Contacts of the strand formed by residues 46 - 58 (chain X) in PDB entry 5OA3
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 HIS 46 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272 A 3.5 45.1 + + - -
282 U 4.1 12.9 + - - -
4832 C 3.7 27.6 + - - +
6472 U 5.1 3.6 + - - -
6482 A 3.6 26.0 + - - -
41X PHE* 3.8 3.6 - - - -
44X ALA* 3.5 18.2 - - - +
45X SER* 1.3 98.8 - - - +
47X ALA* 1.3 64.1 + - - +
76X LYS* 4.6 0.2 + - - -
101X LEU* 4.4 20.6 - - + +
102X VAL 3.3 9.9 - - - +
103X ALA* 3.6 23.5 - - + +
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Residues in contact with ALA 47 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4832 C 3.4 9.0 - - - +
41X PHE* 3.9 22.6 - - + -
46X HIS* 1.3 77.1 - - - +
48X LYS* 1.3 63.0 + - - +
74X LEU* 3.6 26.7 - - + -
76X LYS* 4.2 11.0 - - - -
101X LEU* 3.7 4.3 - - - -
102X VAL* 2.9 36.3 + - - +
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Residues in contact with LYS 48 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4822 G 6.6 0.7 - - + -
4832 C 3.1 44.1 + - - +
4842 A 5.5 6.4 + - - +
47X ALA* 1.3 75.0 - - - +
49X GLY* 1.3 58.4 + - - +
74X LEU* 3.4 11.9 - - - +
75X ILE* 3.5 23.8 + - + +
76X LYS* 5.2 1.4 + - - +
99X GLU* 3.5 33.6 - - - +
100X VAL 3.5 10.1 - - - +
101X LEU* 3.7 13.0 - - + +
127X ASN* 4.0 20.9 + - - +
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Residues in contact with GLY 49 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X ALA 3.8 0.6 + - - -
48X LYS* 1.3 76.1 - - - +
50X ILE* 1.3 64.1 + - - -
72X VAL* 4.9 6.1 - - - -
73X GLN 3.5 11.4 - - - -
74X LEU* 4.2 7.9 - - - -
75X ILE* 4.0 4.5 - - - -
98X ASP 3.3 0.5 - - - +
99X GLU* 3.3 9.5 + - - +
100X VAL* 2.9 38.6 + - - -
102X VAL* 5.3 1.3 - - - +
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Residues in contact with ILE 50 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49X GLY* 1.3 77.6 - - - -
51X VAL* 1.3 68.7 + - - +
52X LEU* 3.5 8.2 + - + +
72X VAL* 3.1 5.6 - - - -
73X GLN* 2.8 39.1 + - + +
75X ILE* 4.4 15.7 - - + -
97X ASN* 4.2 25.1 - - + +
98X ASP 3.2 10.3 - - - +
99X GLU* 3.7 16.2 - - - +
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Residues in contact with VAL 51 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X ILE* 1.3 75.7 - - - +
52X LEU* 1.3 63.7 + - - +
53X GLU 4.0 12.3 - - - +
54X LYS* 5.3 2.7 - - + -
70X VAL* 3.5 27.4 - - + -
71X ARG 3.8 3.4 - - - -
72X VAL* 4.3 2.5 - - + -
94X ILE* 4.2 7.0 - - + -
95X GLU 3.4 28.7 - - - +
96X GLU* 4.0 7.0 - - + -
97X ASN* 2.8 36.4 + - - +
98X ASP* 3.3 11.3 + - + +
100X VAL* 3.6 31.4 - - + -
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Residues in contact with LEU 52 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X ILE* 4.3 9.2 - - + +
51X VAL* 1.3 76.6 - - - +
53X GLU* 1.3 63.1 + - + +
71X ARG* 2.8 29.9 + - + +
73X GLN* 4.0 29.2 - - + +
80X LYS* 3.6 44.6 - - + +
96X GLU* 2.7 25.1 - - - +
97X ASN* 5.2 6.6 + - - +
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Residues in contact with GLU 53 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51X VAL* 3.7 4.1 - - - +
52X LEU* 1.3 85.7 - - - +
54X LYS* 1.3 65.2 + - - +
55X VAL* 3.8 16.8 - - + +
70X VAL* 3.5 7.3 - - - +
71X ARG* 2.9 65.4 + - + +
96X GLU* 3.2 14.1 - - - +
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Residues in contact with LYS 54 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51X VAL* 5.3 4.3 - - + -
53X GLU* 1.3 79.5 - - - +
55X VAL* 1.3 63.3 + - - +
69X CYS 3.8 6.5 - - - +
70X VAL* 4.7 2.7 - - + +
91X LEU* 2.6 52.9 + - + +
92X ASN* 4.5 2.8 + - - +
94X ILE* 2.7 30.2 + - - -
95X GLU* 4.3 16.9 + - - +
96X GLU* 3.9 14.0 + - + +
6e LEU* 3.3 25.8 - - + +
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Residues in contact with VAL 55 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53X GLU* 3.8 27.1 - - + +
54X LYS* 1.3 79.5 - - - +
56X GLY* 1.3 77.0 + - - +
57X VAL* 4.1 11.7 - - + -
69X CYS* 2.9 48.5 + - + +
70X VAL 5.2 0.4 - - - -
71X ARG* 4.4 15.0 - - + +
82X THR* 6.0 7.2 - - + -
6e LEU* 3.9 5.9 - - - +
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Residues in contact with GLY 56 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55X VAL* 1.3 85.5 - - - +
57X VAL* 1.3 60.0 + - - +
58X GLU 4.3 0.3 + - - -
66X ILE* 3.8 11.4 - - - -
67X ARG 3.7 4.0 - - - -
4e GLY* 4.6 19.8 + - - +
6e LEU* 3.5 24.7 - - - +
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Residues in contact with VAL 57 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55X VAL* 4.1 9.2 - - + -
56X GLY* 1.3 78.4 - - - +
58X GLU* 1.3 76.6 + - - +
59X ALA 3.4 0.9 + - - -
66X ILE* 3.5 5.5 - - - +
67X ARG* 2.8 46.7 + - + +
69X CYS* 4.1 24.7 - - + -
82X THR* 6.1 3.1 - - + -
115X ILE* 3.7 24.7 - - + -
116X PRO* 3.7 12.8 - - + +
118X VAL* 5.1 4.0 - - + -
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Residues in contact with GLU 58 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18232 A 4.5 11.8 + - - -
18242 A 4.2 19.0 + - - -
56X GLY 4.2 1.0 - - - -
57X VAL* 1.3 77.0 - - - +
59X ALA* 1.3 73.1 + - - +
65X ALA 3.9 6.1 - - - +
66X ILE* 4.8 7.5 - - + +
116X PRO* 3.4 22.3 - - - +
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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