Contacts of the helix formed by residues 142 - 150 (chain A) in PDB entry 2R2N
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 TYR 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A GLN* 3.5 27.3 + - - -
121A LEU* 5.7 0.7 - - + -
141A ALA* 1.3 71.3 - - - +
143A SER* 1.3 63.7 + - - +
144A GLY* 3.6 19.1 - - - -
145A THR* 2.6 50.8 + - + +
146A LEU* 3.3 2.9 + - - +
195A TYR* 4.1 10.8 + - - +
197A VAL* 5.1 1.1 - - + -
201A ASN* 4.8 2.0 - - - +
202A ASN* 3.2 33.2 + - - +
230A ASP* 4.6 0.4 - - - -
387A PHE* 4.4 2.0 - + - -
426A PMP 3.5 54.6 - + + -
428A KYN 2.9 54.3 + - + +
293B LEU* 4.7 1.0 - - - +
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Residues in contact with SER 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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141A ALA 3.1 3.9 + - - -
142A TYR* 1.3 79.7 - - - +
144A GLY* 1.3 56.6 + - - +
146A LEU* 3.3 5.1 + - - +
147A GLN* 2.9 36.6 + - - +
386A ALA 3.4 27.8 - - - -
387A PHE* 3.9 5.3 - - - -
428A KYN 5.7 1.2 + - - +
18B PRO* 3.9 20.0 - - - +
19B ILE* 3.1 28.3 - - - +
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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
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118A GLN* 4.1 14.5 + - - -
142A TYR* 3.2 27.1 - - - -
143A SER* 1.3 78.6 + - - +
145A THR* 1.3 64.5 + - - +
147A GLN* 3.9 4.9 - - - +
148A SER* 3.0 24.9 + - - -
428A KYN 5.2 4.2 + - - -
290B VAL* 4.2 4.1 - - - +
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Residues in contact with THR 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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118A GLN* 4.9 1.8 + - - -
121A LEU* 6.2 1.3 - - - -
125A PHE* 3.7 19.1 - - - -
137A LEU* 5.3 1.1 - - + -
141A ALA* 4.1 10.1 - - + -
142A TYR* 2.6 49.5 + - - +
144A GLY* 1.3 76.4 - - - +
146A LEU* 1.3 59.7 + - + +
148A SER* 3.2 6.1 + - - -
149A LEU* 2.9 39.8 + - - +
195A TYR* 3.5 44.7 - - + +
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Residues in contact with LEU 146 (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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137A LEU* 4.4 14.1 - - + -
139A GLU* 5.2 0.9 - - + +
141A ALA* 3.9 22.9 - - + +
142A TYR 3.3 10.0 + - - +
143A SER 3.3 5.6 + - - +
145A THR* 1.3 78.8 - - + +
147A GLN* 1.3 60.5 + - + +
149A LEU* 4.2 4.6 - - + +
150A HIS* 3.1 29.5 + - - +
156A ILE* 4.7 5.2 - - + -
386A ALA 3.9 8.1 - - - +
387A PHE 3.5 20.9 - - - +
388A TYR 3.4 34.5 - - - +
389A VAL* 3.7 24.5 - - + +
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Residues in contact with GLN 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 SER 2.9 22.9 + - - +
144A GLY* 4.1 4.5 - - - +
146A LEU* 1.3 80.0 - - + +
148A SER* 1.3 58.7 + - - +
150A HIS* 4.7 5.9 + - - +
151A PRO* 3.1 24.1 - - - +
14B ARG* 5.0 1.9 + - - +
15B ASN* 3.5 43.8 + - - +
17B SER* 3.0 31.6 + - - +
18B PRO* 3.9 23.7 - - + +
290B VAL* 4.0 17.1 - - + +
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Residues in contact with SER 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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118A GLN* 5.5 1.1 - - - -
122A CYS* 4.1 18.9 - - - -
125A PHE* 3.5 25.1 - - - +
144A GLY 3.0 19.1 + - - -
145A THR* 3.5 5.8 - - - -
147A GLN* 1.3 78.3 - - - +
149A LEU* 1.3 61.2 + - - +
151A PRO* 3.5 13.4 - - - +
152A LEU* 3.8 15.1 - - - +
14B ARG* 4.9 1.7 + - - -
290B VAL* 3.9 24.1 - - - +
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Residues in contact with LEU 149 (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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125A PHE* 3.6 28.9 - - + -
129A ILE* 3.5 31.0 - - + -
135A VAL* 4.5 5.6 - - + -
137A LEU* 3.8 25.4 - - + -
145A THR* 2.9 34.7 + - - +
146A LEU* 4.2 2.2 - - - +
147A GLN 3.5 0.2 - - - -
148A SER* 1.3 75.9 - - - +
150A HIS* 1.3 65.2 + - - +
152A LEU* 3.1 20.8 + - - +
153A GLY 3.7 0.9 + - - -
154A CYS* 3.6 17.8 + - - -
156A ILE* 4.2 20.9 - - + -
193A PHE* 4.0 8.3 - - + -
195A TYR* 5.8 0.4 - - + -
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Residues in contact with HIS 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 LEU 3.1 18.6 + - - +
147A GLN* 4.3 7.3 + - - +
149A LEU* 1.3 75.6 - - - +
151A PRO* 1.4 70.4 - - + +
152A LEU 3.1 1.2 + - - -
153A GLY* 3.1 13.7 + - - -
154A CYS 6.1 0.2 - - - -
156A ILE* 5.3 3.8 - - - +
389A VAL* 6.6 0.2 - - + -
13B ALA* 3.2 38.8 + - + +
14B ARG* 5.2 0.4 - - - -
15B ASN* 3.8 19.3 + - - -
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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