Contacts of the strand formed by residues 68 - 75 (chain K) in PDB entry 1S72
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 VAL 68 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19930 C 3.7 39.7 - - - +
25960 A 4.6 17.5 - - - +
25970 U 5.6 0.2 - - - +
32K ILE* 4.5 2.2 - - + -
54K THR* 3.8 21.3 - - + -
55K VAL 3.2 11.7 - - - +
56K SER* 4.4 3.1 - - - -
66K ARG 3.6 3.3 + - - +
67K GLN* 1.3 74.8 - - - +
69K LEU* 1.3 67.5 + - - +
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Residues in contact with LEU 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K LEU* 6.5 0.2 - - + -
54K THR* 3.5 7.9 - - - +
55K VAL* 2.6 43.5 + - + +
57K VAL* 4.2 14.4 - - + -
64K MET* 4.1 15.5 - - + -
67K GLN* 3.7 30.5 + - + +
68K VAL* 1.3 83.7 - - - +
70K GLU* 1.3 64.3 + - - +
97K ILE* 3.9 35.4 - - + -
98K VAL 5.3 0.4 - - - +
105K ARG* 4.3 15.3 - - - +
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Residues in contact with GLU 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25970 U 4.6 5.9 + - - -
35K HIS* 5.4 4.0 + - - -
52K LYS* 4.1 32.5 + - + +
53K ILE 3.6 9.9 - - - +
54K THR* 4.5 12.2 + - - +
69K LEU* 1.3 77.4 - - - +
71K ALA* 1.3 65.2 + - - +
97K ILE* 3.5 8.0 - - - +
98K VAL* 2.9 36.8 + - + +
99K ASP 3.9 17.7 - - - +
100K GLU* 4.6 5.5 - - - +
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Residues in contact with ALA 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K LEU* 4.7 6.1 - - + -
52K LYS* 3.3 8.6 - - - +
53K ILE* 2.9 31.3 + - + -
55K VAL* 4.2 21.1 - - + -
70K GLU* 1.3 77.5 - - - +
72K VAL* 1.3 67.3 + - - +
95K ALA* 4.2 12.3 - - + -
96K VAL 3.3 20.6 - - - +
97K ILE* 4.0 3.8 - - + +
98K VAL* 3.9 4.2 - - - +
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Residues in contact with VAL 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50K GLY 4.8 0.9 - - - -
51K ASP 3.5 6.5 - - - +
52K LYS* 4.3 9.4 - - + -
71K ALA* 1.3 81.8 - - - +
73K VAL* 1.3 75.5 + - - +
74K VAL* 3.3 6.7 + - + +
95K ALA* 3.1 5.3 - - - -
96K VAL* 3.0 31.7 + - + +
98K VAL* 4.7 15.0 - - + -
117K VAL* 4.1 10.1 - - + -
121K PHE* 3.3 57.9 - - + -
124K VAL* 5.2 6.7 - - + -
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Residues in contact with VAL 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K LEU* 4.1 22.9 - - + -
48K GLY* 3.3 36.8 - - - +
49K LEU* 3.4 7.7 - - - +
50K GLY* 3.0 24.7 + - - +
51K ASP* 3.1 14.2 + - + +
53K ILE* 3.9 33.0 - - + -
72K VAL* 1.3 74.4 - - - +
74K VAL* 1.3 63.2 + - - +
75K ARG 3.9 14.1 - - - +
76K GLN* 5.0 1.6 - - - +
94K ALA 3.6 11.2 - - - +
95K ALA* 4.1 3.4 - - + -
117K VAL* 4.1 1.6 - - - +
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Residues in contact with VAL 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K ALA* 5.5 2.9 - - + -
49K LEU* 3.1 18.5 - - - +
72K VAL* 3.3 15.7 + - + +
73K VAL* 1.3 73.1 - - - +
75K ARG* 1.3 63.9 + - + +
94K ALA* 2.7 17.1 + - + +
96K VAL* 3.7 24.0 - - + -
112K PRO 3.8 6.3 - - - +
113K ILE* 3.0 51.1 - - + -
114K ALA* 3.6 12.0 + - - +
117K VAL* 4.2 12.7 - - + +
124K VAL* 4.6 4.0 - - + -
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Residues in contact with ARG 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K THR* 4.8 4.2 - - - +
21K ALA* 3.3 19.1 - - - +
49K LEU* 4.2 4.0 - - - -
73K VAL* 3.7 8.9 - - - +
74K VAL* 1.3 85.9 - - + +
76K GLN* 1.3 64.2 + - - +
90K PHE* 3.3 34.3 - - + -
92K ASP* 3.4 31.7 + - - +
93K ASN* 3.2 2.6 - - - +
94K ALA* 2.8 56.3 + - - +
110K LYS 3.7 5.6 + - - -
111K GLY* 3.8 5.3 - - - -
112K PRO* 3.2 48.4 + - - +
24U LYS* 4.5 10.7 + - - +
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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