Contacts of the strand formed by residues 28 - 35 (chain A) in PDB entry 3SOQ
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 ARG 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ASN* 1.3 73.5 - - - +
29A ARG* 1.3 80.9 + - - +
30A ASP 3.3 1.1 - - - -
50A LEU* 3.5 6.2 - - - +
51A GLU 3.2 14.3 - - - +
52A ASP* 2.9 30.3 + - - +
53A ALA* 2.9 45.0 + - - +
70A VAL* 4.8 1.2 - - - +
242A TRP* 4.5 8.1 - - - -
266A PHE* 4.3 5.2 - - + -
267A SER* 2.9 30.4 + - - +
269A MET* 3.9 26.6 - - + +
42Z ILE* 2.8 40.0 + - - +
43Z LYS* 4.9 3.8 + - - +
44Z ASN* 3.9 15.9 - - - +
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Residues in contact with ARG 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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27A ASN* 2.6 12.7 + - - +
28A ARG* 1.3 91.6 - - - +
30A ASP* 1.3 65.8 + - - +
49A GLY* 3.4 6.9 + - - -
50A LEU* 3.0 33.5 + - - +
51A GLU* 3.0 29.8 + - - +
52A ASP* 3.9 9.2 + - - -
266A PHE* 3.8 36.3 - - + -
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Residues in contact with ASP 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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27A ASN* 2.9 42.3 + - - +
28A ARG 3.3 2.3 + - - -
29A ARG* 1.3 84.9 - - - +
31A LEU* 1.3 65.8 + - - +
32A ARG* 3.0 44.9 + - - +
45A ILE* 4.0 15.0 - - + +
47A VAL 3.0 16.8 - - - +
48A GLY* 3.8 6.5 - - - -
50A LEU* 3.8 8.5 - - - -
53A ALA* 4.4 0.9 - - - +
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Residues in contact with LEU 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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24A LEU* 4.7 3.8 - - + -
25A TYR 3.5 4.0 - - - +
26A ALA* 3.6 31.0 - - + -
30A ASP* 1.3 75.1 - - - +
32A ARG* 1.3 67.3 + - - +
45A ILE* 3.6 1.6 - - - +
46A VAL* 2.9 36.8 + - + +
47A VAL* 2.8 20.1 + - + +
50A LEU* 3.9 8.7 - - + -
53A ALA* 4.0 12.8 - - + -
56A VAL* 4.0 8.3 - - + -
65A ILE* 3.7 22.0 - - + -
67A TRP* 3.6 41.5 - - + -
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Residues in contact with ARG 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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23A LEU 3.6 0.9 - - - +
24A LEU* 3.4 8.3 - - - +
25A TYR* 2.9 68.3 + - + +
27A ASN* 3.5 16.8 - - + +
30A ASP* 3.0 37.2 + - - +
31A LEU* 1.3 79.9 - - - +
33A LEU* 1.3 60.8 + - - +
34A VAL 4.2 0.2 - - - -
42A ASN* 5.0 9.9 - - - +
43A ALA* 3.8 22.6 + - + +
44A THR 3.2 11.2 - - - +
45A ILE* 4.0 20.2 - - + +
46A VAL* 4.4 3.4 - - - +
266A PHE* 6.1 0.4 - - - +
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Residues in contact with LEU 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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22A LEU* 4.3 19.5 - - + -
23A LEU 3.4 5.8 - - - +
24A LEU* 3.5 39.0 - - + +
32A ARG* 1.3 74.7 - - - +
34A VAL* 1.3 60.3 + - - +
43A ALA* 3.5 1.9 - - - -
44A THR* 2.8 48.7 + - - +
46A VAL* 3.8 17.9 - - + -
65A ILE* 5.8 0.2 - - + -
274A PHE* 3.9 27.6 - - + -
401A FUC 3.7 30.7 - - + +
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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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22A LEU* 3.5 4.0 - - - -
23A LEU* 2.8 56.0 + - + +
25A TYR* 3.8 14.6 - - + -
32A ARG 4.2 0.2 - - - -
33A LEU* 1.3 74.8 - - - +
35A ASP* 1.3 65.9 + - - +
36A ALA* 3.4 1.3 + - - -
38A ASN 4.7 2.5 - - - +
39A GLY* 4.0 20.0 - - - +
41A GLU* 4.6 4.3 - - + +
42A ASN 5.3 0.7 - - - +
43A ALA* 4.0 14.4 - - + +
247A ILE* 4.3 7.0 - - + -
261A ILE* 5.8 0.9 - - + -
262A HIS* 3.8 34.8 - - + +
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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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20A ALA 4.3 4.8 - - - +
21A PRO 4.1 2.6 - - - +
22A LEU* 3.7 27.3 - - + +
34A VAL* 1.3 74.1 - - - +
36A ALA* 1.3 54.8 + - - +
37A THR* 2.8 35.8 + - - +
38A ASN* 2.8 44.3 + - + +
39A GLY* 3.2 3.6 + - - -
41A GLU* 5.9 1.8 - - - +
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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