Contacts of the helix formed by residues 232 - 242 (chain H) in PDB entry 1AVG
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 PHE 232 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H PRO* 3.6 37.1 - - + +
125H ASP 3.6 22.0 - - - -
126H LYS* 3.6 35.9 - - + -
129H ALA* 3.6 21.5 - - + -
130H LEU* 5.0 2.0 - - + -
210H MET* 4.2 4.4 + - + +
230H HIS* 3.4 19.1 + + + -
231H VAL* 1.3 77.7 - - - +
233H ARG* 1.3 75.7 + - - +
235H LYS* 3.2 30.0 - - + +
236H LYS* 5.2 5.3 + - - -
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Residues in contact with ARG 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165H ARG* 5.6 2.8 - - - +
178H ASP* 3.8 29.0 + - - +
179H ASN* 3.4 24.2 - - - +
230H HIS* 3.2 49.2 + - + +
231H VAL 3.1 0.8 - - - -
232H PHE* 1.3 91.2 - - - +
234H LEU* 1.3 61.1 + - + +
235H LYS 3.3 2.1 + - - -
236H LYS* 4.9 3.6 + - - +
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Residues in contact with LEU 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H HIS* 4.1 21.5 - - + +
101H ARG* 4.2 20.6 - - + +
103H ILE* 4.4 27.4 - - + -
179H ASN* 4.1 25.1 - - + +
229H THR* 4.0 18.8 - - + -
230H HIS 3.0 24.9 - - - +
231H VAL 2.9 8.9 + - - +
233H ARG* 1.3 81.4 - - + +
235H LYS* 1.3 62.9 + - - +
236H LYS 3.4 2.2 - - - -
237H TRP* 3.4 13.1 + - + +
238H ILE* 3.1 23.6 + - - +
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Residues in contact with LYS 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H LEU* 4.2 25.2 + - + -
124H PRO* 2.9 30.9 + - + +
125H ASP* 4.6 0.4 - - - +
231H VAL* 3.2 6.3 + - + +
232H PHE* 3.2 28.9 + - + +
233H ARG 3.3 0.8 - - - -
234H LEU* 1.3 75.7 - - - +
236H LYS* 1.3 83.5 + - - +
238H ILE* 3.2 11.2 + - + +
239H GLN* 3.1 36.1 + - - +
1L PHE* 3.5 52.6 - - - +
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Residues in contact with LYS 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H LYS* 5.1 9.2 - - - +
232H PHE* 5.2 5.5 - - - -
233H ARG 4.9 3.3 + - - +
234H LEU* 3.4 1.0 - - - +
235H LYS* 1.3 99.3 - - + +
237H TRP* 1.3 62.4 + - - +
239H GLN* 3.5 21.1 + - - +
240H LYS* 3.1 25.3 + - - +
1L PHE* 4.9 10.4 - - - -
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Residues in contact with TRP 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H LEU* 5.0 0.4 - - + -
89H TYR* 4.2 9.6 - - + -
90H ILE 4.4 1.5 + - - -
91H HIS* 3.4 56.3 - + + +
92H PRO* 4.0 15.1 - - + +
93H ARG* 5.5 3.1 - - - +
103H ILE* 3.8 29.8 - - + -
104H ALA* 4.4 2.2 - - - -
105H LEU* 3.7 34.8 - - + -
234H LEU* 3.4 14.4 + - + +
235H LYS 3.2 0.4 - - - -
236H LYS* 1.3 75.9 - - - +
238H ILE* 1.3 100.5 + - + +
240H LYS* 2.9 33.5 + - + +
241H VAL* 3.1 36.3 + - + +
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Residues in contact with ILE 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H ILE* 4.7 1.3 - - + -
53H LEU* 4.6 9.0 - - + -
103H ILE* 4.3 13.9 - - + -
105H LEU* 3.8 18.5 - - + +
123H LEU* 4.4 15.9 - - + -
231H VAL* 4.5 17.9 - - + +
234H LEU 3.1 17.0 - - - +
235H LYS* 3.4 16.4 - - + +
237H TRP* 1.3 99.8 - - + +
239H GLN* 1.3 64.6 + - - +
241H VAL* 3.1 1.2 + - - -
242H ILE* 3.0 45.7 + - + +
1L PHE* 4.2 11.7 - - - +
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Residues in contact with GLN 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235H LYS* 3.1 20.9 + - - +
236H LYS* 3.6 23.1 + - + +
238H ILE* 1.3 78.5 - - - +
240H LYS* 1.3 58.1 + - - +
242H ILE* 4.5 0.4 - - - -
243H ASP* 3.0 40.0 + - - +
1L PHE* 2.9 83.3 + - - +
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Residues in contact with LYS 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93H ARG* 6.2 2.5 - - - +
236H LYS* 3.1 13.8 + - - +
237H TRP* 2.9 32.3 + - + +
239H GLN* 1.3 79.4 - - - +
241H VAL* 1.3 56.9 + - + +
243H ASP* 3.8 4.5 - - - +
244H ARG* 3.1 56.7 + - - +
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Residues in contact with VAL 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H TRP* 4.2 8.7 - - + -
89H TYR* 3.8 43.2 + - + -
105H LEU* 3.3 28.0 - - + -
237H TRP* 3.1 47.0 + - + +
238H ILE 3.1 0.6 + - - +
240H LYS* 1.3 77.5 - - + +
242H ILE* 1.3 69.7 + - - +
244H ARG* 3.7 17.2 - - - +
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Residues in contact with ILE 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H ILE* 4.3 10.5 - - + -
51H TRP* 4.1 28.6 - - + +
105H LEU* 4.2 10.8 - - + -
238H ILE* 3.0 30.2 + - + +
239H GLN 4.0 2.9 - - - +
241H VAL* 1.3 80.6 - - - +
243H ASP* 1.3 61.5 + - - +
244H ARG* 3.0 8.0 + - - +
1L THR* 3.3 99.0 - - + +
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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
------------------------------------------------------------
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