Contacts of the strand formed by residues 25 - 30 (chain C) in PDB entry 4WLU
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 25 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ASN* 1.3 78.4 - - + +
26C LYS* 1.3 59.5 + - - +
27C VAL* 4.5 9.9 - - + -
49C LEU 3.4 17.6 + - - +
50C VAL* 3.8 3.9 - - + +
51C SER* 3.1 24.6 + - - -
52C ARG 3.4 4.3 + - - +
94C ASP* 3.3 16.2 - - + +
95C VAL* 5.6 0.4 - - + -
263C VAL* 4.0 29.8 - - + -
266C MET* 6.0 1.6 - - + -
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Residues in contact with LYS 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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24C ASN 3.7 0.9 + - - +
25C ALA* 1.3 71.4 - - - +
27C VAL* 1.3 63.3 + - - +
52C ARG* 3.5 47.0 - - + +
54C THR* 3.9 13.9 - - - +
88C ASP 4.2 7.3 + - - -
89C CYS 3.8 13.7 + - - -
91C LYS* 2.4 30.5 + - - +
92C GLY* 3.6 24.9 - - - +
93C CYS* 3.8 9.5 - - - +
94C ASP* 2.7 42.4 + - - +
95C VAL 3.2 8.5 + - - +
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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
----------------------------------------------------------
25C ALA* 4.5 12.1 - - + -
26C LYS* 1.3 77.7 - - - +
28C ALA* 1.3 69.7 + - - +
44C LEU* 4.0 26.0 - - + -
50C VAL* 4.2 23.6 - - + -
52C ARG 2.9 9.4 + - - +
53C LEU* 3.5 14.1 - - + +
54C THR* 3.1 25.7 + - - +
93C CYS* 4.5 0.4 - - - -
95C VAL* 3.3 24.7 - - + +
97C VAL* 4.1 13.2 - - + -
259C VAL* 4.6 9.2 - - + -
263C VAL* 5.0 1.1 - - + -
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Residues in contact with ALA 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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27C VAL* 1.3 76.8 - - - +
29C VAL* 1.3 63.1 + - - +
30C LEU* 4.0 2.9 - - + -
54C THR* 3.3 19.7 - - - +
89C CYS* 4.3 12.3 - - - +
90C LEU* 4.4 7.6 - - + -
93C CYS* 3.4 19.3 - - - -
95C VAL 2.9 8.6 + - - +
96C VAL* 3.4 12.4 - - + -
97C VAL 2.8 26.5 + - - -
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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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27C VAL* 4.6 0.7 - - + -
28C ALA* 1.3 77.2 - - - +
30C LEU* 1.3 61.4 + - - +
32C ALA* 3.6 25.6 - - + +
37C GLY 4.4 2.0 - - - +
40C LEU* 4.4 9.0 - - + -
41C SER* 3.8 17.0 - - - +
44C LEU* 3.4 33.7 - - + -
53C LEU* 4.2 9.9 - - + -
54C THR 3.0 7.1 + - - -
55C LEU* 4.2 3.6 - - + -
56C TYR 3.0 27.7 + - - +
97C VAL* 3.4 8.3 - - + +
99C PRO* 4.1 21.3 - - + -
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Residues in contact with LEU 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 ALA* 4.5 4.5 - - + -
29C VAL* 1.3 71.9 - - - +
31C GLY* 1.3 57.9 + - - +
56C TYR* 3.6 27.8 - - + -
86C LEU* 4.1 14.4 - - + -
89C CYS* 4.4 6.5 - - - -
90C LEU* 4.2 13.7 - - + -
96C VAL* 3.7 25.4 - - + -
97C VAL 2.8 12.0 + - - +
98C ILE* 3.6 11.6 - - + -
99C PRO* 3.1 11.5 - - - +
100C ALA* 2.9 23.6 + - - -
124C LEU* 3.9 42.0 - - + +
128C CYS* 4.2 10.1 - - - -
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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