Contacts of the strand formed by residues 25 - 30 (chain C) in PDB entry 4WCI
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 25 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ARG* 3.6 37.6 - - - +
101A SO4 4.0 6.7 + - - +
3C ASP* 4.0 9.2 - - + -
4C TYR 3.5 8.1 - - - +
5C ILE* 3.9 24.9 - - + -
23C GLY 3.7 9.2 - - - +
24C GLU* 1.3 80.0 - - - +
26C ILE* 1.3 63.6 + - - +
27C ARG* 3.6 42.6 + - + +
41C GLU* 4.2 1.2 - - - +
42C LEU* 3.6 15.6 - - - +
57C ILE* 3.9 22.4 - - + -
101C SO4 4.5 2.2 - - - +
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Residues in contact with ILE 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ASP* 3.4 5.2 - - - +
4C TYR* 2.9 34.3 + - + +
6C VAL* 3.7 28.0 - - + -
18C LEU* 4.2 8.5 - - + -
20C ILE* 4.1 13.2 - - + -
25C ILE* 1.3 74.5 - - - +
27C ARG* 1.3 61.2 + - - +
29C VAL* 3.6 7.4 - - + +
40C GLY* 3.7 16.8 - - - -
41C GLU 3.5 12.6 - - - +
42C LEU* 4.6 9.2 - - + -
49C PHE* 3.6 55.0 - - + -
54C VAL* 4.1 5.4 - - + -
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Residues in contact with ARG 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ARG* 3.5 3.2 - - - +
101A SO4 2.9 33.9 + - - -
1C MET* 6.1 0.2 - - - -
3C ASP* 3.3 33.0 + - - +
25C ILE* 3.6 22.6 + - + +
26C ILE* 1.3 77.4 - - - +
28C ASN* 1.3 71.2 + - - +
29C VAL 3.3 2.8 + - - -
40C GLY* 3.6 0.9 - - - -
41C GLU* 2.8 51.1 + - - +
57C ILE* 6.0 0.2 - - - +
101C SO4 3.1 28.5 + - - -
23E GLY* 3.1 30.7 - - - +
24E GLU* 4.5 2.7 - - - +
25E ILE* 3.5 24.7 - - - +
27E ARG* 3.4 11.1 - - - +
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Residues in contact with ASN 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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1C MET* 3.7 31.6 - - - +
2C VAL 3.3 8.9 + - - +
3C ASP* 3.4 3.4 + - - -
27C ARG* 1.3 76.8 - - - +
29C VAL* 1.3 62.6 + - - +
30C LYS* 3.8 23.0 + - - +
46C ARG* 2.9 46.7 + - - +
22E VAL* 3.5 24.4 - - - +
23E GLY* 4.0 18.7 - - - -
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Residues in contact with VAL 29 (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 VAL* 2.9 31.3 + - + +
4C TYR* 3.7 36.1 - - + -
26C ILE* 3.6 44.2 - - + +
28C ASN* 1.3 77.6 + - - +
30C LYS* 1.3 67.3 + - - +
38C LEU* 3.9 13.9 - - + -
39C GLU 3.1 10.1 - - - +
49C PHE* 3.8 13.9 - - + -
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Residues in contact with LYS 30 (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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28C ASN* 3.8 26.9 - - - +
29C VAL* 1.3 81.8 - - - +
31C LYS* 1.3 62.7 + - - +
32C LEU* 3.9 17.5 - - + -
38C LEU* 3.8 6.6 - - - -
39C GLU* 2.8 39.5 + - - +
46C ARG* 3.7 20.4 - - - +
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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