Contacts of the strand formed by residues 22 - 26 (chain D) in PDB entry 3HUU
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 22 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C SER* 3.8 33.0 + - - -
20D THR* 3.1 25.9 + - - -
21D LEU* 1.3 78.0 + - - +
23D ILE* 1.3 67.5 + - - +
56D TYR* 3.9 0.4 - - - -
57D SER* 3.3 12.7 - - - +
58D THR* 3.8 11.7 - - - -
59D ARG* 4.1 8.9 + - - +
81D SER 4.0 14.9 + - - +
82D VAL* 3.4 3.3 - - + +
83D ASP* 2.9 31.3 + - - +
84D GLY 3.9 0.2 + - - -
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Residues in contact with ILE 23 (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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22D THR* 1.3 76.3 - - - +
24D GLY* 1.3 70.1 + - - +
25D LEU* 4.1 8.7 - - + -
51D CYS* 4.1 20.4 - - - -
56D TYR* 3.9 20.0 - - + -
57D SER 2.9 11.4 + - - +
58D THR* 3.2 20.5 + - - +
59D ARG 3.2 9.5 + - - -
82D VAL* 4.1 1.6 - - - -
84D GLY 3.5 7.9 - - - +
86D ILE* 3.9 16.6 - - + -
266D ILE* 3.8 30.7 - - + -
267D ILE* 4.7 2.2 - - + -
270D LEU* 3.5 32.5 - - + -
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Residues in contact with GLY 24 (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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23D ILE* 1.3 73.2 - - - +
25D LEU* 1.3 62.1 + - - +
59D ARG* 3.5 8.5 - - - -
76D MET* 5.4 1.1 - - - -
82D VAL* 3.3 18.8 - - - +
84D GLY 2.8 13.9 + - - -
85D PHE* 3.2 20.1 - - - +
86D ILE 2.9 27.2 + - - +
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Residues in contact with LEU 25 (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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23D ILE* 4.1 7.4 - - + -
24D GLY* 1.3 76.6 - - - +
26D ILE* 1.3 64.3 + - - +
27D GLN 3.8 0.4 - - - -
44D LEU* 3.7 19.3 - - + -
47D ILE* 3.9 31.9 - - + -
58D THR* 3.1 29.2 - - + +
59D ARG 2.8 13.6 + - - +
60D MET* 3.4 37.4 - - + +
61D THR* 3.1 27.0 + - - +
76D MET* 6.1 0.6 - - - -
86D ILE* 3.6 22.2 - - + -
88D LEU* 4.3 6.1 - - + -
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Residues in contact with ILE 26 (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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25D LEU* 1.3 73.2 - - - +
27D GLN* 1.3 69.1 + - - +
61D THR* 3.7 17.5 - - + -
69D LEU* 4.1 15.0 - - + -
73D VAL* 4.1 10.8 - - + -
85D PHE* 3.4 44.2 - - + -
86D ILE 2.9 10.0 + - - +
87D LEU* 3.5 31.6 - - + -
88D LEU* 2.9 28.3 + - - +
89D TYR* 3.7 10.0 - - + +
96D ILE* 4.1 13.7 - - + -
100D LEU* 4.3 7.0 - - + -
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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