Contacts of the strand formed by residues 76 - 79 (chain K) in PDB entry 3STJ
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 TYR 76 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69K ILE* 3.5 4.0 - - - +
70K ILE* 2.8 49.4 + - + +
71K ASN* 3.0 24.9 + - + -
74K LYS* 3.5 38.8 + - + +
75K GLY* 1.4 73.9 - - - +
77K VAL* 1.3 55.5 - - - +
105K ILE* 4.3 10.9 - - + +
115K LEU* 4.2 12.3 - - + -
116K LEU 3.3 9.6 - - - +
117K GLN* 3.6 35.9 + - + -
232K ILE* 3.7 48.7 + - + +
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Residues in contact with VAL 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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27K VAL* 3.9 17.9 - - + -
29K VAL* 4.8 0.7 - - + -
67K GLY* 3.9 4.0 - - - -
68K VAL 3.3 21.8 - - - +
69K ILE* 3.9 14.6 - - + -
75K GLY 4.0 0.4 - - - +
76K TYR* 1.3 76.9 - - - +
78K LEU* 1.3 65.5 + - - +
79K THR 3.9 0.5 + - - -
92K ILE* 4.6 4.3 - - + -
115K LEU* 3.5 6.0 - - - -
116K LEU* 2.8 61.1 + - + +
118K ILE* 3.6 37.0 - - + -
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Residues in contact with LEU 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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67K GLY* 3.2 5.4 - - - -
68K VAL* 2.8 38.7 + - + +
70K ILE* 3.6 34.0 - - + +
76K TYR 4.2 0.8 + - - -
77K VAL* 1.3 71.9 - - - +
79K THR* 1.3 62.3 + - - +
113K ILE* 3.8 26.2 - - + -
114K ALA 3.6 15.9 - - - +
115K LEU* 4.4 5.1 - - + +
188K GLY 3.4 4.2 - - - +
198K LEU* 4.8 3.1 - - + -
201K ILE* 3.6 30.7 - - + -
224K ALA* 3.8 20.2 - - + +
228K ALA* 4.2 13.2 - - + -
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Residues in contact with THR 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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29K VAL* 4.5 2.8 - - - +
66K SER 2.8 23.2 + - - -
67K GLY* 4.4 2.7 - - - -
78K LEU* 1.3 76.7 - - - +
80K ASN* 1.3 79.8 + - - +
83K VAL* 3.9 12.1 - - - +
84K ILE* 3.8 22.2 - - + -
113K ILE* 3.8 10.0 - - - +
114K ALA* 3.1 35.2 + - + +
116K LEU* 3.8 20.9 - - + -
188K GLY* 3.7 13.2 - - - -
201K ILE* 4.5 3.8 - - - +
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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