Contacts of the strand formed by residues 81 - 86 (chain K) in PDB entry 4FAO
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 81 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G ILE* 3.9 29.2 - - + +
30G LYS* 6.1 0.7 - - - -
85G LEU* 5.1 4.3 - - + -
87G LYS* 5.8 2.9 - - - -
93G PRO* 4.5 22.0 - - + -
44K SER* 4.2 14.6 - - - +
45K TRP* 4.0 9.4 - - - +
46K ARG* 4.8 16.8 - - + +
55K VAL* 5.5 4.5 - - + -
76K GLU* 5.9 0.9 - - - +
79K PRO* 3.5 12.2 - - - +
80K GLN* 1.3 98.4 + - + +
82K TYR* 1.3 77.1 + - - +
83K PHE* 3.6 5.2 + - + +
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Residues in contact with TYR 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44K SER* 3.0 28.1 - - - -
45K TRP* 2.9 58.6 + + + +
47K ASN* 3.4 49.5 + - + +
74K ALA* 4.8 2.2 - - + -
77K GLU 5.2 0.3 + - - -
78K ASN* 3.4 17.5 + - - -
79K PRO* 3.0 42.5 - - + +
80K GLN 4.1 2.7 - - - -
81K VAL* 1.3 73.7 - - - +
83K PHE* 1.3 60.1 + - - +
97K HIS* 3.6 42.5 + + + -
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Residues in contact with PHE 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G ILE* 5.5 3.6 - - + +
28G ALA* 3.6 27.6 - - + -
29G PRO* 5.6 2.9 - - + -
85G LEU* 4.1 15.9 - - + -
42K TYR* 3.8 30.5 - + + -
43K ALA 3.5 7.9 - - - -
44K SER* 4.4 1.6 - - - -
45K TRP* 4.4 1.3 - - - -
60K TRP* 3.7 43.3 - + - -
63K ASP* 5.6 0.9 - - - -
74K ALA* 3.1 23.8 - - - +
75K THR 4.5 1.4 + - - -
76K GLU* 5.8 7.5 - - + +
81K VAL* 3.6 6.8 + - + +
82K TYR* 1.3 76.9 - - - +
84K CYS* 1.3 86.2 + - - +
85K CYS* 3.8 16.4 - - + -
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Residues in contact with CYS 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K TYR* 3.1 5.2 - - - +
43K ALA* 2.9 34.5 + - - +
45K TRP* 3.8 20.9 - - + -
72K CYS* 2.1 54.5 - - - -
73K VAL 3.4 28.3 - - - +
74K ALA* 3.6 2.0 - - - +
83K PHE* 1.3 85.8 - - - +
85K CYS* 1.3 60.7 + - - +
95K PHE* 4.0 4.3 - - - -
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Residues in contact with CYS 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40K HIS* 4.9 0.2 - - + -
41K CYS 3.0 14.6 - - - +
60K TRP* 4.4 5.2 - - + -
63K ASP* 4.4 5.4 - - - -
65K ASN* 4.3 8.3 - - - -
66K CYS* 2.0 48.0 - - - -
69K ARG* 3.5 21.1 - - - -
71K GLU 4.2 1.6 - - - +
72K CYS* 4.0 4.3 - - - -
73K VAL 4.4 2.2 + - - +
83K PHE* 3.9 22.4 - - + -
84K CYS* 1.3 76.6 - - - +
86K CYS* 1.3 64.6 + - - +
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Residues in contact with CYS 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40K HIS* 3.2 12.6 - - - +
41K CYS* 2.9 38.1 + - - -
66K CYS* 3.9 6.9 - - - +
69K ARG* 3.5 15.5 - - - +
71K GLU 3.8 13.7 - - - +
72K CYS* 3.9 9.0 - - - -
85K CYS* 1.3 78.7 - - - +
87K GLU* 1.3 60.5 + - - +
91K CYS* 2.0 59.9 - - + -
92K ASN 3.9 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