Contacts of the strand formed by residues 53 - 58 (chain D) in PDB entry 4ZHF
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 ALA 53 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LYS* 4.1 18.6 - - + -
31D TRP 3.3 11.4 - - - +
32D TYR* 4.1 11.2 - - + -
52D TYR* 1.3 76.6 - - - +
54D THR* 1.3 63.5 + - - +
55D ILE* 5.1 1.6 - - + -
67D THR 4.5 0.2 - - - -
68D SER* 3.1 4.9 - - - -
69D VAL* 2.8 36.5 + - + +
176D ILE* 4.0 24.3 - - + +
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Residues in contact with THR 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D GLY 3.7 1.4 - - - +
31D TRP* 2.8 38.2 + - - +
33D VAL* 4.3 1.6 - - - +
52D TYR* 3.8 6.1 - - - -
53D ALA* 1.3 74.4 - - - +
55D ILE* 1.3 64.2 + - - +
56D TYR* 3.6 16.8 - - + -
66D VAL* 3.4 29.4 - - + -
67D THR 3.3 3.4 - - - +
68D SER* 2.6 16.3 + - - +
81D ARG* 4.0 1.1 - - - +
138D TYR* 4.2 11.7 - - - +
203D SO4 2.6 28.1 + - - +
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Residues in contact with ILE 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ASN* 3.8 39.0 - - + +
29D GLY* 3.4 15.3 - - - +
30D LYS* 4.1 33.2 - - + +
53D ALA 5.1 0.2 - - - -
54D THR* 1.3 79.1 - - - +
56D TYR* 1.3 66.6 + - - +
57D GLU* 3.9 11.4 + - + +
65D ASN 3.4 2.4 - - - +
66D VAL* 3.3 5.2 - - - -
67D THR* 2.6 40.6 + - - +
69D VAL* 4.1 24.9 - - + -
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Residues in contact with TYR 56 (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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27D PHE* 3.9 33.8 - + - +
28D GLN* 3.4 6.5 - - - +
29D GLY* 2.8 38.0 + - - +
31D TRP* 3.9 18.2 - + - -
54D THR* 3.6 21.3 - - + +
55D ILE* 1.3 76.7 - - - +
57D GLU* 1.3 62.9 + - - +
58D LEU 4.1 0.4 - - - -
64D TYR* 3.9 34.3 - + + -
65D ASN 3.7 3.1 - - - -
66D VAL* 4.0 11.6 - - + +
83D PHE* 3.8 32.1 - + - -
92D PHE* 6.2 1.6 - + - -
108D VAL* 6.1 0.7 - - + -
121D VAL* 4.9 3.8 - - - +
123D PHE* 4.3 5.7 - - - -
138D TYR* 2.7 36.0 + + - -
203D SO4 5.3 0.3 + - - -
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLN* 5.8 0.7 - - - -
129C ASN* 3.1 39.1 + - - +
28D GLN* 4.0 4.5 - - - +
55D ILE* 4.3 8.3 - - + +
56D TYR* 1.3 76.8 - - - +
58D LEU* 1.3 65.7 + - - +
59D LYS* 3.4 2.3 + - + +
64D TYR* 3.2 5.1 - - - -
65D ASN* 2.8 59.0 + - + +
67D THR* 5.2 1.2 + - - -
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Residues in contact with LEU 58 (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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24D ASP* 3.7 36.1 - - + +
25D ASN* 3.8 21.8 - - + -
28D GLN* 2.9 30.8 + - + +
57D GLU* 1.3 73.0 - - - +
59D LYS* 1.3 67.0 + - - +
62D LYS* 3.7 43.3 - - + +
63D SER 3.8 2.7 - - - +
64D TYR* 3.7 20.4 - - + -
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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