Contacts of the strand formed by residues 68 - 74 (chain X) in PDB entry 2AW2
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 HIS 68 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67X PRO* 1.3 70.1 - - - +
69X VAL* 1.3 63.3 + - - +
70X THR* 3.4 30.1 + - + +
116X SER 4.0 0.5 - - - +
117X ALA* 3.3 2.4 - - - -
118X ASN* 2.7 54.5 + - + +
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Residues in contact with VAL 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X LEU* 5.2 0.2 - - + -
58X CYS* 4.5 6.5 - - - -
60X VAL* 4.5 6.7 - - + -
67X PRO* 3.4 27.1 + - + +
68X HIS* 1.3 86.3 + - - +
70X THR* 1.3 71.6 + - - +
89X TRP* 3.8 24.1 - - + -
98X PHE* 3.3 46.4 - - + -
115X CYS* 4.5 10.3 - - + -
116X SER 3.3 13.0 - - - +
117X ALA* 4.2 8.3 - - + -
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Residues in contact with THR 70 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X HIS* 3.4 31.4 - - + +
69X VAL* 1.3 79.9 - - - +
71X TRP* 1.3 67.3 + - - +
72X CYS* 5.6 1.2 - - - +
81X LYS* 4.4 29.3 - - + +
98X PHE* 4.0 5.8 - - - -
114X ARG 3.8 0.5 - - - +
115X CYS* 3.2 6.4 - - - +
116X SER* 3.0 46.3 + - - -
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Residues in contact with TRP 71 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40X ILE* 4.0 21.8 - - + -
56X LEU* 3.8 25.6 - - + -
57X GLU 4.9 0.7 - - - -
58X CYS* 3.4 30.1 - - + -
70X THR* 1.3 75.8 - - - +
72X CYS* 1.3 64.3 + - - +
81X LYS* 3.4 7.6 - - - +
82X LEU* 3.4 22.3 + - + +
87X THR* 4.5 3.3 - - + +
98X PHE* 3.3 45.9 + + - -
100X LEU* 3.6 50.6 - - + +
113X TYR* 3.8 20.0 - - + -
114X ARG* 3.4 44.2 - - - -
115X CYS* 3.7 3.4 - - + -
129X THR* 4.2 5.4 - - + -
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Residues in contact with CYS 72 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70X THR* 5.6 0.9 - - - +
71X TRP* 1.3 78.7 - - - +
73X LYS* 1.3 56.8 + - - +
79X CYS* 2.0 49.1 - - - -
80X VAL 3.2 25.1 - - - +
81X LYS* 3.7 8.1 - - + +
82X LEU* 4.4 3.1 - - - -
113X TYR* 3.3 9.4 - - - +
114X ARG* 3.0 47.4 + - - -
116X SER* 5.3 7.4 - - - -
125X GLU* 5.9 0.7 - - - -
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Residues in contact with LYS 73 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72X CYS* 1.3 71.4 - - - +
74X LEU* 1.3 71.2 + - - +
75X ASN 3.8 0.2 + - - -
79X CYS* 4.0 1.3 - - - -
80X VAL* 2.9 42.1 + - + +
82X LEU* 4.3 15.6 - - + +
108X ASN 2.7 21.4 + - - -
109X ASP* 3.3 14.7 + - - +
110X ASN 2.7 30.8 + - - -
111X GLY* 4.2 4.7 - - - -
112X SER 3.6 9.6 - - - +
113X TYR* 3.5 27.8 + - + +
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Residues in contact with LEU 74 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73X LYS* 1.3 83.0 - - - +
75X ASN* 1.3 59.4 + - - +
76X GLY 3.6 6.7 - - - +
78X THR 4.2 3.1 - - - -
79X CYS* 3.6 32.3 - - + +
111X GLY* 5.8 0.5 - - - -
112X SER* 2.9 47.8 + - - +
113X TYR* 4.2 2.5 - - - +
114X ARG* 4.2 15.0 - - + +
128X SER* 3.8 17.3 - - - +
7Y ASP* 3.7 40.4 - - + +
49Y LEU* 5.5 2.0 - - + -
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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