Contacts of the helix formed by residues 233 - 238 (chain B) in PDB entry 1P7L
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 GLY 233 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B MET 4.5 5.0 - - - +
83B GLY* 5.0 1.9 - - - -
163B ASP* 3.7 1.8 - - - -
188B GLN* 2.9 27.3 + - - +
230B PHE* 3.7 12.1 - - - -
232B ILE* 1.3 76.0 - - - +
234B GLY* 1.3 69.9 + - - +
236B MET* 3.5 10.4 + - - +
237B GLY* 3.3 15.0 + - - -
484B ANP 5.2 1.3 - - - -
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Residues in contact with GLY 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PRO* 3.6 13.1 - - - +
77B TYR* 3.2 23.5 + - - -
163B ASP* 2.8 18.4 + - - -
233B GLY* 1.3 66.5 - - - -
235B PRO* 1.3 70.7 - - - +
236B MET 2.8 12.8 + - - -
237B GLY 2.9 10.0 + - - -
238B ASP* 2.9 10.6 + - - +
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Residues in contact with PRO 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PRO* 3.9 3.8 - - + -
18B ILE* 4.1 21.8 - - + -
45B VAL* 3.6 21.5 - - + +
46B LYS* 3.1 57.3 - - - +
47B THR 3.4 3.6 + - - +
77B TYR* 4.7 1.6 - - + -
83B GLY 6.0 0.2 - - - -
84B PHE* 3.5 33.7 - - + -
234B GLY* 1.3 81.2 - - - +
236B MET* 1.3 60.7 + - - +
238B ASP 3.2 15.7 + - - +
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Residues in contact with MET 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU* 4.7 0.3 - - - +
97A LYS 5.1 5.4 - - - +
99A SER* 5.4 1.2 + - - -
46B LYS* 3.5 14.6 + - - -
47B THR* 3.9 22.3 + - + +
80B SER 5.6 0.2 - - - +
83B GLY* 3.6 36.9 + - - +
84B PHE* 5.4 0.2 - - - -
232B ILE* 4.0 25.5 - - + +
233B GLY 3.6 9.4 - - - +
234B GLY 2.8 6.3 + - - -
235B PRO* 1.3 76.7 - - - +
237B GLY* 1.3 59.3 + - - +
87C ASN* 3.7 25.1 - - + +
88C SER* 3.9 11.4 - - - -
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Residues in contact with GLY 237 (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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55A GLU* 4.2 12.3 - - - +
99A SER* 4.3 14.0 + - - -
102A ILE* 4.2 17.7 - - - +
485A MET* 4.4 1.9 - - - +
232B ILE* 4.1 17.5 - - - +
233B GLY* 3.3 9.6 + - - -
234B GLY 2.9 5.7 + - - -
236B MET* 1.3 81.2 - - - +
238B ASP* 1.3 65.1 + - - +
484B ANP 5.4 3.6 - - - -
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Residues in contact with ASP 238 (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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55A GLU* 3.9 4.2 + - - -
485A MET* 2.9 37.1 + - - +
14B HIS* 4.5 1.6 + - - -
15B PRO* 3.0 24.7 - - + +
234B GLY 2.9 5.6 + - - +
235B PRO* 3.2 13.7 + - - +
236B MET 3.4 2.0 - - - -
237B GLY* 1.3 79.0 - - - +
239B CYS* 1.3 63.4 + - - +
484B ANP 3.0 56.8 + - + +
486B K 3.1 13.2 - - - -
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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