Contacts of the strand formed by residues 48 - 51 (chain O) in PDB entry 3H1J
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 48 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47O ILE* 1.3 84.5 - - - +
49O VAL* 1.3 62.1 + - - -
50O PHE* 3.3 17.1 - - - -
107O TYR 3.1 12.8 - - - -
108O CYS* 3.2 7.6 - - - -
123O LEU* 4.1 1.3 - - - -
206O LEU* 3.8 2.5 - - - -
207O VAL 3.0 31.4 + - - +
379O LEU* 4.7 0.9 - - - +
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Residues in contact with VAL 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33O LEU* 6.5 0.2 - - + -
48O GLY* 1.3 70.8 - - - -
50O PHE* 1.3 62.0 + - - +
51O ILE* 3.6 20.9 + - + +
105O MET 3.7 0.7 - - - +
106O THR* 3.7 0.3 - - - -
107O TYR* 2.6 31.0 + - - +
123O LEU* 4.1 14.1 - - + +
124O LEU* 5.9 0.9 - - - +
127O THR* 4.0 31.4 - - + +
204O MET* 3.6 30.7 - - + -
205O ALA 3.6 6.5 - - - +
206O LEU* 4.1 17.7 - - + -
224O LEU* 5.4 8.3 - - + -
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Residues in contact with PHE 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48O GLY* 3.3 16.2 - - - -
49O VAL* 1.3 72.9 - - - +
51O ILE* 1.3 60.1 + - - +
104O LYS* 3.4 27.8 - - - +
105O MET 3.7 4.9 - - - +
106O THR* 3.4 25.1 - - + -
204O MET* 3.4 3.3 - - - +
205O ALA* 2.8 42.7 + - + +
207O VAL* 3.3 35.0 - - + -
379O LEU* 3.1 39.9 - - + -
380O ASN* 4.0 12.3 - - + -
383O GLY* 4.0 15.3 - - - +
387O LEU* 3.6 17.9 - - + +
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Residues in contact with ILE 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49O VAL* 3.7 25.4 - - + +
50O PHE* 1.3 79.7 - - - +
52O LYS* 1.3 63.7 + - - +
53O ALA* 3.0 28.7 + - + +
104O LYS* 3.9 5.2 - - - +
105O MET* 2.8 30.8 + - + +
107O TYR* 4.4 12.6 - - + -
127O THR* 5.0 2.2 - - - -
198O ASN 4.0 11.2 - - - +
199O PHE* 3.3 48.5 - - + -
203O ARG 3.5 7.2 - - - +
204O MET* 3.7 13.9 - - + -
387O LEU* 3.9 9.3 - - - +
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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