Contacts of the strand formed by residues 23 - 30 (chain C) in PDB entry 4D2W
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 23 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B GLY 4.1 7.2 - - - +
21B GLY* 4.0 18.6 - - - -
19C THR* 3.6 3.6 - - - +
20C GLY 3.0 34.1 + - - +
21C GLY 4.1 0.7 - - - +
22C PHE* 1.4 99.2 - - + +
24C LYS* 1.3 62.7 + - - +
40C LYS* 5.3 5.2 - - + -
41C ILE 3.5 4.5 - - - -
42C MET* 4.2 11.0 - - - -
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Residues in contact with LYS 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLY* 4.9 0.9 - - - -
93B GLU* 2.8 28.4 + - - +
95B PHE* 6.6 0.2 - - + -
136B GLU* 4.3 23.7 + - - +
4C TYR* 5.8 2.2 - - - +
16C THR* 3.8 15.3 - - + +
18C GLY 3.3 17.5 - - - +
19C THR* 3.0 30.5 + - + +
22C PHE 5.5 0.2 - - - +
23C ALA* 1.3 75.9 - - - +
25C VAL* 1.3 64.6 + - - +
26C LYS* 4.4 14.6 - - + +
39C ILE 3.6 0.7 - - - +
40C LYS* 3.5 2.6 - - - +
41C ILE* 2.7 51.4 + - + +
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Residues in contact with VAL 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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19B THR 3.7 22.9 - - - +
20B GLY 4.0 11.9 - - - +
16C THR* 2.5 32.0 - - - +
17C ILE* 4.5 12.8 - - + -
18C GLY 2.9 17.0 + - - +
24C LYS* 1.3 74.8 - - - +
26C LYS* 1.3 59.7 + - - +
38C ALA* 4.2 23.8 - - + -
39C ILE 3.3 8.7 - - - +
40C LYS* 4.1 21.3 - - + +
86C LEU* 6.5 0.9 - - + -
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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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93B GLU* 4.2 7.1 + - - -
95B PHE* 4.1 18.0 - - + -
96B ASP* 2.7 29.8 + - - -
99B ILE* 4.9 0.4 - - - -
13C LEU* 4.2 23.3 - - + -
14C HIS 3.5 12.6 - - - -
15C GLU 4.2 0.4 - - - +
16C THR* 2.8 42.6 + - - +
24C LYS* 4.2 10.4 - - + +
25C VAL* 1.3 77.7 - - - +
27C LEU* 1.3 66.1 + - - +
38C ALA* 4.8 0.2 - - - -
39C ILE* 2.8 43.4 + - + +
41C ILE* 3.8 29.2 - - + -
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Residues in contact with LEU 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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13C LEU* 3.9 1.0 - - - -
14C HIS* 2.8 49.2 + - + +
15C GLU* 3.0 42.4 + - - +
16C THR 3.6 2.0 + - - -
17C ILE* 4.0 18.3 - - + +
26C LYS* 1.3 77.2 - - - +
28C ALA* 1.3 57.0 + - - +
36C MET* 4.7 11.9 - - + -
37C VAL 3.7 7.0 - - - +
38C ALA* 4.7 3.4 - - + +
88C TYR* 3.7 37.9 - - + +
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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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11C TYR* 4.2 4.3 - - + -
12C GLU 3.3 13.9 - - - +
13C LEU* 4.1 8.5 - - + -
14C HIS* 4.2 4.3 - - - +
26C LYS 3.8 0.2 + - - -
27C LEU* 1.3 75.8 - - - +
29C CYS* 1.3 58.3 + - - +
36C MET* 3.4 12.7 - - - +
37C VAL* 2.8 42.0 + - + +
39C ILE* 3.5 32.5 - - + -
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Residues in contact with CYS 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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11C TYR* 3.2 7.8 - - - -
12C GLU* 2.8 40.9 + - + +
14C HIS* 4.0 17.7 - - + +
28C ALA* 1.3 72.3 - - - +
30C HIS* 1.3 63.5 + - - +
31C ILE* 3.4 4.3 + - - +
34C GLY* 3.2 40.2 - - - -
35C GLU 3.7 3.1 - - - -
36C MET* 4.1 15.7 - - + -
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Residues in contact with HIS 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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10C TYR 4.0 3.4 - - - -
11C TYR* 3.5 37.7 - + + -
28C ALA 4.2 0.2 - - - -
29C CYS* 1.3 67.3 - - - +
31C ILE* 1.3 54.4 + - - +
32C LEU* 3.8 20.2 - - + -
33C THR* 2.8 29.7 + - + +
34C GLY* 2.8 33.8 + - - -
35C GLU 2.8 19.0 + - - +
37C VAL* 4.5 2.1 - - + +
312C HIS* 3.0 30.9 + + - -
315C ALA* 4.3 1.1 - - + +
316C THR* 3.4 32.4 + - - -
319C LEU* 3.6 21.9 - - + +
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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