Contacts of the strand formed by residues 22 - 28 (chain C) in PDB entry 4IHB
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 ALA 22 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C VAL* 4.1 19.3 - - + -
20C SER* 3.6 4.0 + - - -
21C ASP* 1.3 75.0 - - - +
23C TYR* 1.3 58.7 + - - +
37C VAL* 4.4 0.4 - - - -
38C ILE* 3.1 29.5 + - - +
41C SER 5.2 0.6 + - - +
44C PRO* 4.1 10.1 - - + +
46C TRP* 3.1 19.6 + - + -
69C VAL* 3.9 19.7 - - + -
70C LYS 3.2 11.9 - - - +
71C ASP* 4.6 0.2 - - - +
81C LEU* 4.7 1.8 - - + -
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Residues in contact with TYR 23 (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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22C ALA* 1.3 72.3 - - - +
24C CYS* 1.3 74.8 + - - +
25C SER* 4.5 7.0 - - - -
34C ARG* 4.0 27.7 + - + -
35C THR* 3.4 17.3 - - - +
36C LYS 3.4 21.1 - - - +
37C VAL* 4.0 6.5 - - + -
46C TRP* 3.6 4.0 - - - +
69C VAL* 3.4 4.7 - - - +
70C LYS* 3.0 74.1 + - + +
72C HIS* 3.7 20.0 - + + -
79C ARG* 3.1 39.8 + - - -
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Residues in contact with CYS 24 (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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6C ILE* 3.8 34.1 - - + +
23C TYR* 1.3 78.1 - - - +
25C SER* 1.3 60.7 + - - +
26C ALA 4.0 0.2 - - - -
33C LYS 3.9 0.3 - - - +
34C ARG* 3.3 5.4 - - - -
35C THR* 2.9 32.8 + - + +
46C TRP* 3.4 37.0 - - - -
67C VAL* 4.3 7.9 - - + -
68C VAL 3.3 4.5 - - - +
69C VAL* 3.9 17.0 - - - -
117C LEU* 3.9 5.6 - - - -
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Residues in contact with SER 25 (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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23C TYR* 4.1 10.7 + - - -
24C CYS* 1.3 74.5 - - - +
26C ALA* 1.3 58.8 + - - +
27C VAL* 4.2 3.4 - - - +
32C LYS* 3.4 36.6 + - - +
33C LYS 3.6 4.0 + - - -
34C ARG* 4.3 9.7 + - - +
66C HIS 3.6 1.2 - - - +
67C VAL* 3.3 2.1 - - - -
68C VAL* 2.7 50.9 + - - +
70C LYS* 4.9 11.0 - - - -
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Residues in contact with ALA 26 (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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4C VAL* 5.9 1.1 - - + -
6C ILE* 4.2 17.3 - - + -
24C CYS 4.0 0.6 - - - -
25C SER* 1.3 75.1 + - - +
27C VAL* 1.3 62.4 + - - +
32C LYS* 3.4 0.9 - - - -
33C LYS* 2.8 43.4 + - + +
50C PHE* 5.5 2.2 - - + -
52C TRP* 3.7 23.3 - - + -
65C LEU* 4.4 4.7 - - + -
66C HIS 3.3 4.3 - - - +
67C VAL* 4.0 18.4 - - + -
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Residues in contact with VAL 27 (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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25C SER* 4.4 4.5 - - - +
26C ALA* 1.3 78.9 - - - +
28C PHE* 1.3 64.5 + - - +
29C ALA 5.0 0.2 - - - +
30C GLY* 4.1 24.5 - - - +
31C VAL 3.4 7.6 - - - +
32C LYS* 3.7 35.2 - - + -
64C GLU 3.9 2.1 - - - +
65C LEU* 3.8 3.5 - - - +
66C HIS* 2.7 50.3 + - + +
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Residues in contact with PHE 28 (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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2C LEU* 3.7 19.1 - - + -
27C VAL* 1.3 75.1 - - - +
29C ALA* 1.3 76.5 - - + +
30C GLY 3.1 1.3 - - - -
31C VAL* 2.8 36.7 + - - +
52C TRP* 3.6 37.0 + + + +
53C ASP 5.5 1.6 - - - -
54C LEU* 3.4 33.7 - - + -
57C ILE* 5.0 6.1 - - + -
59C LEU* 4.8 9.0 - - + -
63C SER* 3.5 25.4 - - - -
64C GLU 3.6 17.0 - - - -
65C LEU* 4.2 8.3 - - + -
88C LEU* 3.5 19.7 - - + -
123C TYR* 5.5 1.3 - - - -
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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