Contacts of the strand formed by residues 24 - 31 (chain B) in PDB entry 2ONL
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 TYR 24 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B TYR* 2.5 38.8 + - - -
20B VAL* 3.4 15.7 - - + -
21B PRO* 3.2 47.3 + - + -
22B GLU 2.9 1.2 - - - -
23B ARG* 1.3 110.4 + - + +
25B GLN* 1.3 55.7 + - - +
27B LEU* 4.0 10.5 - - + -
41B ALA* 5.0 3.4 - - + -
42B PHE 3.6 2.9 - - - +
43B ASP* 4.0 20.0 - - + -
50B VAL* 4.4 9.4 - - + -
52B VAL* 4.9 8.3 - - + -
88B ASP* 2.4 39.0 + - - +
90B PHE* 3.8 9.2 - + - -
105B VAL* 4.0 20.4 - - + -
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Residues in contact with GLN 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B TYR* 3.8 13.5 + - - -
22B GLU* 2.5 34.0 + - - +
24B TYR* 1.3 80.4 + - - +
26B ASN* 1.3 86.2 + - - +
27B LEU* 3.4 6.8 - - - +
42B PHE* 3.0 35.0 + - + +
44B THR* 3.9 19.3 - - + -
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Residues in contact with ASN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B TYR* 4.3 2.2 + - - -
25B GLN* 1.3 90.8 + - - +
27B LEU* 1.3 69.6 + - - +
28B SER* 3.2 8.7 + - - -
40B ALA 4.0 3.2 - - - +
41B ALA* 4.6 2.0 - - - -
42B PHE* 4.6 16.6 - - + +
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B TYR* 2.8 28.0 - - + +
11B GLN* 2.8 26.8 + - + +
13B LEU* 3.6 21.9 - - + +
18B TRP* 5.3 7.0 - - + +
20B VAL* 4.9 15.5 - - + -
24B TYR* 4.0 6.1 - - + -
25B GLN 3.4 17.9 - - - +
26B ASN* 1.3 72.8 - - - +
28B SER* 1.3 59.2 + - - +
29B PRO* 3.7 2.1 - - - +
39B CYS* 3.3 22.0 - - + -
40B ALA 3.4 4.9 - - - +
41B ALA* 3.1 26.5 - - + -
52B VAL* 5.4 5.2 - - + -
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Residues in contact with SER 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASN 3.2 6.3 + - - -
27B LEU* 1.3 73.6 - - - +
29B PRO* 1.3 74.1 + - - +
30B VAL* 2.9 3.1 + - - +
39B CYS* 3.2 3.1 - - - -
40B ALA* 2.8 41.1 + - - +
49B ARG* 5.5 1.4 + - - -
96D GLN* 5.5 11.3 + - - -
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Residues in contact with PRO 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 3.9 28.3 - - + +
14B ASN* 4.3 27.8 - - + +
18B TRP* 6.0 1.1 - - + +
27B LEU 3.7 5.2 - - - +
28B SER* 1.3 86.2 + - - +
30B VAL* 1.3 59.9 + - - +
31B GLY 3.5 3.9 + - - +
38B VAL 3.6 11.2 - - - +
39B CYS* 3.4 13.5 - - - -
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Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B SER* 2.9 9.6 + - - +
29B PRO* 1.3 71.7 - - - +
31B GLY* 1.3 55.8 + - - +
38B VAL* 3.0 43.2 + - + +
40B ALA* 3.7 22.0 - - + +
49B ARG* 5.3 5.4 - - - +
51B ALA* 6.0 0.7 - - + -
108B LEU* 5.6 7.4 - - + -
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PRO* 3.5 4.4 - - - +
30B VAL* 1.3 79.2 - - - +
32B SER* 1.3 53.3 + - - -
37B SER* 3.8 1.6 - - - -
38B VAL* 2.6 40.6 + - - +
357D THR* 6.0 0.9 - - - -
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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