Contacts of the strand formed by residues 76 - 81 (chain K) in PDB entry 6R90
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 LEU 76 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23K PHE* 4.5 0.7 - - - -
66K LEU* 3.5 8.5 - - - +
67K PHE* 2.6 56.8 + - + +
68K ARG* 4.7 0.2 - - - +
69K PRO* 4.4 18.8 - - + -
72K GLU* 4.6 10.3 - - + +
74K LYS* 3.7 5.1 + - + +
75K ASP* 1.3 77.2 - - - +
77K LEU* 1.3 60.5 + - - +
88K ILE* 3.8 17.9 - - + -
89K LEU 3.5 16.2 - - - +
90K GLU* 3.6 30.3 - - + -
103K ARG* 4.1 26.9 - - + +
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Residues in contact with LEU 77 (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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23K PHE* 3.6 26.7 - - + -
32K LEU* 3.6 27.8 - - + -
39K LEU* 4.1 10.5 - - + -
64K MET* 4.0 14.6 - - + -
65K GLU 3.6 18.4 - - - +
66K LEU* 3.6 13.9 - - + -
67K PHE* 3.9 3.6 - - - -
76K LEU* 1.3 74.4 - - - +
78K PHE* 1.3 64.4 + - - +
79K ILE* 4.1 23.9 + - + -
87K CYS 3.7 0.9 - - - +
88K ILE* 3.3 2.8 - - - -
89K LEU* 2.8 51.2 + - + +
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Residues in contact with PHE 78 (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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63K VAL* 3.8 12.5 - - + +
64K MET* 3.7 2.3 + - - -
65K GLU 3.3 27.3 + - - -
67K PHE* 3.8 9.3 - - + -
77K LEU* 1.3 73.1 - - - +
79K ILE* 1.3 71.8 + - - +
80K LEU* 4.3 14.1 - - + -
86K ALA* 3.7 31.9 - - + -
87K CYS 3.1 27.6 - - - -
88K ILE* 3.9 6.5 - - + +
122K GLY* 5.9 0.2 - - - -
124K ILE* 3.7 29.4 - - + -
131K ILE* 3.6 43.1 - - + -
133K LEU* 4.2 12.6 - - + -
143K ILE* 4.2 11.7 - - + -
152K LEU* 4.6 3.8 - - + -
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Residues in contact with ILE 79 (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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39K LEU* 4.3 8.7 - - + -
57K MET* 3.7 38.8 - - + -
61K ILE* 4.1 26.5 - - + -
63K VAL 3.4 11.7 - - - +
64K MET* 4.5 6.7 - - + -
77K LEU* 4.1 27.3 + - + -
78K PHE* 1.3 84.9 - - - +
80K LEU* 1.3 73.8 + - - +
81K THR* 4.8 3.8 - - + -
85K ASN 3.7 0.3 - - - +
86K ALA* 3.5 2.1 - - - -
87K CYS* 2.9 44.7 + - - +
89K LEU* 4.5 5.4 - - + -
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Residues in contact with LEU 80 (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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60K LYS 3.7 0.5 - - - +
62K ALA* 2.9 25.9 + - - +
63K VAL* 3.4 23.3 + - + +
78K PHE* 4.3 7.0 - - + -
79K ILE* 1.3 78.3 - - - +
81K THR* 1.3 69.9 + - - +
84K TYR* 3.9 5.8 - - - -
85K ASN 3.3 26.0 - - - +
86K ALA* 3.6 15.0 - - + +
108K VAL* 3.8 15.5 - - + -
120K ILE* 4.1 23.1 - - + -
133K LEU* 3.6 35.2 - - + -
135K LEU* 4.3 9.4 - - + -
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Residues in contact with THR 81 (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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57K MET* 5.2 3.8 - - + -
59K GLY* 4.2 20.9 - - - -
60K LYS 3.3 16.2 - - - +
61K ILE* 6.2 0.2 - - + -
62K ALA* 4.4 3.8 - - - -
79K ILE* 4.8 9.4 - - + -
80K LEU* 1.3 84.5 - - - +
82K ALA* 1.3 59.9 + - - +
83K LYS* 3.5 2.9 + - - -
84K TYR* 3.0 19.4 + - - -
85K ASN* 2.7 60.0 + - + +
87K CYS* 6.2 0.9 - - - -
120K ILE* 4.1 6.8 - - - +
1068K ILE* 4.4 9.0 - - + -
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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