Contacts of the helix formed by residues 141 - 148 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B PRO* 2.8 14.6 + - + +
139B PRO 4.8 2.7 - - - +
140B GLY* 1.3 84.1 - - - +
142B VAL* 1.3 65.5 + - - +
143B PRO* 3.7 2.9 - - - -
144B TRP* 3.8 12.1 + - + -
145B HIS* 3.0 39.7 + - + +
203B TYR* 3.2 49.4 - - + +
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Residues in contact with VAL 142 (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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135B HIS* 5.6 1.1 - - + -
137B ALA* 3.6 44.6 - - + +
138B PRO 3.8 7.0 - - - +
139B PRO* 4.9 1.8 - - + -
140B GLY 3.7 3.3 - - - +
141B MET* 1.3 76.6 - - - +
143B PRO* 1.3 79.3 - - + +
144B TRP 2.9 1.6 + - - -
145B HIS* 3.0 14.0 + - - +
146B VAL* 3.1 14.6 + - + +
308C LEU* 3.3 23.3 - - + -
312C PHE* 3.2 42.8 - - + -
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Residues in contact with PRO 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLY 5.7 0.2 - - - -
141B MET* 4.9 1.6 - - - -
142B VAL* 1.3 99.4 - - + +
144B TRP* 1.3 59.9 + - - +
146B VAL* 4.7 0.2 - - + -
147B VAL* 2.8 32.9 + - - +
210B MET* 3.6 17.9 - - + -
249B ASN* 4.7 0.4 - - - +
308C LEU* 3.9 31.0 - - + +
309C ILE* 4.1 5.8 - - + +
312C PHE* 3.4 32.1 - - + -
313C GLU* 4.2 14.6 - - + +
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Residues in contact with TRP 144 (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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60B HIS* 6.1 1.1 - - + -
62B MET* 3.9 24.2 - - + -
93B LEU* 3.8 31.0 - - + -
141B MET* 3.8 15.9 + - + +
142B VAL 2.9 1.0 + - - -
143B PRO* 1.3 82.0 - - - +
145B HIS* 1.3 73.9 + + - +
147B VAL* 2.8 21.5 - - + +
148B SER* 2.7 27.4 + - - -
199B PRO* 3.2 34.1 - - + -
200B GLY* 4.4 6.3 - - - -
202B ALA* 4.7 1.3 + - + +
203B TYR* 3.5 47.3 - + + +
206B THR* 4.3 25.0 + - + +
207B VAL* 5.9 0.4 - - + -
210B MET* 3.9 9.1 - - + +
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Residues in contact with HIS 145 (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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62B MET* 3.6 14.9 - - - +
93B LEU* 4.5 8.0 - - + +
94B MET 3.6 7.4 - - - -
95B HIS* 3.2 17.6 + + - -
136B CYS* 4.0 11.9 - - - +
138B PRO* 3.2 25.6 - - + +
141B MET* 3.0 34.3 - - + +
142B VAL 3.0 7.2 + - - +
144B TRP* 1.3 100.5 - + - +
146B VAL* 1.3 62.1 + - - +
148B SER* 3.5 5.9 + - - -
150B MET* 2.9 26.4 + - + +
345B CU 2.1 34.6 - - - -
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Residues in contact with VAL 146 (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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135B HIS* 4.4 8.3 - - + -
136B CYS 3.6 18.4 - - - +
142B VAL* 3.1 12.9 + - + +
143B PRO 4.1 1.8 - - - +
145B HIS* 1.3 74.4 - - - +
147B VAL* 1.3 65.7 + - - +
149B GLY 3.0 10.9 + - - -
150B MET 4.2 6.5 - - - +
151B ASN* 3.1 33.7 + - + +
181B GLN* 3.2 3.2 + - - -
248B ALA* 2.7 37.5 - - + +
249B ASN* 3.9 5.4 - - + +
308C LEU* 2.9 31.4 - - + -
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Residues in contact with VAL 147 (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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143B PRO 2.8 22.1 + - - +
144B TRP* 2.8 39.0 - - + +
146B VAL* 1.3 75.2 - - - +
148B SER* 1.3 57.6 + - - +
149B GLY 2.9 1.4 + - - -
181B GLN* 3.2 11.5 + - - +
182B ASP 4.3 0.4 - - - +
183B PHE* 2.8 32.5 - - + -
184B TYR* 4.0 25.8 - - + -
206B THR* 5.1 3.4 - - + -
210B MET* 4.1 17.7 - - + -
249B ASN* 3.4 29.2 - - - +
309C ILE* 4.9 1.1 - - + -
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Residues in contact with SER 148 (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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59B VAL* 4.7 4.8 - - - +
60B HIS 4.0 10.6 + - - -
61B ALA* 3.3 27.0 - - - +
62B MET* 3.3 36.0 + - - +
144B TRP* 2.7 34.8 + - - -
145B HIS 3.6 7.0 - - - -
146B VAL 3.1 0.4 - - - -
147B VAL* 1.3 77.0 - - - +
149B GLY* 1.3 57.2 + - - +
183B PHE* 3.8 10.9 - - - -
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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