Contacts of the strand formed by residues 99 - 104 (chain O) in PDB entry 6XXD
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 VAL 99 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O ASP* 4.7 0.3 - - - +
93O GLY* 4.7 2.6 - - - -
94O HIS 5.3 0.5 + - - -
98O THR* 1.3 98.4 + - - +
100O TRP* 1.3 61.9 + - - +
101O PHE* 3.2 23.7 - - + -
111O LYS* 4.0 30.1 - - + -
112O THR 3.4 20.4 - - - +
113O ASN* 4.2 6.3 - - - +
114O THR 3.3 20.9 - - - +
115O ALA* 4.2 3.4 - - + -
116O VAL* 3.6 14.3 - - - +
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Residues in contact with TRP 100 (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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77O THR* 3.2 36.3 - - + -
91O ILE* 3.6 20.9 - - + -
92O ALA 3.8 2.9 - - - -
93O GLY* 3.6 26.2 - - - -
99O VAL* 1.3 77.1 - - - +
101O PHE* 1.3 61.0 + - - +
111O LYS* 3.7 2.4 - - - -
112O THR* 3.0 41.7 + - + +
114O THR* 3.2 13.1 + - + -
115O ALA 2.9 30.6 + - - -
116O VAL* 3.7 13.8 - - + +
118O SER 3.5 11.9 + - - -
119O SER* 3.6 3.2 + - - -
120O GLN* 3.7 42.0 - - + -
121O PRO* 3.6 19.7 - - + -
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Residues in contact with PHE 101 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33O ASP* 3.8 42.2 - - + -
36O VAL* 3.6 17.9 - - + -
37O THR* 3.3 24.2 - - + -
40O LEU* 3.3 24.0 - - + +
91O ILE* 3.5 3.6 - - - -
92O ALA 2.8 36.4 + - - +
93O GLY* 5.2 0.2 - - - -
98O THR* 4.5 3.1 - - - -
99O VAL* 3.2 23.3 - - + -
100O TRP* 1.3 73.0 - - - +
102O ALA* 1.3 58.5 + - - +
109O VAL* 4.8 6.5 - - + -
110O TYR 3.4 12.6 - - - +
111O LYS* 3.7 30.3 - - + -
112O THR* 5.5 0.2 - - - -
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Residues in contact with ALA 102 (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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40O LEU* 3.9 0.2 - - - +
90O MET 3.4 6.5 - - - -
91O ILE* 3.8 10.3 - - + +
100O TRP 4.2 1.0 + - - -
101O PHE* 1.3 74.6 - - - +
103O ALA* 1.3 65.5 + - - +
108O GLY 4.6 0.7 - - - -
109O VAL* 3.6 6.8 - - - +
110O TYR* 2.8 58.8 + - + +
111O LYS* 4.7 0.4 - - - +
112O THR* 5.0 4.5 - - - +
124O CYS* 3.7 21.1 - - + -
125O PRO* 4.4 4.5 - - + -
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Residues in contact with ALA 103 (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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40O LEU* 3.8 17.9 - - + -
44O VAL* 4.3 3.6 - - + -
88O TYR* 3.3 13.6 - - - -
89O CYS* 3.8 0.5 - - - -
90O MET* 2.9 48.4 + - + +
102O ALA* 1.3 80.5 - - - +
104O THR* 1.3 61.9 + - - +
108O GLY 3.5 7.2 - - - -
109O VAL* 4.1 16.4 - - + -
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Residues in contact with THR 104 (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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24K LEU* 5.3 0.3 - - - +
44O VAL* 5.3 0.9 - - - +
88O TYR* 3.7 16.6 + - - +
103O ALA* 1.3 76.4 - - - +
105O PRO* 1.4 70.8 - - - +
106O ASP* 2.7 23.8 + - - -
107O LYS* 3.2 17.0 + - + +
108O GLY* 2.9 29.4 + - - -
110O TYR* 4.2 11.2 - - + +
124O CYS* 3.5 36.6 - - + -
125O PRO* 5.1 1.8 - - - +
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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