Contacts of the strand formed by residues 35 - 40 (chain B) in PDB entry 4R2G
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 LYS 35 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B HIS* 3.9 29.6 - - + +
28B TRP 4.0 3.4 - - - -
29B LYS* 4.4 7.9 - - + -
33B GLN 3.8 0.4 + - - -
34B ILE* 1.3 74.9 - - - +
36B ILE* 1.3 59.8 + - - +
47B GLY* 3.0 34.8 - - - +
48B PRO* 3.5 9.7 - - + +
49B SER 3.5 6.6 + - - -
280O ASN* 3.0 39.6 + - - +
281O ALA* 4.2 10.5 - - - +
455O THR* 3.6 21.2 + - - -
456O ARG 2.8 29.7 + - - -
457O ASP* 3.9 10.9 + - - +
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Residues in contact with ILE 36 (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 TRP* 2.8 23.9 + - + +
29B LYS 3.8 16.4 - - - +
30B ASN* 4.0 13.2 - - + -
34B ILE 4.3 1.3 - - - +
35B LYS* 1.3 71.4 - - - +
37B LEU* 1.3 62.6 + - + +
46B LYS* 3.7 4.2 - - - +
47B GLY* 2.9 23.8 + - - +
49B SER* 3.5 30.7 + - - +
51B LEU* 4.2 11.4 - - + -
52B ASN* 5.5 2.1 - - - -
55B ALA* 4.2 14.5 - - + +
69B LEU* 4.0 28.7 - - + -
82B TYR* 3.9 25.4 - - + -
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 4.8 3.1 - - + -
27B HIS* 3.2 10.6 - - - -
28B TRP* 2.8 35.8 + - + +
35B LYS* 3.7 0.6 - - - +
36B ILE* 1.3 92.6 - - + +
38B GLY* 1.3 60.2 + - - +
44B LEU* 3.7 19.3 - - + -
45B THR 3.3 20.0 - - - +
46B LYS* 3.8 26.5 - - + -
47B GLY 4.4 1.1 - - - +
55B ALA* 4.2 9.2 - - + +
56B ASP* 4.2 5.4 - - - -
57B SER* 3.7 28.3 - - - -
68B PRO 4.3 3.6 - - - +
69B LEU* 3.7 23.1 - - + -
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Residues in contact with GLY 38 (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 PHE* 3.7 25.8 - - - -
27B HIS* 4.1 5.2 - - - -
37B LEU* 1.3 77.8 - - - +
39B ASN* 1.3 60.3 + - - +
44B LEU* 3.3 14.7 - - - +
45B THR* 2.9 35.8 + - - -
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Residues in contact with ASN 39 (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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23B SER* 4.4 3.4 + - - -
24B ILE 3.2 23.8 + - - -
25B GLN* 2.5 25.8 + - - +
26B PHE* 3.0 40.9 + - + +
27B HIS* 4.8 1.8 + - - -
38B GLY* 1.3 75.5 - - - +
40B GLN* 1.3 73.4 + - - +
41B GLY 3.5 16.5 + - - +
43B PHE 3.2 15.7 - - - +
45B THR* 3.3 4.1 + - - +
62B TRP* 3.5 20.4 - - + -
67B PHE* 5.3 0.2 - - - -
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Residues in contact with GLN 40 (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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25B GLN* 3.4 7.5 + - - +
27B HIS* 4.5 15.8 - - - -
39B ASN* 1.3 86.9 + - - +
41B GLY* 1.3 61.4 + - - +
42B SER 3.4 2.1 + - - -
43B PHE* 3.1 18.4 + - + +
45B THR* 3.5 23.4 - - + +
281O ALA 4.8 5.9 + - - -
283O THR* 3.5 22.3 + - - -
371O ILE* 5.3 0.4 - - + -
471O GLY* 6.1 0.4 - - - -
472O GLY 3.3 33.9 + - - +
473O GLY* 3.0 18.7 - - - +
474O ASP* 3.5 14.0 - - - +
477O ASP* 4.2 9.0 - - - +
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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