Contacts of the strand formed by residues 26 - 31 (chain C) in PDB entry 5A15
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 26 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ALA* 6.4 0.9 - - + -
67B LYS 3.8 8.1 - - - +
68B ASP* 3.4 39.0 - - + +
69B SER 4.5 1.6 - - - +
74B PHE* 3.4 47.3 - - + -
24C PRO* 3.5 15.8 - - + +
25C GLU* 1.3 79.1 - - + +
27C VAL* 1.3 64.2 + - - +
28C GLU* 3.9 1.4 + - - +
37C PHE* 4.2 9.1 - - + -
38C THR 3.3 17.7 - - - +
39C ARG* 4.2 0.9 - - + +
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Residues in contact with VAL 27 (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 PHE* 5.0 2.7 - - + -
24C PRO* 4.0 16.4 - - + +
26C VAL* 1.3 75.6 - - - +
28C GLU* 1.3 64.8 + - - +
29C LEU* 3.8 11.0 + - + +
36C TYR 3.8 0.2 - - - +
37C PHE* 3.5 5.1 - - - -
38C THR* 2.7 34.9 + - + +
40C HIS* 3.9 29.2 - - + -
43C LEU* 3.8 32.8 - - + -
55C PHE* 4.3 2.9 - - + -
73C PHE* 3.3 34.5 - - + -
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Residues in contact with GLU 28 (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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69B SER* 4.9 7.8 + - - -
24C PRO* 5.5 0.8 - - - +
26C VAL 3.9 2.6 + - - +
27C VAL* 1.3 72.8 - - - +
29C LEU* 1.3 61.9 + - - +
35C VAL* 4.0 5.8 - - + +
36C TYR 3.7 2.5 - - - -
37C PHE* 3.1 46.9 - - + -
72C ARG* 3.2 44.2 + - + +
73C PHE* 3.4 27.7 + - - -
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Residues in contact with LEU 29 (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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27C VAL* 4.2 13.9 - - + +
28C GLU* 1.3 75.0 - - - +
30C ASN* 1.3 61.5 + - - +
31C VAL* 4.0 11.9 - - + -
35C VAL* 3.3 11.1 - - - +
36C TYR* 2.6 42.9 + - + +
38C THR* 4.1 10.5 - - + -
43C LEU* 3.9 22.9 - - + -
51C LEU* 5.8 0.7 - - + -
55C PHE* 3.7 30.3 - - + -
72C ARG* 4.5 2.0 - - - -
73C PHE* 3.7 17.0 - - + +
75C ILE* 4.5 11.4 - - + -
82C PHE* 3.8 29.6 - - + -
86C LEU* 5.4 0.2 - - + -
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Residues in contact with ASN 30 (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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29C LEU* 1.3 73.4 - - - +
31C VAL* 1.3 59.8 + - - +
32C GLY 4.0 0.2 + - - -
33C GLY* 3.0 32.2 + - - -
34C GLN 3.8 2.9 - - - -
35C VAL* 4.6 4.7 - - - +
68C ASP* 3.0 39.0 + - - +
72C ARG* 4.1 13.9 - - + +
73C PHE 2.7 16.5 + - - +
74C PHE* 3.3 15.0 - - + -
75C ILE 2.9 25.1 + - - -
37D PHE* 3.9 21.6 - - - -
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Residues in contact with VAL 31 (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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29C LEU* 4.3 8.1 - - + -
30C ASN* 1.3 75.4 + - - +
32C GLY* 1.3 59.1 + - - +
33C GLY 3.0 2.5 - - - -
34C GLN* 2.8 30.2 + - - +
36C TYR* 4.0 9.0 - - + -
75C ILE* 3.6 29.4 - - + -
77C ARG* 3.6 17.9 - - + +
78C ASP 3.8 5.8 - - - +
79C GLY* 3.0 16.2 - - - -
82C PHE* 3.7 54.1 - - + -
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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