Contacts of the strand formed by residues 41 - 48 (chain A) in PDB entry 5CH3
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 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A VAL* 3.9 24.9 - - + -
35A ALA 3.4 5.4 - - - +
36A GLU* 2.7 41.5 + - - +
40A GLY* 1.3 72.9 - - - -
42A VAL* 1.3 59.6 + - - +
82A TRP* 2.9 10.7 + - - +
84A GLY 3.6 15.9 + - - +
85A VAL* 4.1 17.5 - - + -
86A ARG 2.9 23.5 + - - -
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Residues in contact with VAL 42 (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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34A VAL* 3.3 3.3 - - - -
35A ALA* 2.8 42.6 + - + +
37A THR* 3.8 24.2 - - + -
41A LYS* 1.3 80.3 - - - +
43A LYS* 1.3 61.4 + - - +
58A PHE* 3.7 22.1 - - + -
61A ILE* 4.5 10.5 - - + -
82A TRP* 3.8 22.2 - - + -
85A VAL* 4.1 3.4 - - - -
86A ARG* 3.5 4.3 - - + -
88A CYS* 3.9 25.4 - - - -
205A PHE* 4.0 11.4 - - + -
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Residues in contact with LYS 43 (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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32A THR* 4.0 24.2 - - + +
33A VAL 3.3 12.8 - - - +
34A VAL* 4.5 6.7 - - + +
42A VAL* 1.3 71.4 - - - +
44A GLY* 1.3 67.6 + - - +
58A PHE* 3.9 2.7 - - - -
85A VAL* 3.7 22.8 - - + +
86A ARG 2.9 11.9 + - - +
87A ASP* 4.5 11.3 - - - +
88A CYS* 2.8 34.1 + - - -
89A CYS* 3.5 14.2 + - - -
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Residues in contact with GLY 44 (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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32A THR* 3.1 10.2 - - - -
33A VAL* 2.8 33.1 + - - +
43A LYS* 1.3 74.7 - - - +
45A VAL* 1.3 59.8 + - - +
57A SER 3.2 13.7 - - - -
58A PHE* 3.2 22.5 - - - -
88A CYS 4.3 1.1 - - - -
89A CYS* 3.6 6.9 - - - -
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Residues in contact with VAL 45 (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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28A THR* 4.1 9.0 - - + -
29A THR 3.2 26.9 - - - +
31A GLU 3.5 14.1 - - - +
32A THR* 4.3 7.0 - - + -
33A VAL* 4.7 1.0 - - - +
44A GLY* 1.3 74.6 - - - +
46A LYS* 1.3 71.2 + - - +
47A ARG* 3.6 34.3 - - + +
56A TYR* 4.4 3.8 - - - -
57A SER* 2.9 35.4 + - - +
89A CYS* 3.8 21.3 - - + +
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Residues in contact with LYS 46 (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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29A THR* 2.6 47.0 + - + +
31A GLU* 3.0 42.4 + - - +
45A VAL* 1.3 78.4 - - - +
47A ARG* 1.4 70.0 + - - +
48A LEU* 5.5 1.1 - - + -
54A SER* 3.9 23.7 + - - +
55A TYR* 3.2 14.6 - - - +
56A TYR* 3.3 42.6 + - + +
119A ASN 5.3 3.6 + - - -
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Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ASN* 3.5 12.7 + - - +
27A LEU* 3.2 12.1 - - + +
28A THR* 3.4 26.8 + - - +
29A THR* 4.3 0.2 - - - -
45A VAL* 3.6 15.3 - - + +
46A LYS* 1.4 78.6 - - - +
48A LEU* 1.3 67.4 + - - +
54A SER* 3.2 7.4 - - - -
55A TYR* 2.8 63.9 + - + +
57A SER* 3.1 29.3 + - - -
59A GLU* 3.4 11.5 + - - -
89A CYS* 2.8 29.7 + - - +
90A ASN* 4.5 3.8 + - - -
145A ARG* 3.3 29.6 - - - +
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Residues in contact with LEU 48 (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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26A ARG 4.4 6.7 - - - +
27A LEU* 2.8 56.2 + - + +
28A THR 5.0 1.6 - - - +
29A THR* 4.0 18.8 - - + -
46A LYS* 5.4 0.9 - - + -
47A ARG* 1.3 77.5 - - - +
49A THR* 1.3 67.4 + - - +
52A ASP* 6.3 0.4 - - - -
53A ASP 3.5 6.1 - - - +
54A SER* 3.9 21.3 - - - -
55A TYR* 3.9 7.1 + - - -
151A ASP* 4.2 2.3 - - - +
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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