Contacts of the strand formed by residues 43 - 48 (chain C) in PDB entry 4BPW
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 ARG 43 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30C LEU* 3.6 29.0 + - + +
32C TYR* 3.7 15.0 - - - -
39C TYR* 3.5 10.4 + - - +
40C PHE* 3.3 20.0 + - + +
42C HIS* 1.3 79.0 - - - +
44C GLU* 1.3 67.6 + - - +
45C PHE* 3.2 33.2 - - + -
58C GLN 3.3 13.0 - - - +
59C SER* 3.8 8.0 + - - -
80C ILE* 3.7 11.4 - - - +
81C GLY 3.2 24.7 + - - -
82C ALA 3.7 5.4 - - - -
83C VAL* 3.6 24.2 - - - +
88C PRO* 3.7 5.4 - - - +
104C LYS* 4.4 3.0 - - - +
105C GLU* 2.9 41.4 + - - -
175C ARG* 5.2 0.6 - - - +
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Residues in contact with GLU 44 (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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42C HIS 3.6 0.6 + - - -
43C ARG* 1.3 77.0 - - - +
45C PHE* 1.3 80.2 + - - +
56C ARG* 2.6 41.3 + - - +
57C TYR* 3.3 25.2 + - - +
58C GLN 3.7 2.5 - - - -
80C ILE* 3.9 0.5 - - - -
81C GLY* 2.9 21.7 + - - -
82C ALA 3.0 17.3 + - - +
84C TYR* 2.8 44.2 + - + -
88C PRO* 3.9 5.8 - - + -
314C ASN 4.9 1.0 - - - +
316C LEU* 3.9 15.7 - - + +
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Residues in contact with PHE 45 (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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26C TYR* 3.4 30.7 - + - -
30C LEU* 3.4 26.9 - - + -
40C PHE* 4.3 13.5 - + - -
43C ARG* 3.2 29.4 - - + -
44C GLU* 1.3 81.6 - - - +
46C SER* 1.3 60.8 + - - +
47C PHE* 4.9 8.3 - + + -
57C TYR 3.4 9.5 + - - -
58C GLN* 2.9 47.9 + - + +
60C PHE* 3.8 26.2 - + + -
66C LEU* 4.7 5.4 - - + -
70C MET* 5.6 1.1 - - + -
78C ILE* 4.3 11.7 - - + -
79C ASP 3.3 15.0 - - - -
80C ILE* 4.0 7.9 - - + -
316C LEU* 4.5 0.7 - - - -
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Residues in contact with SER 46 (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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45C PHE* 1.3 76.3 - - - +
47C PHE* 1.3 70.6 + - - +
48C THR* 5.3 0.2 + - - -
54C TYR* 3.3 27.5 + - - -
55C ILE 3.2 12.1 - - - -
56C ARG* 3.7 7.0 - - - -
58C GLN* 4.5 0.9 - - - -
77C LYS 3.3 3.6 - - - +
78C ILE* 3.5 0.2 - - - -
79C ASP* 3.1 50.9 + - - +
316C LEU* 4.2 8.7 - - - -
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Residues in contact with PHE 47 (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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45C PHE* 4.9 5.2 - - + -
46C SER* 1.3 82.8 - - - +
48C THR* 1.3 62.7 + - - +
49C LEU* 4.0 7.2 - - + -
53C ILE 3.6 0.7 - - - +
54C TYR* 3.3 5.2 - - - -
55C ILE* 2.7 52.1 + - + +
58C GLN* 3.8 32.8 - - + -
60C PHE* 3.9 24.7 - + - -
69C GLU* 4.9 6.3 - - + -
70C MET* 3.9 30.3 - - + -
73C ALA* 4.9 9.6 - - + -
75C PRO* 3.7 26.0 - - + -
77C LYS 3.4 3.4 - - - -
78C ILE* 3.8 28.9 - - + -
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Residues in contact with THR 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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47C PHE* 1.3 71.5 - - - +
49C LEU* 1.3 61.0 + - - +
52C ASP* 4.1 18.8 - - + +
53C ILE 3.2 8.7 - - - +
54C TYR* 3.3 24.8 - - + -
75C PRO* 4.5 0.7 - - - -
76C TYR* 2.6 37.3 + - + +
77C LYS* 3.2 53.7 + - + +
79C ASP* 5.0 1.7 + - - -
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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