162A GLN* 4.2 19.3 - - - +
163A PRO* 5.4 1.4 - - - +
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Residues in contact with ARG 147 (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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143A LEU 3.2 9.0 + - - +
144A GLY 3.8 2.2 - - - +
146A ARG* 1.4 77.7 - - - +
148A LEU* 1.4 59.4 + - - +
150A GLN* 3.4 30.7 + - - +
151A ARG* 3.3 33.8 + - - +
114B GLU 3.1 24.5 - - - +
115B LEU 3.4 20.2 - - - +
116B GLY* 3.7 28.4 + - - -
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Residues in contact with LEU 148 (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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144A GLY 3.2 20.1 + - - +
145A LEU* 3.9 3.8 - - - +
147A ARG* 1.4 70.9 - - - +
149A ARG* 1.4 62.6 + - - +
151A ARG* 3.5 8.1 + - - +
153A ARG* 3.2 38.3 + - + +
154A LEU* 3.6 17.2 + - + -
108B LEU* 4.4 5.8 - - + -
110B VAL* 3.7 29.2 - - + -
114B GLU* 3.8 31.6 - - + +
115B LEU* 3.8 13.9 - - + -
127B PHE* 3.8 32.3 - - + -
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Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU 2.9 18.0 + - - +
146A ARG* 3.3 31.1 + - - +
148A LEU* 1.4 76.7 - - - +
150A GLN* 1.4 59.9 + - - +
152A ARG* 3.4 15.8 + - - +
154A LEU* 3.7 23.7 - - + +
159A VAL* 3.4 35.4 + - + +
160A ARG* 4.7 0.2 - - - +
161A ALA* 3.4 27.7 - - - +
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Residues in contact with GLN 150 (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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146A ARG* 3.1 18.0 + - - +
147A ARG* 3.4 36.0 + - - +
149A ARG* 1.4 74.6 - - - +
151A ARG* 1.3 59.9 + - + +
152A ARG* 3.3 16.6 + - - +
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Residues in contact with ARG 151 (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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147A ARG* 3.3 36.3 + - - +
148A LEU* 3.8 4.2 - - - +
149A ARG 3.2 1.4 - - - -
150A GLN* 1.3 77.4 - - + +
152A ARG* 1.3 60.2 + - - +
153A ARG* 3.1 40.9 + - + +
113B SER 4.6 3.0 + - - -
114B GLU* 2.7 56.3 + - - +
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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