Contacts of the strand formed by residues 21 - 26 (chain C) in PDB entry 5UK7
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 PRO 21 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ARG 3.6 5.6 - - - +
20C VAL* 1.3 88.4 - - + +
22C VAL* 1.3 53.0 + - - +
34C GLY 3.6 10.3 - - - +
35C GLN* 4.7 4.0 - - + -
65C SER 1.5 44.6 + - - +
66C ARG* 2.7 29.3 + - + +
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Residues in contact with VAL 22 (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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15C LEU* 3.6 35.0 - - + -
20C VAL* 3.7 16.2 - - + +
21C PRO* 1.3 81.1 - - - +
23C SER* 1.3 65.1 + - - +
24C ILE* 4.2 3.8 - - + -
32C LEU 3.9 0.3 - - - +
33C GLN* 3.4 4.5 - - - +
34C GLY 2.9 36.9 + - - +
35C GLN* 4.1 0.2 - - - -
36C ILE* 3.5 35.4 - - + +
46C LEU* 4.0 10.3 - - + -
62C VAL* 4.7 6.1 - - + -
63C VAL 3.7 3.8 - - - +
64C PRO* 4.4 4.9 - - + -
65C SER 3.1 3.3 - - - +
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Residues in contact with SER 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C VAL* 1.3 76.8 + - - +
24C ILE* 1.3 62.3 + - - +
25C TYR* 3.7 4.8 + - - -
31C LYS* 3.1 37.7 + - - +
32C LEU 3.7 3.8 - - - -
33C GLN* 3.5 10.4 + - - +
61C THR 3.8 0.5 - - - +
62C VAL* 3.7 0.7 - - - -
63C VAL* 2.8 45.6 + - - +
65C SER* 2.6 22.0 + - - -
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Residues in contact with ILE 24 (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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22C VAL* 4.5 4.7 - - + -
23C SER* 1.3 74.3 - - - +
25C TYR* 1.3 62.6 + - - +
26C LEU* 3.6 8.0 + - + -
30C ILE 3.7 0.9 - - - +
31C LYS* 4.7 0.4 - - - -
32C LEU* 2.9 46.1 + - + +
36C ILE* 4.2 15.3 - - + -
44C ILE* 4.4 14.1 - - + -
46C LEU* 3.8 31.9 - - + -
54C VAL* 4.7 6.7 - - + -
59C ILE* 3.6 46.2 - - + -
61C THR 3.6 3.4 - - - +
62C VAL* 4.5 14.1 - - + -
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Residues in contact with TYR 25 (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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23C SER 4.0 6.1 - - - -
24C ILE* 1.3 72.3 - - - +
26C LEU* 1.3 63.5 + - - +
29C GLY* 4.9 8.5 - - - +
30C ILE 3.5 4.3 - - - +
31C LYS* 2.9 48.8 + - + +
59C ILE* 3.8 3.8 - - - +
60C SER* 2.9 32.3 + - - +
61C THR* 3.0 36.0 + - - +
63C VAL* 4.0 18.3 - - + +
52G GLN* 5.9 1.1 - - - -
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Residues in contact with LEU 26 (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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60B SER* 3.9 27.1 - - - +
61B THR* 4.9 1.8 - - + -
24C ILE* 4.3 3.1 - - + +
25C TYR* 1.3 82.7 - - - +
27C VAL* 1.3 64.0 + - - +
28C ASN* 3.1 30.5 + - - +
29C GLY* 3.2 11.7 + - - -
30C ILE* 2.8 28.2 + - + +
32C LEU* 4.1 30.5 - - + -
54C VAL* 4.1 17.5 - - + -
58C ALA* 3.2 19.3 - - + +
59C ILE* 4.2 4.3 - - + -
60C SER* 3.5 7.7 + - - -
28G ASN* 4.3 3.3 + - - -
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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