Contacts of the strand formed by residues 85 - 88 (chain K) in PDB entry 6T9L
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 PHE 85 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4K CYS* 4.6 0.7 - - - -
6K HIS* 3.7 28.5 - - + -
7K ILE* 3.6 37.7 - - + -
10K VAL* 5.6 4.9 - - + -
61K LEU* 3.4 49.0 + - + +
74K PHE* 4.7 4.1 - - - -
83K HIS* 3.3 5.6 - - - +
84K ILE* 1.3 106.3 - - + +
86K GLY* 1.3 59.3 + - - +
87K ILE* 5.7 0.3 - - - +
94K LEU* 3.8 23.8 - - + -
95K PHE 3.5 5.4 - - - -
96K CYS* 4.2 13.2 - - + -
103K ILE* 4.6 2.7 - - + -
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Residues in contact with GLY 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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58K PHE* 4.3 8.5 - - - -
59K MET 3.5 10.5 - - - -
74K PHE* 3.8 18.0 - - - -
84K ILE 3.8 1.6 + - - -
85K PHE* 1.3 73.7 - - - +
87K ILE* 1.3 64.7 + - - -
88K ASN 4.0 0.6 + - - -
93K LEU 3.7 0.7 - - - +
94K LEU* 3.4 2.8 - - - +
95K PHE* 3.0 36.7 + - - +
97K PHE* 5.7 0.8 - - - -
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Residues in contact with ILE 87 (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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24K CYS* 5.1 17.3 - - + -
27K ALA* 5.3 10.3 - - + -
28K ARG* 5.9 4.3 - - + +
31K LEU* 6.3 2.9 - - + -
58K PHE* 3.4 2.8 - - - -
59K MET* 3.0 57.7 + - + +
61K LEU* 5.3 11.7 - - + -
86K GLY* 1.3 72.8 - - - -
88K ASN* 1.3 73.4 + - - +
89K SER* 3.5 1.0 + - - -
92K GLY* 3.8 19.1 - - - +
93K LEU 3.3 16.6 - - - +
94K LEU* 3.7 28.9 - - + -
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Residues in contact with ASN 88 (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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56K ALA* 4.2 5.2 - - - +
57K THR 3.2 16.3 + - - +
58K PHE* 3.6 26.4 - - + -
86K GLY 4.0 0.6 + - - -
87K ILE* 1.3 71.6 - - - +
89K SER* 1.3 64.5 + - - +
90K ASN* 3.1 35.7 + - - +
91K ASN* 3.3 28.3 + - - +
92K GLY* 2.7 33.8 + - - -
93K LEU 3.1 10.6 + - - +
102K TYR* 4.1 12.5 + - + +
25M GLN* 5.2 7.1 + - - +
26M ASP* 5.5 1.4 - - - +
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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