Contacts of the strand formed by residues 48 - 52 (chain D) in PDB entry 4AFZ
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 THR 48 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B THR* 4.7 7.7 - - + +
28B LYS* 3.3 39.8 + - + +
19D LEU* 3.8 6.3 - - - +
30D LEU* 3.9 21.4 - - + +
39D GLU* 4.3 15.9 - - + +
40D ALA 3.2 9.0 - - - +
41D ARG* 3.5 22.2 - - - +
46D GLY 4.1 0.5 + - - -
47D GLU* 1.3 78.9 - - - +
49D GLY* 1.3 61.5 + - - +
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Residues in contact with GLY 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D THR 3.6 12.1 - - - -
18D ASP 4.9 0.2 - - - -
19D LEU* 3.7 17.0 - - - +
39D GLU* 4.4 6.3 - - - -
40D ALA* 3.0 30.7 + - - +
48D THR* 1.3 77.8 - - - +
50D TYR* 1.3 68.2 + - - -
51D ILE 3.7 0.2 + - - -
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Residues in contact with TYR 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B HIS* 3.7 21.7 - + + +
77B ARG* 5.6 2.1 + - - -
81B TYR* 2.7 37.6 + - - -
83B THR* 3.6 17.7 - - + +
86B LEU* 4.0 12.1 - - + -
15D ARG* 4.6 2.5 - - - +
17D THR* 3.1 22.6 + - - -
18D ASP* 3.3 23.1 - - - +
19D LEU 2.9 24.6 + - - +
33D GLY 4.3 5.0 + - - -
34D PRO* 5.2 0.5 - - - +
37D TRP* 4.1 23.1 - - + -
38D TRP 3.2 17.9 - - - +
39D GLU* 3.6 31.6 + - + -
49D GLY* 1.3 74.5 - - - -
51D ILE* 1.3 60.0 + - - +
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Residues in contact with ILE 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 3.8 25.4 - - + -
21D PHE* 3.8 20.0 - - + -
27D PHE* 3.9 13.9 - - + -
29D ILE* 4.0 15.3 - - + -
37D TRP* 3.4 5.7 - - - -
38D TRP* 2.9 44.5 + - + +
40D ALA* 4.0 18.2 - - + -
50D TYR* 1.3 79.0 - - - +
52D PRO* 1.4 74.3 - - + +
53D SER 3.4 0.2 + - - -
56D VAL* 3.6 34.8 - - + -
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Residues in contact with PRO 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D TYR* 4.3 13.0 - - + -
21D PHE* 3.8 17.3 - - + -
36D ASP 4.1 1.6 - - - +
37D TRP* 3.6 43.4 - - + +
51D ILE* 1.4 87.3 - - + +
53D SER* 1.3 64.8 + - - +
54D ASN* 3.2 15.9 - - - +
55D TYR* 3.0 39.5 + - + +
56D VAL* 4.3 4.0 + - - +
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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