Contacts of the strand formed by residues 21 - 26 (chain C) in PDB entry 5D0A
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 LYS 21 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LYS* 4.7 4.5 - - - +
19C VAL* 3.4 5.8 - - - +
20C ASP* 1.3 80.6 - - - +
22C ILE* 1.3 67.2 + - - +
73C ILE* 3.4 4.0 - - - -
74C ALA* 2.9 42.8 + - + -
148C GLY 3.9 13.2 + - - -
149C ILE* 3.1 40.7 + - + +
160C THR* 4.6 4.9 - - + -
161C PRO* 3.7 10.5 - - - +
162C GLU* 3.0 42.6 + - - +
163C TYR* 4.4 9.2 - - + -
184C ILE* 4.8 3.8 - - - +
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Residues in contact with ILE 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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10C LEU* 4.3 10.3 - - + -
11C ILE* 3.9 38.0 - - + +
14C ALA* 3.7 26.2 - - + -
15C LYS* 4.8 11.8 - - + +
19C VAL* 4.5 6.7 - - + -
21C LYS* 1.3 83.0 - - - +
23C GLY* 1.3 60.6 + - - +
24C PHE* 4.1 16.9 - - + -
71C VAL* 3.6 26.2 - - + -
72C ALA 3.3 11.0 - - - +
73C ILE* 4.3 7.2 - - + -
116C LEU* 4.6 1.8 - - + -
149C ILE* 3.7 5.5 - - - +
181C ASP* 4.5 2.3 - - - +
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Residues in contact with GLY 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 1.3 76.5 - - - +
24C PHE* 1.3 71.6 + - - -
71C VAL* 3.7 3.8 - - - +
72C ALA 3.0 31.3 + - - +
147C ALA* 3.5 20.4 - - - -
148C GLY 5.7 0.2 - - - -
149C ILE* 3.7 4.4 - - - +
181C ASP* 3.4 11.0 - - - -
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Residues in contact with PHE 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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7C LYS* 3.5 32.5 - - + +
10C LEU* 3.7 31.9 - - + -
11C ILE* 3.7 28.5 - - + -
22C ILE* 4.1 14.6 - - + -
23C GLY* 1.3 82.6 - - - -
25C THR* 1.3 61.0 + - - +
69C SER* 5.7 0.2 - - - -
70C ILE 3.7 3.6 - - - -
71C VAL* 3.8 11.0 - - + -
146C ARG 4.1 0.5 - - - +
147C ALA* 3.4 14.0 - - - +
178C PHE* 3.7 38.4 - + + -
179C GLU 3.5 19.3 - - - +
180C PRO* 4.0 1.3 - - + +
181C ASP* 2.8 37.4 + - - +
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Residues in contact with THR 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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24C PHE* 1.3 75.6 - - - +
26C THR* 1.3 73.7 + - - +
30C PHE* 5.0 1.6 - - + -
69C SER* 3.3 9.7 - - - -
70C ILE* 2.9 49.3 + - + +
143C VAL* 4.3 11.7 - - + +
146C ARG* 2.9 51.0 + - + +
147C ALA* 4.0 8.3 - - + -
178C PHE 5.2 2.0 - - - +
180C PRO* 3.9 12.0 - - - +
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Residues in contact with THR 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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25C THR* 1.3 89.0 + - - +
27C ALA* 1.3 59.8 + - - +
28C ASP* 3.2 36.9 + - - +
68C LYS 3.8 9.6 - - - +
69C SER* 3.9 3.1 - - - -
70C ILE* 3.6 6.2 - - - +
146C ARG* 3.1 21.7 + - - -
178C PHE 5.6 2.5 - - - +
180C PRO* 3.9 26.9 - - + -
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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