Contacts of the strand formed by residues 29 - 35 (chain A) in PDB entry 3S4S
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 ASP 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ASP* 2.9 5.2 - - - -
26A PHE 2.6 38.3 + - - +
27A ASP* 3.4 1.8 - - - +
28A GLY* 1.3 77.8 - - - +
30A GLU* 1.3 62.1 + - - +
138A LEU* 6.0 0.4 - - - -
123B TYR* 3.8 21.5 - - - -
149B GLN* 3.3 26.1 + - - +
151B GLY* 3.8 18.1 - - - +
153B TRP* 3.2 53.9 + - + +
154B THR 4.9 0.3 + - - -
155B PHE* 4.9 1.0 - - - -
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Residues in contact with GLU 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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23A MET* 3.9 16.8 - - + +
24A PHE 3.7 4.3 - - - -
25A ASP* 4.1 3.1 - - - +
28A GLY 4.2 0.6 + - - -
29A ASP* 1.3 72.4 + - - +
31A ILE* 1.3 58.3 + - - +
32A PHE* 3.6 18.9 - - - +
33A HIS* 2.7 37.5 + - - +
42A VAL 4.3 1.6 - - - +
44A ARG* 2.8 44.5 + - + +
135A THR* 4.4 3.5 - - - -
136A VAL* 3.8 23.9 + - - +
138A LEU* 4.1 15.4 - - + +
151B GLY 5.5 2.4 + - - +
153B TRP* 2.7 26.6 + - - +
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Residues in contact with ILE 31 (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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7A ILE* 4.8 9.6 - - + -
24A PHE* 2.8 23.2 + - + +
25A ASP 4.2 5.4 - - - +
26A PHE* 3.7 37.2 - - + +
30A GLU* 1.3 73.5 - - - +
32A PHE* 1.3 77.3 + - + +
43A TRP* 3.5 11.5 - - + -
44A ARG 3.0 18.4 + - - -
48A PHE* 3.4 20.3 - - + -
89B PHE* 4.2 5.4 - - + -
90B THR* 4.7 4.9 - - + -
153B TRP* 4.1 9.4 - - + -
5C TYR* 3.6 33.7 - - + +
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Residues in contact with PHE 32 (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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22A PHE* 4.3 10.3 - + - -
23A MET* 3.3 5.2 - - - +
24A PHE* 3.1 69.4 + + + +
30A GLU* 3.5 9.5 - - - +
31A ILE* 1.3 88.2 - - + +
33A HIS* 1.3 72.6 + - - +
34A VAL* 4.7 1.1 - - + -
41A THR* 3.9 9.2 - - + -
42A VAL 3.1 18.4 - - - +
43A TRP* 3.5 33.2 - + + +
44A ARG 4.1 0.2 - - - +
54A PHE* 3.8 33.0 - + - -
5C TYR* 3.9 24.0 - + + -
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Residues in contact with HIS 33 (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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21A GLU* 5.4 4.9 - - + -
22A PHE 3.2 16.6 - - - +
23A MET* 3.6 8.5 - - + -
30A GLU* 2.7 23.3 + - - +
32A PHE* 1.3 80.2 - - - +
34A VAL* 1.3 76.4 + - - +
35A ASP* 4.0 6.0 + - - +
41A THR* 3.5 2.9 - - - -
42A VAL* 2.7 63.8 + - + +
136A VAL* 3.5 33.2 - - + +
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Residues in contact with VAL 34 (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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21A GLU* 5.7 0.3 - - - -
22A PHE* 3.1 13.5 + - + +
32A PHE* 4.7 1.8 - - + -
33A HIS* 1.3 87.8 - - - +
35A ASP* 1.3 67.6 + - - +
36A MET* 3.0 39.8 + - + +
40A GLU 3.2 9.0 - - - +
41A THR* 4.0 8.5 - - - +
54A PHE* 3.8 25.1 - - + -
56A ALA* 4.1 15.7 - - + +
59A ALA* 3.7 19.1 - - + -
60A LEU* 4.1 14.8 - - + -
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Residues in contact with ASP 35 (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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33A HIS* 4.0 12.3 + - - +
34A VAL* 1.3 69.0 - - - +
36A MET* 1.3 56.3 + - - +
37A ALA* 3.0 10.9 + - - +
38A LYS* 2.7 51.9 + - + +
39A LYS* 2.8 27.2 + - - -
40A GLU* 2.7 19.8 + - + +
42A VAL* 4.1 16.5 - - + +
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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