Contacts of the strand formed by residues 49 - 57 (chain C) in PDB entry 1S4Y
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 GLU 49 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C TRP* 3.3 0.2 - - - -
42C ARG* 2.7 80.2 + - + +
47C THR* 3.7 2.7 + - + +
48C ILE* 1.3 76.0 - - - +
50C LEU* 1.3 71.7 + - - +
51C VAL* 3.9 5.0 - - - +
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Residues in contact with LEU 50 (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* 3.7 42.8 + - + +
12C ALA* 4.0 11.8 - - - +
39C ALA* 6.1 0.2 - - + -
40C SER 4.1 8.5 - - - +
41C TRP* 4.1 2.5 - - - -
48C ILE* 3.9 6.1 - - + +
49C GLU* 1.3 83.8 - - - +
51C VAL* 1.4 65.2 + - - +
52C LYS 4.9 1.1 - - - +
53C LYS* 4.1 35.4 - - + -
91C PHE* 4.6 17.5 - - + -
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Residues in contact with VAL 51 (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* 3.4 5.2 - - - -
12C ALA* 2.9 39.3 + - + +
40C SER* 2.9 24.3 + - - +
41C TRP* 3.9 13.9 - - - +
42C ARG* 3.6 27.1 - - + +
49C GLU* 3.5 11.4 + - - +
50C LEU* 1.4 76.0 - - - +
52C LYS* 1.4 65.6 + - + +
77C VAL* 4.8 1.8 - - + -
100D ILE* 3.5 43.7 - - + +
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Residues in contact with LYS 52 (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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9C TYR* 5.3 1.7 + - + -
10C TYR* 3.2 11.2 - - - +
11C ASN* 2.7 30.4 + - - +
13C ASN* 4.7 0.6 - - - +
17C GLU* 2.7 24.2 + - - -
38C TYR* 3.2 26.5 - - - +
39C ALA* 3.4 1.4 - - - -
40C SER* 2.8 37.0 + - - +
50C LEU* 5.0 0.4 - - - -
51C VAL* 1.4 93.5 - - + +
53C LYS* 1.3 62.8 + - - +
92D LEU* 4.7 2.9 - - + -
100D ILE 3.5 24.2 + - - -
101D ILE* 3.9 0.9 - - - +
102D LYS* 3.7 28.0 + - + +
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Residues in contact with LYS 53 (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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8C ILE* 3.5 31.7 - - + +
9C TYR* 3.4 10.2 - - - -
10C TYR* 2.9 43.0 + - + +
38C TYR* 3.2 16.7 + - - +
39C ALA* 4.2 9.4 - - + -
50C LEU* 4.1 16.2 - - + -
52C LYS* 1.3 79.4 - - - +
54C GLY* 1.3 58.3 + - - +
88C ASN* 3.4 19.0 + - - +
89C GLU* 3.0 30.7 + - - +
91C PHE* 3.8 24.3 - - - -
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Residues in contact with GLY 54 (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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7C CYS* 3.8 7.4 - - - -
8C ILE 3.3 10.9 + - - -
9C TYR* 4.4 2.7 - - - -
25C GLU* 3.7 10.3 - - - -
37C CYS* 3.3 5.0 - - - -
38C TYR* 2.9 43.3 + - - -
53C LYS* 1.3 75.8 - - - +
55C CYS* 1.3 60.8 + - - -
88C ASN* 3.5 2.4 + - - -
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Residues in contact with CYS 55 (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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7C CYS* 3.6 6.3 - - - -
25C GLU* 3.0 46.2 + - - +
27C CYS* 2.1 50.9 - - + -
28C GLU 5.7 0.4 - - - +
36C HIS 3.4 5.4 - - - -
38C TYR* 3.5 8.5 - - - -
54C GLY* 1.3 73.0 - - - -
56C TRP* 1.3 62.5 + - - +
102D LYS* 3.1 22.4 + - - +
104D ASP* 5.9 0.2 - - - -
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Residues in contact with TRP 56 (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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35C LEU* 4.0 2.3 - - - +
36C HIS* 2.9 41.4 + - + +
38C TYR* 3.7 35.7 - + + -
55C CYS* 1.3 77.6 - - - +
57C LEU* 1.3 81.1 + - - +
59C ASP* 3.1 27.0 + - - +
62C CYS* 3.8 21.5 - - - -
79C PHE* 3.8 29.8 - + - -
81C CYS* 4.5 0.7 - - + -
31D ALA* 3.9 15.0 - - + -
32D PRO* 4.7 2.0 - - + -
90D SER* 3.4 48.7 - - - +
91D MET* 3.8 4.5 - - - -
92D LEU* 3.9 13.2 - - + -
102D LYS* 3.8 21.8 - - + +
104D ASP* 5.8 0.2 - - - -
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Residues in contact with LEU 57 (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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28C GLU 4.1 20.2 - - - +
29C GLY* 5.0 7.0 - - - -
34C ARG 4.6 1.3 - - - +
35C LEU* 5.4 3.4 - - + +
36C HIS* 3.3 1.6 - - - -
56C TRP* 1.3 89.7 + - - +
58C ASP* 1.4 68.3 + - - +
59C ASP* 3.2 4.5 + - - +
87D ARG* 4.1 17.5 - - - +
88D PRO* 3.6 35.9 - - + -
89D MET* 3.8 13.9 - - - +
90D SER* 3.0 23.1 + - - +
104D ASP* 3.7 33.0 + - + +
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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