Contacts of the helix formed by residues 141 - 148 (chain A) in PDB entry 2P80
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 MET 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A LEU* 6.2 3.4 - - + -
94A MET* 5.7 5.2 - - + +
138A PRO* 2.8 21.9 + - + +
139A PRO 3.3 7.4 - - - +
140A GLY* 1.3 83.1 - - - +
142A VAL* 1.3 66.3 + - - +
143A PRO* 3.6 4.0 - - - -
144A TRP* 3.6 27.0 + - + +
145A HIS* 3.0 41.7 + - + +
203A TYR* 4.2 21.1 - - + +
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Residues in contact with VAL 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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135A HIS* 5.6 2.0 - - + -
137A ALA* 3.6 44.9 - - + +
138A PRO 3.9 6.3 - - - +
139A PRO* 4.9 1.6 - - + -
140A GLY 3.7 2.9 - - - +
141A MET* 1.3 80.8 - - - +
143A PRO* 1.3 75.5 - - + +
144A TRP 3.0 1.6 + - - -
145A HIS* 3.1 10.2 + - - +
146A VAL* 3.1 13.8 + - + +
308B LEU* 3.6 23.1 - - + -
312B PHE* 3.3 41.0 - - + -
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Residues in contact with PRO 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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140A GLY 5.5 0.9 - - - +
141A MET* 3.8 2.5 - - - -
142A VAL* 1.3 102.0 - - + +
144A TRP* 1.3 50.3 + - - +
146A VAL* 4.0 0.4 - - - +
147A VAL* 2.6 42.4 + - + +
210A MET* 3.6 18.4 - - + -
308B LEU* 3.8 27.1 - - + +
309B ILE* 4.1 10.3 - - + +
312B PHE* 3.4 30.5 - - + -
313B GLU* 4.3 14.4 - - + +
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Residues in contact with TRP 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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60A HIS* 6.0 1.6 - - + -
62A MET* 3.5 26.5 - - + -
93A LEU* 3.7 22.7 - - + -
141A MET* 3.6 18.1 + - - +
142A VAL 3.0 1.0 + - - -
143A PRO* 1.3 80.0 - - - +
145A HIS* 1.3 81.4 + + - +
147A VAL* 2.8 21.8 - - + +
148A SER* 2.8 31.3 + - - -
199A PRO* 3.0 39.3 - - + -
200A GLY* 4.0 8.1 - - - -
202A ALA* 4.9 0.8 + - - +
203A TYR* 3.4 45.5 - + + +
206A THR* 4.4 25.9 + - + +
207A VAL* 5.9 1.8 - - + -
210A MET* 4.0 8.0 - - + +
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Residues in contact with HIS 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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62A MET* 3.7 11.8 - - - -
93A LEU* 4.6 6.5 - - + +
94A MET 3.4 8.9 + - - -
95A HIS* 3.2 19.2 + + - -
136A CYS* 3.3 13.9 - - + +
138A PRO* 3.1 28.0 - - + +
141A MET* 3.0 39.4 - - + +
142A VAL 3.1 7.4 + - - +
144A TRP* 1.3 100.0 - + - +
146A VAL* 1.3 61.7 + - - +
148A SER* 3.6 5.9 + - - -
150A MET* 2.9 26.1 + - - +
345A CU 2.1 33.7 - - - -
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Residues in contact with VAL 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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135A HIS* 4.1 15.5 - - + -
136A CYS 3.5 21.5 - - - +
142A VAL* 3.1 9.4 + - + +
143A PRO 4.1 1.3 - - - +
145A HIS* 1.3 75.9 - - - +
147A VAL* 1.3 66.8 + - - +
149A GLY 2.9 11.4 + - - -
150A MET 4.2 5.8 - - - +
151A ASN* 3.1 21.9 + - - +
181A GLN* 3.2 4.4 + - - +
248A ALA* 3.7 27.1 - - + -
249A ASN* 3.9 12.1 - - + +
308B LEU* 3.0 36.8 - - + -
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Residues in contact with VAL 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 PRO* 2.6 26.7 - - + +
144A TRP* 2.8 30.1 - - + +
146A VAL* 1.3 74.3 - - + +
148A SER* 1.3 57.2 + - - +
149A GLY 2.9 0.6 + - - -
181A GLN* 3.3 11.5 + - - +
182A ASP* 4.2 1.8 - - - +
183A PHE* 2.8 33.9 - - + -
184A TYR* 3.8 35.7 - - + +
206A THR* 5.2 2.9 - - + -
210A MET* 4.2 16.8 - - + -
249A ASN* 4.2 20.2 - - + +
309B ILE* 4.9 1.8 - - + -
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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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59A VAL* 4.6 4.4 - - - +
60A HIS 3.9 10.0 + - - -
61A ALA* 3.3 13.0 - - - +
62A MET* 3.3 53.7 + - - +
68A VAL* 4.4 0.2 - - - +
144A TRP* 2.8 34.8 + - - -
145A HIS 3.7 4.3 - - - -
146A VAL 3.1 0.6 - - - -
147A VAL* 1.3 77.1 - - - +
149A GLY* 1.3 57.5 + - - +
183A PHE* 3.7 10.6 - - - -
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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