Contacts of the strand formed by residues 72 - 77 (chain h) in PDB entry 5KZ5
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 72 (chain h).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H ARG* 3.7 52.7 - - + +
56H SER* 5.0 6.7 - - - +
439T LEU* 3.2 27.7 + - - +
442T MET* 3.7 20.4 - - + -
443T VAL* 5.1 2.5 - - + +
64h VAL* 3.0 29.4 - - - +
65h GLY* 4.0 10.1 - - - -
66h ALA 5.5 0.4 - - - -
70h GLY 4.3 2.5 - - - +
71h ASP* 1.3 72.8 - - - +
73h MET* 1.4 88.5 + - - +
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Residues in contact with MET 73 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56H SER* 5.5 0.4 + - - -
439T LEU* 4.1 23.4 + - + +
63h LEU* 3.6 16.3 - - - +
64h VAL* 3.7 14.2 + - + +
71h ASP* 3.7 21.3 - - + -
72h VAL* 1.4 107.2 - - - +
74h LYS* 1.4 58.4 + - - +
91h LYS* 3.4 27.6 - - + +
92h THR* 5.1 4.3 - - - +
93h PHE* 3.8 49.6 - - + +
94h GLY 4.8 2.0 - - - +
141h LEU* 4.2 31.6 - - + +
145h ALA* 5.7 2.7 - - + -
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Residues in contact with LYS 74 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H ARG* 3.5 43.2 - - - +
432T ARG* 3.4 31.2 + - - +
439T LEU* 4.6 3.1 - - + -
61h THR* 3.4 21.9 - - - +
62h GLY 3.7 5.4 - - - +
63h LEU* 3.5 28.9 - - + +
73h MET* 1.4 73.9 - - - +
75h LEU* 1.4 71.7 + - - +
76h GLN* 3.4 37.6 + - - -
91h LYS* 3.1 27.1 - - - +
145h ALA* 6.2 0.2 - - - -
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Residues in contact with LEU 75 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61h THR 3.7 0.3 - - - -
62h GLY* 2.9 31.0 + - - +
74h LYS* 1.4 78.7 - - - +
76h GLN* 1.4 63.8 + - - +
77h ILE* 4.0 17.5 - - + -
89h ARG* 3.9 38.4 - - + +
91h LYS* 3.7 29.2 - - + +
106h THR* 5.1 6.5 - - + -
145h ALA* 3.8 40.2 - - + +
146h ILE* 4.0 16.6 - - + +
149h ALA* 3.8 5.5 - - + +
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Residues in contact with GLN 76 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64H GLN* 5.6 0.2 + - - -
428T GLN* 4.8 11.2 + - - +
432T ARG* 4.9 9.7 - - - -
59h VAL* 3.9 19.6 - - + +
60h GLY 3.2 16.8 - - - +
61h THR* 3.7 15.8 + - + +
74h LYS* 3.4 25.5 + - - +
75h LEU* 1.4 74.3 - - - +
77h ILE* 1.4 60.9 + - - +
89h ARG* 2.9 59.4 + - + +
149h ALA* 4.7 0.4 - - - -
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Residues in contact with ILE 77 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425T LYS* 4.2 3.1 - - - +
59h VAL* 3.7 4.5 - - - -
60h GLY 3.1 25.1 + - - -
75h LEU* 4.0 21.3 - - + -
76h GLN* 1.4 78.9 - - - +
78h GLN* 1.3 66.1 + - - +
79h VAL* 3.6 14.8 + - + +
85h ILE* 4.8 8.5 - - + -
88h ALA* 4.5 10.1 - - + -
89h ARG 3.8 19.7 - - - +
106h THR* 6.3 0.4 - - + -
109h VAL* 5.9 2.2 - - + -
146h ILE* 4.2 11.7 - - + +
149h ALA* 3.7 25.5 - - + +
150h LEU* 3.7 33.2 - - + +
153h TYR* 3.9 0.2 - - - -
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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
------------------------------------------------------------
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