Contacts of the strand formed by residues 78 - 83 (chain I) in PDB entry 5AKF
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 78 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I THR* 3.2 3.5 - - - -
42I ALA 2.7 35.0 + - - +
43I LYS 3.8 10.5 - - - -
45I GLU* 3.0 61.4 + - + -
48I ILE* 3.6 19.5 - - + +
71I ILE* 4.3 12.8 - - + -
72I VAL 3.4 5.6 - - - -
73I LYS* 2.7 65.3 + - + +
77I ARG* 1.3 80.0 - - - +
79I GLU* 1.3 60.1 + - - +
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Residues in contact with GLU 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I ARG* 4.7 2.3 + - - -
39I VAL* 3.4 31.6 - - + +
40I ILE 3.8 2.9 - - - -
41I THR* 4.1 2.2 - - + +
48I ILE* 4.5 2.2 - - - -
70I GLN 3.4 0.5 - - - +
71I ILE* 3.4 5.0 - - - -
72I VAL* 2.7 46.7 + - + +
77I ARG* 3.5 31.3 + - - +
78I TYR* 1.3 75.5 - - - +
80I LEU* 1.3 71.8 - - - +
81I ARG* 2.8 44.0 + - + +
16K T 5.0 4.3 - - - +
17K T 5.1 1.2 - - - +
9L A 3.9 6.5 + - - -
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Residues in contact with LEU 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I VAL 4.5 2.7 - - - +
39I VAL* 3.2 6.9 - - - -
40I ILE* 2.8 47.4 + - + +
48I ILE* 4.0 22.1 - - + +
52I ILE* 4.2 13.0 - - + -
53I ALA* 3.9 34.5 - - + +
56I MET* 4.2 21.3 - - + -
69I ILE* 3.8 18.8 - - + -
70I GLN 3.4 3.6 - - - +
71I ILE* 4.7 2.2 - - + +
79I GLU* 1.3 76.8 - - - +
81I ARG* 1.3 65.2 + - - +
82I VAL* 4.1 20.0 - - + +
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Residues in contact with ARG 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I GLU* 4.5 1.6 - - - -
37I ARG* 3.4 47.5 - - + +
38I VAL 3.4 3.4 - - - +
39I VAL* 4.2 3.4 - - + -
68I LYS 3.6 1.2 - - - +
69I ILE 3.8 0.3 - - - -
70I GLN* 2.8 67.1 + - + +
72I VAL* 4.2 12.4 - - + +
79I GLU* 2.8 45.2 + - + +
80I LEU* 1.3 77.0 - - - +
82I VAL* 1.3 68.6 + - - +
83I SER* 5.0 0.2 - - - -
7L G 3.1 34.6 + - - -
8L G 3.1 25.1 + - - -
9L A 3.6 11.7 - - - +
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Residues in contact with VAL 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I ARG* 3.5 1.9 - - - -
38I VAL* 2.9 34.3 + - - +
56I MET* 3.9 29.4 - - + -
60I ILE* 4.1 13.0 - - + -
65I VAL* 4.8 1.1 - - + -
67I SER* 4.0 15.7 - - - -
68I LYS 4.0 10.8 - - - +
69I ILE* 4.1 15.0 - - + -
80I LEU* 4.1 7.6 - - + -
81I ARG* 1.3 79.7 - - - +
83I SER* 1.3 59.9 + - - +
84I SER* 3.4 10.5 + - - -
87I LEU* 3.7 27.1 - - + -
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Residues in contact with SER 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I GLU* 2.4 42.3 + - - +
36I TYR 3.3 4.9 - - - -
37I ARG* 4.7 2.7 - - - -
67I SER* 2.4 29.1 + - - -
68I LYS 4.4 2.6 + - - -
70I GLN* 3.8 17.0 - - - +
81I ARG* 4.0 3.0 + - - -
82I VAL* 1.3 72.5 - - - +
84I SER* 1.3 52.5 + - - +
5L C 3.3 33.4 - - - +
6L C 4.4 1.1 - - - -
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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