Contacts of the strand formed by residues 23 - 30 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A THR* 3.5 3.3 - - - +
20A GLY 2.9 40.2 + - - +
21A GLY 3.2 1.3 - - - -
22A PHE* 1.3 97.8 - - + +
24A LYS* 1.3 61.8 + - - +
25A VAL* 6.0 0.7 - - + -
40A LYS* 5.4 6.1 - - + -
41A ILE 3.6 4.0 - - - -
42A MET* 4.5 10.1 - - - -
20D GLY 4.3 1.1 - - - -
21D GLY* 3.9 22.7 - - - +
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Residues in contact with LYS 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 5.9 2.5 - - - +
16A THR* 3.8 15.5 - - + +
18A GLY 3.3 13.2 - - - +
19A THR* 3.0 32.0 + - + +
22A PHE 3.9 0.6 + - - +
23A ALA* 1.3 76.3 - - - +
25A VAL* 1.3 66.9 + - - +
26A LYS* 4.3 15.3 - - + +
39A ILE 3.6 0.5 - - - +
40A LYS* 3.6 1.9 - - - +
41A ILE* 2.7 54.4 + - + +
93D GLU* 2.8 30.0 + - - +
95D PHE* 6.5 0.4 - - + -
136D GLU* 4.3 24.6 + - + +
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A THR* 3.6 4.0 - - - +
17A ILE* 2.8 53.9 + - + -
18A GLY 2.9 13.5 + - - +
23A ALA* 5.7 0.7 - - + -
24A LYS* 1.3 77.5 - - - +
26A LYS* 1.3 59.9 + - - +
38A ALA* 4.2 22.9 - - + -
39A ILE 3.3 10.1 - - - +
40A LYS* 4.1 23.3 - - + +
86A LEU* 6.5 0.7 - - + -
19D THR 3.7 20.2 - - - +
20D GLY* 4.3 6.7 - - - -
21D GLY 5.4 1.1 - - - +
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 4.2 22.2 - - + -
14A HIS 3.6 12.3 - - - -
15A GLU 3.7 3.4 - - - +
16A THR* 2.7 37.8 + - - +
17A ILE* 5.2 0.2 - - - -
24A LYS* 4.1 11.1 - - + +
25A VAL* 1.3 80.4 - - - +
27A LEU* 1.3 65.2 + - - +
38A ALA* 4.7 0.7 - - - -
39A ILE* 2.8 38.5 + - + +
41A ILE* 3.9 27.6 - - + -
93D GLU* 4.2 7.3 + - - -
95D PHE* 4.0 18.9 - - + -
96D ASP* 2.8 30.1 + - - -
99D ILE* 4.8 0.4 - - - -
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.8 1.9 - - - -
14A HIS* 2.8 42.0 + - + +
15A GLU* 3.0 42.3 + - - +
17A ILE* 4.6 12.3 - - + +
26A LYS* 1.3 75.5 - - - +
28A ALA* 1.3 57.2 + - - +
36A MET* 3.4 28.5 - - + -
37A VAL 3.4 13.5 - - - +
38A ALA* 4.8 2.7 - - - +
88A TYR* 3.0 48.0 - - + +
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 4.2 4.3 - - + -
12A GLU 3.3 14.8 - - - +
13A LEU* 4.1 8.5 - - + -
14A HIS* 4.2 2.9 - - - +
26A LYS 3.8 0.4 + - - +
27A LEU* 1.3 76.7 - - - +
29A CYS* 1.3 60.8 + - - +
36A MET* 3.4 13.5 - - - +
37A VAL* 2.9 39.0 + - + +
39A ILE* 3.5 31.9 - - + -
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Residues in contact with CYS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 3.2 7.3 - - - -
12A GLU* 2.8 44.7 + - + +
14A HIS* 3.9 21.0 - - + +
28A ALA* 1.3 74.1 - - - +
30A HIS* 1.4 63.2 + - - +
31A ILE* 3.3 4.6 + - + +
34A GLY* 3.5 37.0 - - - -
35A GLU 3.6 4.3 - - - -
36A MET* 4.0 10.1 - - - -
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Residues in contact with HIS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A TYR 4.1 3.1 - - - -
11A TYR* 3.6 36.8 - + + -
28A ALA 4.2 0.6 - - - -
29A CYS* 1.4 69.0 - - - +
31A ILE* 1.3 57.6 + - - +
32A LEU* 3.8 9.9 - - + -
33A THR* 2.6 48.3 + - + +
34A GLY* 2.9 27.7 + - - -
35A GLU 2.8 17.8 + - - +
37A VAL* 4.5 2.1 - - + +
312A HIS* 3.2 30.2 + + - -
315A ALA* 4.5 0.9 - - + -
316A THR* 3.3 25.9 + - - -
319A LEU* 3.4 22.5 - - + +
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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