Contacts of the strand formed by residues 47 - 53 (chain C) in PDB entry 3VZC
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 ILE 47 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C CYS* 3.5 18.2 - - - -
17C VAL* 4.1 24.9 - - + -
42C LEU* 2.9 46.5 + - + +
43C ALA* 4.4 2.2 + - - -
45C ALA* 3.9 9.9 - - + +
46C GLU* 1.3 76.5 - - - +
48C SER* 1.3 67.8 + - - +
49C PHE* 4.0 3.8 + - - -
142C LEU* 3.6 37.0 - - + +
143C CYS* 3.9 15.3 - - - +
145C ARG* 3.5 25.1 - - + +
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Residues in contact with SER 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ARG* 4.1 20.2 - - - -
15C CYS 2.9 14.4 + - - +
16C ARG* 3.1 31.5 + - - +
17C VAL* 2.8 31.9 + - - +
46C GLU 3.6 3.6 + - - -
47C ILE* 1.3 74.2 - - - +
49C PHE* 1.3 56.6 + - - +
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Residues in contact with PHE 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B ARG* 2.8 26.9 + - - +
59B HIS* 3.8 3.4 + + - -
17C VAL* 3.0 18.2 - - + +
19C VAL* 3.8 14.4 - - + -
34C PHE* 3.5 35.9 - + - -
35C ARG* 4.2 7.6 - - - -
39C GLN* 3.7 33.2 - - + -
42C LEU* 3.7 21.5 - - + -
43C ALA* 6.0 2.0 - - + -
47C ILE 4.2 5.2 - - - -
48C SER* 1.3 77.3 - - - +
50C THR* 1.3 72.4 + - - +
51C LEU* 4.0 18.2 - - + -
72C TRP* 5.1 0.4 - - - -
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Residues in contact with THR 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B MET* 4.4 5.8 - - - +
53B LEU 4.9 0.2 - - - -
56B ARG* 4.8 1.1 - - - +
59B HIS* 2.9 36.8 - - + +
63B LEU* 3.9 14.5 - - + +
17C VAL 2.9 6.7 + - - -
18C LEU* 3.8 11.1 - - - +
19C VAL 2.9 24.9 + - - +
49C PHE* 1.3 79.7 - - - +
51C LEU* 1.3 66.0 + - - +
52C MET* 3.7 0.5 + - - +
72C TRP* 3.3 35.1 - - + -
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Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B MET* 3.3 9.2 - - - +
53B LEU* 3.1 47.7 + - + -
19C VAL* 3.5 26.0 - - + -
21C LEU* 3.8 29.4 - - + -
31C LEU* 3.8 15.9 - - + -
34C PHE* 3.8 29.4 - - + -
35C ARG* 3.8 29.6 - - - +
49C PHE* 4.0 9.5 - - + -
50C THR* 1.3 72.5 - - - +
52C MET* 1.3 58.8 + - - +
53C LEU* 4.2 3.8 - - + -
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Residues in contact with MET 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B THR* 3.8 12.8 - - - +
51B LEU 3.3 13.0 - - - +
52B MET* 2.7 45.1 - - + -
71B ARG* 5.1 1.3 - - - +
72B TRP* 5.7 0.4 - - - -
18C LEU* 3.6 26.7 - - + -
19C VAL 2.8 8.8 + - - +
20C LEU* 3.4 21.6 - - + +
21C LEU* 3.1 23.7 + - - -
50C THR* 4.5 1.6 - - - +
51C LEU* 1.3 73.3 - - - +
53C LEU* 1.3 65.3 + - - +
54C THR 3.8 0.2 + - - -
63C LEU* 4.0 33.0 - - + -
67C GLU* 4.6 13.0 - - - +
71C ARG* 5.1 2.2 - - - +
72C TRP* 5.3 0.4 - - + -
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Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 4.3 22.4 - - + -
35B ARG* 4.4 8.5 - - - +
50B THR* 4.4 1.7 - - - -
51B LEU* 2.9 44.5 + - + +
53B LEU* 4.3 25.6 - - + -
21C LEU* 3.4 36.3 - - + +
23C PRO* 4.5 10.8 - - + -
31C LEU* 4.7 8.1 - - + -
51C LEU* 4.8 6.5 - - + -
52C MET* 1.3 77.2 - - - +
54C THR* 1.3 61.0 + - - +
55C GLU* 4.1 15.3 - - - +
59C HIS* 3.3 18.9 - - - -
63C LEU* 5.1 0.2 - - - +
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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