Contacts of the strand formed by residues 31 - 37 (chain J) in PDB entry 1S7X
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 LYS 31 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27J TYR* 3.9 3.9 - - - -
28J VAL 3.0 31.8 + - - +
29J ASP* 4.1 3.4 - - + +
30J ASN* 1.3 78.1 - - - +
32J GLU* 1.3 73.3 + - - +
33J PHE* 3.4 2.3 + - - +
51J TRP* 5.9 0.3 - - - -
179J LEU* 4.7 21.1 - - + +
181J ARG* 4.4 25.6 - - - +
209J TYR* 3.8 25.1 - - + +
239J GLY* 5.8 9.6 - - - -
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Residues in contact with GLU 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J VAL* 3.5 19.8 - - + +
26J GLY 3.4 7.6 - - - +
27J TYR* 3.7 16.6 + - + -
31J LYS* 1.3 80.2 + - - +
33J PHE* 1.3 61.6 + - - +
34J VAL 4.0 3.4 - - - +
35J ARG* 2.7 34.3 + - - -
48J ARG* 2.8 49.8 + - + +
49J ALA* 4.1 6.6 - - - +
53K ASP* 4.7 0.4 - - - +
55K SER* 4.8 4.3 + - - -
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Residues in contact with PHE 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J MET* 4.2 3.8 - - + -
7J TYR* 3.5 23.6 - + - -
26J GLY* 3.0 25.2 + - - -
27J TYR 3.3 20.4 - - - -
28J VAL* 3.6 20.0 - - + -
31J LYS 4.2 3.4 - - - +
32J GLU* 1.3 74.6 - - - +
34J VAL* 1.3 80.8 + - + +
47J PRO* 3.7 2.9 - - - +
48J ARG* 3.0 22.8 + - - -
49J ALA* 4.0 5.8 + - + +
51J TRP* 3.5 28.7 - + + +
52J MET* 3.6 27.9 - - + +
59J TYR* 4.3 1.1 - - - -
171J TYR* 3.7 34.5 - + - -
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Residues in contact with VAL 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7J TYR* 3.8 19.1 - - + +
25J VAL* 3.7 2.3 - - - -
26J GLY* 3.1 43.0 + - - +
32J GLU* 4.0 3.3 - - - +
33J PHE* 1.3 109.3 - - + +
35J ARG* 1.3 66.3 + - - +
45J TYR* 3.9 13.5 - - + -
46J GLU 3.3 8.1 - - - +
48J ARG* 3.7 5.0 - - - +
52J MET* 3.7 18.2 - - + -
59J TYR* 4.4 4.7 - - + +
60J TRP* 3.9 15.7 - - + -
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Residues in contact with ARG 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J ILE* 4.0 14.5 - - - +
24J SER 3.2 12.1 - - - +
25J VAL* 3.3 24.7 - - + +
32J GLU* 2.7 43.8 + - - +
34J VAL* 1.3 79.1 - - - +
36J PHE* 1.3 68.1 + - - +
37J ASP* 5.2 10.2 + - + -
44J ARG 3.4 3.8 - - - +
45J TYR* 3.7 5.9 - - - -
46J GLU* 2.9 36.3 + - + +
48J ARG* 3.5 32.1 - - + +
53K ASP* 3.2 29.4 + - - +
54K MET* 3.0 29.5 + - - +
55K SER* 4.8 3.2 + - - -
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Residues in contact with PHE 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J TYR* 3.6 35.2 - + - -
23J ILE* 3.4 6.8 - - - +
24J SER* 2.9 33.9 + - - +
35J ARG* 1.3 75.0 - - - +
37J ASP* 1.3 61.7 + - - +
38J SER* 3.8 18.4 - - - -
43J PRO* 3.7 20.6 - - + -
44J ARG* 3.4 40.6 - - - -
45J TYR* 3.4 26.2 - - + -
64J THR* 4.4 9.2 - - + -
67J ALA* 3.6 24.9 - - + -
68J LYS* 4.7 7.6 - - + -
71J GLU* 4.4 11.9 - - - -
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Residues in contact with ASP 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J ARG* 2.5 44.9 + - - -
22J TYR 3.7 2.9 - - - -
23J ILE* 3.6 13.2 - - + +
35J ARG* 5.2 11.2 + - + +
36J PHE* 1.3 81.4 - - - +
38J SER* 1.3 66.4 + - - +
39J ASP* 3.1 8.3 + - - -
40J ALA* 3.1 29.8 + - + +
43J PRO* 4.0 5.9 - - - +
44J ARG 4.4 2.8 + - - -
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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