Contacts of the strand formed by residues 77 - 84 (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 LYS 77 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C SER 3.3 7.1 - - - +
47C PHE* 3.4 3.3 - - - -
48C THR* 3.2 56.0 + - - +
52C ASP* 4.7 8.1 + - - -
75C PRO* 3.8 2.3 - - - +
76C TYR* 1.3 89.3 - - - +
78C ILE* 1.3 67.0 + - - +
79C ASP* 4.1 15.0 - - - +
318C LYS* 5.8 10.8 - - + +
322C SER* 4.3 3.8 - - - +
323C VAL 5.3 0.4 - - - +
325C PRO* 3.6 31.8 - - + +
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Residues in contact with ILE 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C TYR* 3.6 33.7 - - + +
21C PHE* 4.8 9.9 - - + -
26C TYR* 4.3 11.0 - - + +
45C PHE* 4.3 13.7 - - + -
46C SER 3.5 3.4 - - - +
47C PHE* 3.8 14.6 - - + -
70C MET* 4.0 25.4 - - + -
75C PRO* 3.8 17.0 - - + -
77C LYS* 1.3 78.9 - - - +
79C ASP* 1.3 62.0 + - - +
318C LYS* 4.0 0.5 - - - +
319C SER* 2.8 40.2 + - - -
322C SER* 3.7 18.0 + - - +
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Residues in contact with ASP 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C PHE* 3.3 10.6 - - - +
46C SER* 3.1 48.8 + - - +
48C THR* 5.0 1.7 + - - -
54C TYR* 4.3 9.2 + - - -
77C LYS* 4.5 14.8 - - - +
78C ILE* 1.3 80.0 + - - +
80C ILE* 1.3 61.7 + - - +
316C LEU* 3.8 18.3 - - + +
317C LEU 3.4 8.5 - - - +
318C LYS* 3.4 20.6 + - - +
1412C UTP 4.2 14.8 + - - -
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Residues in contact with ILE 80 (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 20.2 - - + +
29C TRP* 3.5 31.9 - - + -
30C LEU* 4.3 7.0 - - + -
43C ARG* 3.7 37.2 - - + +
44C GLU 4.0 3.1 - - - +
45C PHE* 4.0 6.7 - - + -
79C ASP* 1.3 73.2 - - - +
81C GLY* 1.3 63.5 + - - +
104C LYS* 4.2 4.2 + - - -
168C TRP* 3.8 18.3 - - + -
315C HIS 3.6 3.3 - - - +
316C LEU* 3.4 3.1 - - - -
317C LEU* 2.9 30.4 + - - +
319C SER* 3.3 28.7 - - - +
320C PRO* 4.1 3.6 - - + -
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Residues in contact with GLY 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ARG* 3.2 23.0 + - - -
44C GLU* 2.9 20.6 + - - -
80C ILE* 1.3 74.3 - - - +
82C ALA* 1.3 62.9 + - - +
104C LYS* 3.3 13.8 - - - +
314C ASN 5.4 0.2 - - - -
315C HIS 3.9 7.4 - - - -
316C LEU* 3.3 20.8 - - - +
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Residues in contact with ALA 82 (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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43C ARG* 3.7 0.6 - - - -
44C GLU* 3.0 25.7 + - - -
81C GLY* 1.3 74.3 - - - -
83C VAL* 1.3 64.1 + - - +
84C TYR* 3.4 18.9 + - + -
101C ALA* 3.8 25.6 - - + -
103C GLU 3.4 11.9 - - - +
104C LYS* 3.8 4.6 - - + +
313C ILE* 3.3 23.5 + - + +
314C ASN* 4.1 4.9 - - - +
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Residues in contact with VAL 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C TYR* 3.6 54.3 - - + +
42C HIS* 3.7 16.2 - - + +
43C ARG* 3.6 35.9 - - - +
82C ALA* 1.3 70.0 - - - +
84C TYR* 1.3 64.9 + - - +
102C GLN* 3.0 25.2 + - + +
103C GLU* 2.5 30.3 + - + +
104C LYS* 5.3 0.4 - - - -
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Residues in contact with TYR 84 (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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244B GLU* 3.4 25.3 - - + +
42C HIS* 3.1 30.5 + - - +
44C GLU* 2.8 38.5 + - + -
56C ARG* 3.3 14.1 + - - -
57C TYR* 5.1 1.8 - + - -
82C ALA* 3.4 26.0 - - + -
83C VAL* 1.3 77.8 - - - +
85C SER* 1.3 63.2 + - - +
86C HIS 3.2 15.9 - - - +
88C PRO* 4.4 5.2 - - + -
99C PHE* 3.7 31.4 - + + -
100C GLN 3.5 7.0 - - - -
101C ALA* 3.5 32.5 - - + -
102C GLN* 4.1 6.6 - - - +
314C ASN* 3.7 9.5 - - - +
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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