Contacts of the strand formed by residues 34 - 38 (chain Y) in PDB entry 1IRA
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 34 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33Y GLY* 1.3 71.9 - - - -
35Y ILE* 1.3 64.2 + - - +
36Y THR* 4.2 5.4 + - - -
59Y GLU* 3.6 11.0 - - - +
77Y VAL 3.1 10.9 - - - +
78Y VAL* 4.4 0.2 - - - -
79Y ARG* 3.4 30.5 + - - +
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Residues in contact with ILE 35 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Y CYS* 3.7 26.0 - - + +
26Y LEU* 3.8 11.2 - - + -
31Y HIS* 5.2 5.4 - - + +
33Y GLY 4.2 4.7 - - - +
34Y THR* 1.3 74.6 - - - +
36Y THR* 1.3 68.3 + - - +
37Y TRP* 4.1 4.3 - - - +
56Y GLN* 4.4 5.4 - - - +
59Y GLU* 3.1 59.6 + - + +
76Y CYS* 3.7 27.4 - - + -
77Y VAL 3.1 6.5 - - - +
78Y VAL* 4.0 14.8 - - + -
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Residues in contact with THR 36 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Y THR* 4.2 9.2 + - - -
35Y ILE* 1.3 78.6 + - - +
37Y TRP* 1.3 67.0 + - - +
38Y TYR* 3.3 36.8 - - + +
45Y PRO* 5.2 4.3 - - + -
56Y GLN* 3.9 16.4 - - - +
76Y CYS* 3.3 1.3 - - - -
77Y VAL* 2.8 32.7 + - - -
79Y ARG* 5.1 9.4 - - - -
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Residues in contact with TRP 37 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22Y ARG 3.2 23.1 - - - -
23Y PRO 3.6 26.2 - - - -
24Y CYS* 3.6 4.7 - - - -
25Y PRO* 4.9 0.2 - - + -
35Y ILE* 4.1 5.9 - - + +
36Y THR* 1.3 75.5 - - - +
38Y TYR* 1.3 70.4 + - - +
45Y PRO* 3.4 5.0 - - - +
46Y VAL* 3.0 35.3 + - + +
56Y GLN* 3.3 31.6 + - + +
59Y GLU* 2.8 28.5 + - - -
60Y LYS 3.6 2.9 - - - -
61Y LEU* 3.7 28.5 - - + -
74Y TYR* 4.2 5.6 - - + -
75Y TYR 3.1 18.4 - - - -
76Y CYS* 3.7 22.2 - - + -
89Y ILE* 3.3 35.7 - - + -
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Residues in contact with TYR 38 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36Y THR* 3.3 43.5 - - + +
37Y TRP* 1.3 73.5 - - - +
39Y LYS* 1.3 63.1 + - - +
41Y ASP 4.0 8.7 - - - +
42Y SER* 3.4 25.1 - - - +
43Y LYS* 3.9 8.1 - - - -
44Y THR 3.2 8.7 - - - +
45Y PRO* 3.6 29.6 - - + -
46Y VAL* 3.8 6.4 - - - +
74Y TYR* 3.4 8.5 - - - +
75Y TYR* 2.7 41.5 + - + +
77Y VAL* 3.7 25.8 - - + +
79Y ARG* 5.5 6.6 + - - -
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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