Contacts of the strand formed by residues 46 - 51 (chain A) in PDB entry 1CVU
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 GLU 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A CYS* 3.8 2.7 - - - -
44A ARG 4.0 8.9 - - - +
45A GLY* 1.3 74.2 - - - -
47A CYS* 1.3 62.7 + - - +
48A MET* 3.8 0.3 + - - +
56A LYS 3.4 1.6 - - - +
57A CYS* 3.1 3.5 - - - -
58A ASP* 2.7 37.3 + - + +
130A TYR* 3.7 17.1 + - - +
137A LYS* 2.9 35.6 + - - +
2543B GLN* 4.0 2.4 - - - +
2546B LYS* 3.1 32.0 + - + +
2548B SER* 3.0 26.6 + - - +
2549B THR 4.8 0.2 + - - -
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Residues in contact with CYS 47 (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 CYS* 2.0 56.5 - - + +
39A ASN* 5.9 1.1 - - - -
40A PRO* 3.6 23.1 - - + -
41A CYS* 3.4 15.7 - - + +
45A GLY 4.0 0.8 + - - -
46A GLU* 1.3 74.0 - - - +
48A MET* 1.3 61.6 + - - +
55A TYR* 3.7 15.0 - - - -
56A LYS 3.5 0.7 - - - -
2548B SER* 5.9 0.2 - - - -
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Residues in contact with MET 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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36A CYS* 3.9 4.9 - - - -
46A GLU 5.0 0.4 - - - +
47A CYS* 1.3 76.5 - - - +
49A SER* 1.3 70.9 + - - +
50A THR* 4.0 23.8 - - + -
55A TYR* 3.1 1.4 - - - -
56A LYS* 2.8 49.2 + - + +
2320B HIS* 3.8 10.8 - - + -
2323B TRP* 4.3 9.6 - - + +
2327B GLN* 5.9 0.7 - - - +
2548B SER* 4.3 24.2 - - - +
2551B GLY* 3.4 34.8 - - - +
2552B GLY* 3.6 17.5 - - - -
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Residues in contact with SER 49 (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 ASN* 4.3 9.0 + - - -
35A PRO* 3.6 27.4 - - - -
36A CYS* 4.1 3.0 - - - -
48A MET* 1.3 77.0 - - - +
50A THR* 1.3 59.3 + - - +
51A GLY 3.5 1.1 - - - -
54A GLN 3.3 6.5 - - - -
55A TYR* 4.1 1.3 - - - +
2320B HIS* 2.9 27.4 + - - -
2322B GLU* 2.6 28.3 + - - -
2323B TRP* 3.3 13.7 + - - +
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Residues in contact with THR 50 (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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48A MET* 3.6 13.4 + - + +
49A SER* 1.3 77.9 - - - +
51A GLY* 1.3 57.7 + - - +
54A GLN* 2.9 38.9 + - - +
55A TYR 3.4 4.8 + - - +
56A LYS* 3.5 33.0 - - + -
2319B GLU 3.9 10.5 - - - +
2320B HIS* 4.3 4.7 - - + -
2321B PRO* 5.2 0.5 - - - +
2322B GLU* 3.2 6.7 - - - +
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Residues in contact with GLY 51 (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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35A PRO* 3.9 4.9 - - - +
49A SER* 3.9 0.3 - - - -
50A THR* 1.3 79.0 + - - +
52A PHE* 1.3 66.8 + - - +
53A ASP 3.2 3.7 + - - -
54A GLN* 3.4 24.9 + - - +
2321B PRO* 4.9 7.4 - - - -
2322B GLU* 2.9 25.1 + - - +
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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