Contacts of the strand formed by residues 34 - 40 (chain A) 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 MET 34 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU* 3.9 17.9 - - + -
22A CYS* 4.7 2.9 - - - +
24A ALA* 4.4 1.1 - - + -
27A TYR* 3.2 26.7 - - - +
29A PHE* 4.0 17.9 - - + -
32A TYR 3.6 3.6 + - - +
33A ASN* 1.3 74.1 - - - +
35A HIS* 1.3 62.2 + - - +
36A TRP* 4.2 7.0 - - - +
50A ALA* 3.1 2.0 - - - -
51A ILE* 2.8 49.2 + - + +
53A PRO* 4.8 5.6 - - + -
79A ALA* 3.8 22.4 - - + -
96A CYS* 3.6 26.9 - - - -
97A ALA 3.7 19.5 - - - +
98A ARG* 4.0 5.8 - - + -
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Residues in contact with HIS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASN* 3.9 8.7 - - - +
34A MET* 1.3 80.3 - - - +
36A TRP* 1.3 71.8 + - - +
37A VAL* 5.1 0.7 - - + -
47A TRP* 2.9 24.6 + - + +
49A GLY 3.4 5.6 - - - +
50A ALA* 3.4 14.5 - - + +
96A CYS* 3.5 2.9 - - - -
97A ALA* 2.8 38.0 + - + +
99A SER* 2.9 25.0 + - - -
108A PHE* 3.5 19.2 - + + -
90B TRP* 3.2 26.0 - + - -
170Q ALA 4.0 5.2 - - - -
171Q ASN* 2.8 28.1 + - - -
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Residues in contact with TRP 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A GLN* 3.8 20.2 - - - -
20A MET* 4.1 22.0 - - + -
21A SER 4.2 4.5 - - - -
22A CYS* 3.7 24.2 - - + -
34A MET* 4.2 16.5 + - - +
35A HIS* 1.3 81.7 + - - +
37A VAL* 1.3 64.7 + - - +
47A TRP* 4.0 1.9 - - - -
48A ILE* 2.8 33.7 + - + +
49A GLY 3.0 12.5 + - - +
51A ILE* 5.2 2.6 - - + +
70A LEU* 3.4 29.1 - - + +
79A ALA* 3.7 27.6 - - + +
80A TYR 3.9 12.8 + - - -
81A MET* 3.8 42.2 - - + -
94A TYR* 5.2 0.7 - - + -
95A TYR 3.1 19.5 - - - -
96A CYS* 3.9 5.2 - - + -
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A TRP* 1.3 83.5 - - - +
38A LYS* 1.3 71.3 + - - +
45A LEU* 3.9 25.8 - - + -
46A GLU 3.7 16.2 - - - +
47A TRP* 4.8 10.8 - - + -
48A ILE* 4.2 3.6 - - - -
93A VAL 3.9 0.3 - - - +
94A TYR* 3.4 3.8 - - - +
95A TYR* 2.7 45.8 + - + +
97A ALA* 4.9 9.0 - - + -
108A PHE* 4.9 6.7 - - + -
111A TRP* 4.1 26.7 - - + -
97B PHE* 4.3 13.9 - - + -
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Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 1.3 75.4 - - - +
39A GLN* 1.3 63.5 + - - +
40A THR* 4.4 9.2 - - - -
43A ARG* 3.9 12.8 - - - +
44A GLY 3.4 0.6 - - - +
45A LEU* 3.1 5.9 - - - -
46A GLU* 2.7 66.0 + - + +
48A ILE* 3.9 14.9 - - + +
63A LYS* 5.6 1.8 - - - +
64A PHE* 3.6 26.7 - - + -
89A GLU* 3.2 26.3 + - - +
90A ASP* 4.3 10.1 + - - -
92A ALA* 4.6 5.6 - - + -
93A VAL 3.7 4.3 - - - +
94A TYR* 3.7 27.5 + - + +
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Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LYS* 1.3 77.6 - - - +
40A THR* 1.3 69.3 + - - +
44A GLY* 3.2 7.7 - - - +
45A LEU* 3.5 31.8 - - + +
92A ALA* 3.3 3.2 - - - +
93A VAL* 2.9 45.1 + - + +
95A TYR* 3.2 21.9 + - + -
37B GLN* 2.8 42.2 + - - -
86B TYR* 3.6 14.6 + - - -
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Residues in contact with THR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LYS* 4.4 3.6 - - - -
39A GLN* 1.3 79.3 + - - +
41A PRO* 1.3 72.1 - - + +
42A GLY 3.3 0.2 - - - -
43A ARG* 3.4 62.6 + - - +
44A GLY* 2.9 26.1 + - - +
46A GLU* 3.6 10.6 + - - -
91A SER 4.1 4.7 - - - +
92A ALA* 3.3 28.3 - - + -
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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