Contacts of the strand formed by residues 50 - 54 (chain Z) in PDB entry 4AY9
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 GLU 50 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H ARG* 4.1 7.6 + - - -
28Z ARG 3.6 2.5 + - - +
29Z VAL* 3.6 22.8 - - + +
30Z PHE 2.9 27.4 + - - -
48Z ALA 3.5 0.6 - - - -
49Z ILE* 1.3 85.7 - - + +
51Z LEU* 1.3 69.4 + - - +
52Z ARG* 3.1 43.4 + - + +
72Z LEU* 3.6 0.7 - - - -
74Z LYS* 3.4 46.1 - - + +
76Z GLU* 5.6 1.9 - - - +
101Z ARG* 5.5 2.1 + - - -
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Residues in contact with LEU 51 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Z PHE* 3.6 24.0 - - + +
32Z CYS* 6.2 0.7 - - - -
44Z LEU* 3.9 28.7 - - + -
48Z ALA* 3.9 14.8 - - + -
50Z GLU* 1.3 85.0 - - - +
52Z ARG* 1.3 62.7 + - - +
53Z PHE* 4.3 15.4 - - + -
66Z PHE* 4.2 19.1 - - + -
69Z PHE* 4.2 14.8 - - + -
72Z LEU* 3.9 23.5 - - + +
74Z LYS 3.0 9.5 + - - +
75Z ILE* 3.4 12.5 - - + +
76Z GLU 2.9 25.3 + - - +
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Residues in contact with ARG 52 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H ARG* 3.2 41.9 - - - +
29Z VAL* 4.0 18.9 - - - +
30Z PHE 2.9 14.8 + - - +
31Z LEU* 3.5 31.0 - - + +
32Z CYS* 2.9 28.4 + - - +
50Z GLU* 3.1 34.5 + - + +
51Z LEU* 1.3 79.2 - - - +
53Z PHE* 1.3 66.5 + - - +
54Z VAL* 4.0 4.0 - - + -
76Z GLU* 3.3 32.1 - - + +
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Residues in contact with PHE 53 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Z CYS* 3.5 40.2 - - + -
37Z VAL* 5.1 4.3 - - + -
40Z ILE* 3.2 32.5 - - + -
41Z PRO* 4.5 4.0 - - + -
44Z LEU* 4.3 10.8 - - + -
51Z LEU* 4.3 17.7 - - + -
52Z ARG* 1.3 73.6 - - - +
54Z VAL* 1.3 61.3 + - - +
56Z THR* 4.1 15.5 - - + +
58Z LEU* 5.2 10.3 - - + -
61Z ILE* 5.7 2.2 - - + -
66Z PHE* 3.2 36.1 - + - -
75Z ILE* 5.4 0.9 - - + -
76Z GLU 2.8 10.9 + - - +
77Z ILE* 3.6 22.1 - - + -
78Z SER 3.0 27.0 + - - +
80Z ASN* 3.7 5.4 + - - +
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Residues in contact with VAL 54 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H LEU* 3.8 19.1 - - + -
31Z LEU* 3.8 24.7 - - + -
32Z CYS 3.1 8.0 + - - +
33Z GLN* 3.2 42.3 - - + +
52Z ARG* 4.4 11.0 - - + -
53Z PHE* 1.3 78.2 - - - +
55Z LEU* 1.3 73.4 + - - +
56Z THR* 3.1 3.1 + - - +
76Z GLU* 4.4 8.1 - - - +
78Z SER* 3.3 22.0 - - - +
79Z GLN* 5.1 2.5 - - + +
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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