Contacts of the strand formed by residues 27 - 33 (chain F) in PDB entry 2WA9
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 MET 27 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25F PRO* 3.1 15.8 + - - +
26F SER* 1.3 72.3 - - - +
28F TYR* 1.3 68.7 + - - +
75F VAL* 4.0 15.3 - - + +
76F PHE* 3.2 39.0 - - - +
77F THR* 3.7 23.6 - - + +
105F LYS* 3.9 4.5 - - - +
106F ALA* 3.1 38.0 + - + +
108F ALA* 4.8 10.3 - - - +
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Residues in contact with TYR 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F SER* 3.8 17.0 - - - -
27F MET* 1.3 81.2 - - - +
29F LYS* 1.3 63.6 + - - +
30F VAL* 3.4 4.0 + - - +
75F VAL* 3.3 4.6 - - - -
76F PHE* 2.5 42.3 + - - +
78F ALA* 3.8 21.5 - - + -
81F ALA* 3.8 21.8 - - + -
103F LEU* 4.0 24.5 - - + -
104F GLU 3.5 18.6 - - - -
105F LYS* 2.8 51.3 - - + +
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Residues in contact with LYS 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F TYR* 1.3 71.4 - - - +
30F VAL* 1.3 61.6 + - - +
31F ILE* 3.8 19.4 + - + -
72F ILE* 4.3 29.3 - - + +
74F GLY 3.8 5.2 - - - -
75F VAL* 4.3 10.9 - - + +
103F LEU* 3.7 6.9 - - - +
104F GLU* 2.7 65.6 + - + +
105F LYS 4.6 0.7 - - - -
106F ALA* 4.1 30.2 + - + +
108F ALA 6.2 0.8 - - - -
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Residues in contact with VAL 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F TYR 3.4 0.6 + - - +
29F LYS* 1.3 74.3 - - - +
31F ILE* 1.3 56.4 + - - +
51F PHE* 3.9 27.4 - - + -
72F ILE 3.6 0.9 - - - -
73F CYS* 2.8 32.8 + - + +
74F GLY 2.8 16.2 + - - +
76F PHE* 3.7 24.9 - - + -
81F ALA* 3.7 33.4 - - + +
84F LYS* 4.6 7.4 - - + -
85F VAL* 4.6 4.0 - - + -
101F CYS* 4.0 18.6 - - - -
102F THR 3.7 3.4 - - - +
103F LEU* 4.5 3.4 - - + -
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Residues in contact with ILE 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F LYS* 4.0 12.3 - - + +
30F VAL* 1.3 77.0 - - - +
32F LEU* 1.3 73.6 - - - +
33F VAL* 4.1 2.7 - - + -
70F LYS* 4.0 30.3 - - + +
71F ALA 3.6 8.7 - - - +
72F ILE* 3.9 21.1 - - + -
101F CYS* 3.4 5.4 - - - -
102F THR* 2.8 57.5 + - + +
104F GLU* 3.5 38.1 - - + +
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Residues in contact with LEU 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F VAL 4.3 0.2 + - - -
31F ILE* 1.3 72.3 - - - +
33F VAL* 1.3 63.8 + - - +
43F VAL* 4.1 26.5 - - + -
46F VAL* 4.4 17.0 - - + -
47F LEU* 4.4 4.5 - - + -
51F PHE* 5.1 1.6 - - + -
61F LEU* 6.4 0.2 - - + -
65F VAL* 3.8 16.9 - - + +
70F LYS* 3.2 5.7 - - - -
71F ALA 3.0 35.5 + - - +
73F CYS* 3.6 24.9 - - - -
88F VAL* 4.2 12.1 - - + -
99F LEU* 4.4 17.0 - - + -
100F LEU 4.0 0.4 - - - -
101F CYS* 3.8 32.1 - - + -
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Residues in contact with VAL 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F ILE* 4.3 6.1 - - + -
32F LEU* 1.3 77.1 - - - +
34F ASN* 1.3 70.5 + - - +
35F ASP* 4.0 2.6 - - - +
65F VAL* 4.0 2.5 - - - -
69F GLY 3.8 11.9 - - - +
70F LYS* 4.5 6.5 - - + -
99F LEU* 3.5 19.9 - - - +
100F LEU* 2.9 36.5 + - + +
102F THR* 3.9 28.3 - - + -
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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