Contacts of the strand formed by residues 37 - 42 (chain Y) in PDB entry 1I9R
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 MET 37 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4Y LEU* 3.4 33.2 - - + -
23Y CYS* 3.5 20.9 - - - -
25Y ALA* 4.5 7.2 - - + +
29Y VAL* 4.2 6.5 - - + -
35Y SER 3.0 5.3 + - - -
36Y TYR* 1.3 73.4 - - - +
38Y HIS* 1.3 62.0 + - - +
39Y TRP* 5.2 3.6 - - - +
54Y TYR 2.9 6.9 + - - -
55Y ALA* 2.5 37.9 + - + +
75Y PHE* 3.3 53.2 - - + -
92Y CYS* 4.3 3.8 - - - -
93Y GLN 3.6 30.7 - - - +
94Y HIS* 3.8 2.9 - - + -
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Residues in contact with HIS 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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103X ASN* 3.7 10.3 - - + -
104X ASP* 3.7 20.5 - - + +
36Y TYR 3.8 3.0 + - - -
37Y MET* 1.3 75.6 - - - +
39Y TRP* 1.3 66.5 + - - +
40Y TYR* 3.7 10.0 - - + +
50Y LEU* 4.8 0.7 - - + -
52Y ILE 3.2 12.8 - - - +
53Y LYS* 3.3 8.6 - - - +
54Y TYR* 2.9 45.2 + + - -
92Y CYS* 3.2 3.5 - - - +
93Y GLN* 2.6 77.6 + - - +
94Y HIS 4.0 3.1 - - - -
95Y SER* 3.2 25.9 + - - -
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Residues in contact with TRP 39 (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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6Y GLN* 4.5 5.6 - - - -
21Y ILE* 3.7 22.7 - - + -
22Y SER 3.8 5.2 - - - -
23Y CYS* 3.6 30.5 - - + -
37Y MET* 5.2 3.3 - - - +
38Y HIS* 1.3 80.5 - - - +
40Y TYR* 1.3 68.8 + - - +
50Y LEU* 3.5 2.4 - - - +
51Y LEU* 2.9 28.2 + - + -
52Y ILE* 2.8 38.1 + - + +
55Y ALA* 4.6 7.7 + - - +
75Y PHE* 3.7 13.1 - - + +
76Y THR* 3.3 38.2 + - - -
77Y LEU* 3.4 35.7 - - + -
90Y TYR* 5.0 5.8 - - + -
91Y TYR 3.2 8.5 - - - -
92Y CYS* 3.4 29.6 - - + -
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Residues in contact with TYR 40 (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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104X ASP* 3.7 3.9 - - - -
105X MET* 2.9 50.3 + - + +
108X TRP* 3.9 14.6 - + - -
38Y HIS* 3.7 17.0 - - + -
39Y TRP* 1.3 79.7 - - - +
41Y GLN* 1.3 60.4 + - - +
48Y PRO* 3.8 29.4 - - + -
49Y LYS 3.3 7.4 - - - +
50Y LEU* 4.0 18.4 - - + -
51Y LEU* 3.8 4.0 - - - -
90Y TYR* 3.1 9.2 - - - +
91Y TYR* 2.7 45.1 + - + +
93Y GLN* 2.5 37.9 + - + -
102Y PHE* 4.5 9.9 - + + -
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Residues in contact with GLN 41 (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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40Y TYR* 1.3 76.1 - - - +
42Y GLN* 1.3 63.4 + - - +
43Y LYS* 2.9 36.0 + - + +
47Y PRO 4.4 0.2 - - - +
48Y PRO* 3.4 0.6 - - - +
49Y LYS* 2.9 48.1 + - + +
51Y LEU* 3.2 25.4 - - + +
66Y PHE* 4.6 4.9 - - - -
86Y ASP* 4.0 7.8 - - - +
88Y ALA* 4.0 4.5 - - + +
89Y THR 3.4 4.3 - - - -
90Y TYR* 2.9 34.6 + - + -
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Residues in contact with GLN 42 (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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39X GLN* 2.7 32.3 + - - +
45X LEU* 4.3 0.5 - - - +
95X TYR* 3.7 6.1 + - - -
41Y GLN* 1.3 77.8 - - - +
43Y LYS* 1.3 73.6 + - - +
44Y PRO* 4.3 0.5 - - - +
46Y GLN 2.5 23.3 + - - +
47Y PRO* 3.5 13.4 - - - +
48Y PRO* 3.7 20.2 - - + +
88Y ALA* 4.0 1.5 - - - -
89Y THR* 2.6 43.2 + - + +
91Y TYR* 3.4 27.8 + - + -
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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