Contacts of the strand formed by residues 32 - 37 (chain L) in PDB entry 2OSL
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 ILE 32 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4L LEU* 4.0 19.1 - - + -
23L CYS* 4.2 2.7 - - - -
25L ALA* 5.6 0.2 - - + -
29L VAL* 4.1 11.2 - - + -
31L TYR* 1.3 76.3 - - - +
33L HIS* 1.3 65.0 + - - +
34L TRP* 3.5 26.3 - - + +
47L ILE* 4.5 0.5 - - - +
48L TYR 4.5 0.5 - - - -
49L ALA 3.9 0.2 + - - -
50L THR* 2.9 35.0 + - + +
64L SER 5.3 0.4 - - - +
70L TYR* 3.6 40.5 - - + -
87L CYS* 3.4 29.8 - - - -
88L GLN 3.4 17.3 - - - +
89L GLN* 4.0 7.9 - - + -
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Residues in contact with HIS 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105H ASP* 2.9 32.2 + - - -
106H TRP 3.2 20.8 + - - -
107H TYR* 4.3 10.5 - - + -
31L TYR* 4.6 2.0 - - - +
32L ILE* 1.3 80.8 - - - +
34L TRP* 1.3 66.6 + - - +
35L PHE* 4.1 7.6 - + + -
47L ILE 3.5 3.5 + - - +
48L TYR* 3.3 26.0 - + + +
49L ALA* 3.2 22.2 + - + -
86L TYR 3.5 2.3 - - - +
87L CYS* 3.6 3.3 - - - -
88L GLN* 2.8 58.5 + - + +
90L TRP* 3.8 15.7 - + - -
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Residues in contact with TRP 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L GLN* 3.5 25.4 - - - -
21L MET* 4.0 22.2 - - + -
22L THR 4.3 3.4 - - - -
23L CYS* 3.8 30.5 - - + -
32L ILE* 3.5 22.5 - - + +
33L HIS* 1.3 79.4 - - - +
35L PHE* 1.3 64.8 + - - +
45L PRO* 4.3 0.2 - - - +
46L TRP* 2.9 24.9 + - + -
47L ILE* 2.9 47.5 + - + +
50L THR 4.9 2.7 + - - -
70L TYR 4.6 0.4 - - - -
71L SER* 3.7 17.5 + - - -
72L LEU* 3.6 53.2 - - + -
85L TYR* 4.5 7.0 - - + -
86L TYR 3.3 17.3 - - - -
87L CYS* 4.3 3.6 - - - -
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Residues in contact with PHE 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H LEU* 6.3 0.2 - - + -
107H TYR* 5.1 4.5 - + - -
108H PHE* 3.5 44.2 - + + -
111H TRP* 3.7 16.8 - + - -
33L HIS* 4.1 10.8 - + + -
34L TRP* 1.3 76.5 - - - +
36L GLN* 1.3 60.9 + - - +
37L GLN 4.1 0.2 + - - -
43L PRO* 4.2 16.2 - - + -
44L LYS 3.2 7.9 - - - +
45L PRO* 3.5 26.7 - - + -
46L TRP* 4.2 2.7 - - - -
47L ILE 5.9 0.4 - - - -
84L THR 3.9 0.3 - - - +
85L TYR* 3.3 7.2 - - - +
86L TYR* 2.7 49.5 + - + +
88L GLN* 3.4 34.8 - - + -
97L PHE* 4.0 18.8 - + - -
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Residues in contact with GLN 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L PHE* 1.3 74.5 - - - +
37L GLN* 1.3 62.8 + - - +
38L LYS* 3.7 26.9 + - - +
43L PRO* 3.5 0.2 - - - +
44L LYS* 2.8 55.3 + - + +
46L TRP* 3.3 53.5 - - + +
61L PHE* 4.6 0.9 - - - -
80L GLU 4.4 8.0 + - - +
81L ASP* 4.5 0.7 - - - +
83L ALA* 3.9 16.4 - - + -
84L THR 3.8 2.9 - - - -
85L TYR* 3.2 31.1 + - + -
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Residues in contact with GLN 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H GLN* 2.9 42.7 + - - +
95H TYR* 3.4 11.4 + - - -
35L PHE 4.1 0.2 + - - -
36L GLN* 1.3 76.6 - - - +
38L LYS* 1.3 64.1 + - - +
39L PRO* 3.8 4.5 - - - +
40L GLY 6.2 0.2 - - - -
41L SER 3.5 18.4 - - - +
42L SER 4.8 0.7 - - - -
43L PRO* 3.6 25.6 - - + +
83L ALA* 3.7 4.1 - - - +
84L THR* 2.9 34.4 + - - +
86L TYR* 3.3 30.1 + - + -
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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