Contacts of the strand formed by residues 104 - 109 (chain O) in PDB entry 3H1I
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 LYS 104 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50O PHE* 3.6 28.7 - - - -
51O ILE 3.4 11.4 - - - +
52O LYS* 5.5 0.4 - - - -
53O ALA 2.8 7.3 + - - -
99O TYR* 5.9 0.4 - - - +
100O SER* 2.8 14.0 - - - +
101O THR* 2.6 47.9 + - - +
103O GLU* 1.3 83.3 - - + +
105O MET* 1.3 55.3 + - - +
106O THR* 2.8 25.6 + - - +
380O ASN* 3.6 19.0 + - - -
384O SER* 4.3 19.5 - - - +
387O LEU* 5.0 11.0 - - + -
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Residues in contact with MET 105 (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 0.7 - - - +
50O PHE* 3.5 1.0 - - - -
51O ILE* 2.6 43.8 + - + +
53O ALA* 3.7 26.4 + - + -
54O GLY* 4.1 4.3 - - - +
66O ALA* 3.7 37.7 - - + +
69O LEU* 3.9 13.5 - - + -
70O ARG* 4.3 15.5 - - + +
98O VAL* 5.3 1.8 - - + -
100O SER* 3.4 27.4 - - - +
104O LYS* 1.3 73.3 - - - +
106O THR* 1.3 61.1 + - - +
107O TYR* 4.1 17.5 - - + +
194O PHE* 4.7 1.8 - - - -
199O PHE* 3.8 23.8 - - - -
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Residues in contact with THR 106 (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 3.6 2.2 - - - +
50O PHE* 3.2 50.7 - - + -
97O SER 3.7 2.1 - - - +
98O VAL* 4.9 0.4 - - - +
99O TYR* 2.5 52.6 + - + +
100O SER* 4.8 0.2 - - - -
104O LYS* 2.8 24.8 + - - +
105O MET* 1.3 75.4 - - - +
107O TYR* 1.3 64.7 + - - +
108O CYS* 3.3 13.0 + - + -
380O ASN* 5.6 0.2 - - - +
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Residues in contact with TYR 107 (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 2.7 37.3 + - - +
51O ILE* 4.6 2.0 - - + -
69O LEU* 3.4 39.4 + - - +
70O ARG* 4.7 0.3 - - - -
73O SER* 4.5 6.1 - - - -
96O LEU* 5.2 4.0 - - + -
97O SER 3.8 5.6 - - - -
98O VAL* 3.7 36.6 - - + -
105O MET* 4.3 12.3 - - + -
106O THR* 1.3 74.0 - - - +
108O CYS* 1.3 57.7 + - - +
123O LEU* 3.3 14.7 - - + +
126O VAL* 4.0 28.3 - - + -
127O THR* 3.4 32.3 - - + -
199O PHE* 3.7 29.0 - + - -
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Residues in contact with CYS 108 (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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46O ARG* 3.3 34.1 + - - -
47O ILE 3.0 19.5 - - - +
48O GLY* 3.5 9.2 - - - -
95O SER* 4.4 0.7 + - - +
96O LEU* 4.0 4.8 - - - +
97O SER* 3.2 29.6 + - - -
99O TYR* 3.7 23.3 - - - -
106O THR* 4.2 9.9 - - + +
107O TYR* 1.3 73.8 - - - +
109O VAL* 1.3 62.0 + - - +
110O GLU* 5.2 0.2 - - - +
123O LEU* 4.5 0.4 - - - +
379O LEU* 4.4 6.5 - - + -
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Residues in contact with VAL 109 (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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46O ARG* 3.5 9.5 + - - +
47O ILE* 3.3 40.1 + - + +
89O ILE* 5.2 4.7 - - + -
95O SER 3.4 12.1 - - - +
96O LEU* 3.5 17.7 - - + -
108O CYS* 1.3 77.7 - - - +
110O GLU* 1.3 69.6 + - - +
119O VAL* 3.4 38.6 - - + +
120O MET* 5.2 1.1 - - + -
123O LEU* 3.3 34.0 - - + +
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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
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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