Contacts of the strand formed by residues 47 - 53 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B LEU* 5.5 0.2 - - + -
15B CYS* 3.7 13.5 - - - -
17B VAL* 3.9 27.1 - - + -
42B LEU* 3.0 45.0 + - + +
43B ALA* 4.5 1.4 + - - +
45B ALA* 3.7 9.6 - - + +
46B GLU* 1.3 74.8 - - - +
48B SER* 1.3 73.9 + - - +
49B PHE* 3.9 5.2 + - - -
142B LEU* 3.8 35.9 - - + +
143B CYS* 4.1 13.5 - - - -
145B ARG* 3.2 26.7 - - + +
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Residues in contact with SER 48 (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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14B PRO* 5.7 2.9 - - - +
15B CYS 3.0 13.0 + - - -
16B ARG* 3.3 19.9 + - - -
17B VAL* 3.0 26.9 + - - +
46B GLU 3.8 2.7 + - - -
47B ILE* 1.3 75.7 - - - +
49B PHE* 1.3 60.6 + - - +
56C ARG* 3.9 24.8 + - - +
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Residues in contact with PHE 49 (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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17B VAL* 3.1 13.9 - - + +
19B VAL* 4.0 14.8 - - + -
34B PHE* 3.6 29.2 - + - -
35B ARG* 4.0 0.7 - - - -
39B GLN* 3.8 39.0 - - + -
42B LEU* 3.9 24.0 - - + -
43B ALA* 6.0 0.7 - - - -
47B ILE 4.0 6.5 - - - -
48B SER* 1.3 80.5 - - - +
50B THR* 1.3 66.6 + - - +
51B LEU* 4.0 13.7 - - + -
72B TRP* 5.7 0.2 - - - -
55C GLU* 3.6 37.2 - - + +
56C ARG* 3.0 20.8 + - - +
59C HIS* 3.8 3.3 + - - -
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Residues in contact with THR 50 (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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16B ARG* 6.4 0.2 - - + -
17B VAL 3.0 4.0 + - - -
18B LEU* 3.6 9.7 - - - +
19B VAL* 2.9 23.5 + - - -
49B PHE* 1.3 77.0 - - - +
51B LEU* 1.3 63.2 + - - +
72B TRP* 3.2 37.2 - - + -
52C MET* 3.8 20.8 - - - +
53C LEU 4.4 1.8 - - - -
55C GLU* 5.3 0.2 - - - -
56C ARG* 4.8 1.1 - - - +
59C HIS* 3.0 36.6 - - + +
63C LEU* 4.0 8.1 - - + -
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Residues in contact with LEU 51 (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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19B VAL* 3.4 32.5 - - + +
21B LEU* 4.0 16.4 - - + -
31B LEU* 4.0 15.3 - - + -
34B PHE* 3.9 24.0 - - + -
35B ARG* 3.8 32.8 - - - +
49B PHE* 4.0 9.5 - - + -
50B THR* 1.3 74.4 - - - +
52B MET* 1.3 60.5 + - - +
53B LEU* 4.1 6.5 - - + -
51C LEU 4.2 0.2 - - - +
52C MET* 3.3 6.2 - - - +
53C LEU* 2.9 46.9 + - + -
55C GLU* 3.9 8.9 + - - +
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Residues in contact with MET 52 (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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18B LEU* 3.7 28.0 - - + -
19B VAL 2.9 7.9 + - - +
20B LEU* 3.5 18.2 - - + -
21B LEU 3.2 21.5 + - - -
51B LEU* 1.3 73.9 - - - +
53B LEU* 1.3 65.1 + - - +
54B THR* 3.6 2.1 + - - -
63B LEU* 3.5 42.2 - - + -
67B GLU* 3.8 22.0 - - - +
71B ARG* 5.2 0.9 - - - +
50C THR* 4.4 4.0 - - - +
51C LEU 3.3 13.9 - - - +
52C MET* 2.7 42.6 - - + +
71C ARG* 4.7 3.6 - - - +
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Residues in contact with LEU 53 (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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21B LEU* 3.4 30.3 - - + +
23B PRO* 4.3 12.6 - - + -
31B LEU* 4.4 12.3 - - + -
51B LEU* 4.7 5.2 - - + -
52B MET* 1.3 76.2 - - - +
54B THR* 1.3 60.3 + - - +
55B GLU* 4.3 2.0 - - + -
59B HIS* 3.6 15.4 - - - -
31C LEU* 4.2 20.0 - - + -
35C ARG* 3.8 24.7 - - - +
50C THR* 4.9 0.3 - - - -
51C LEU* 3.1 42.4 + - + +
53C LEU* 4.3 23.3 - - + -
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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