Contacts of the strand formed by residues 21 - 26 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LYS* 4.5 6.1 - - - +
19A VAL* 3.4 5.0 - - - +
20A ASP* 1.3 81.2 - - - +
22A ILE* 1.3 67.0 + - - +
73A ILE* 3.3 3.6 - - - -
74A ALA* 2.8 43.3 + - + -
148A GLY 3.8 14.5 + - - -
149A ILE* 2.9 39.5 + - + +
160A THR* 4.6 6.1 - - + -
161A PRO* 3.6 14.5 - - - +
162A GLU* 3.2 38.5 + - - +
163A TYR* 4.7 6.7 - - + -
184A ILE* 4.7 3.8 - - - +
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Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 4.3 11.4 - - + -
11A ILE* 4.1 27.9 - - + +
14A ALA* 3.7 25.1 - - + -
15A LYS* 4.2 19.4 - - - +
19A VAL* 4.5 6.3 - - + -
21A LYS* 1.3 82.9 - - - +
23A GLY* 1.3 61.6 + - - +
24A PHE* 4.1 17.4 - - + -
71A VAL* 3.6 25.4 - - + -
72A ALA 3.2 11.4 - - - +
73A ILE* 4.3 7.4 - - + -
116A LEU* 4.6 2.0 - - + -
149A ILE* 3.7 5.1 - - - +
181A ASP* 4.5 2.4 - - - +
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Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ILE* 1.3 76.0 - - - +
24A PHE* 1.3 70.4 + - - -
71A VAL* 3.5 5.7 - - - +
72A ALA 2.8 30.6 + - - +
147A ALA* 3.4 23.6 - - - -
148A GLY 5.6 0.2 - - - -
149A ILE* 3.5 7.9 - - - +
181A ASP* 3.5 5.8 - - - -
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Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LYS* 3.5 31.9 - - + -
10A LEU* 3.8 20.9 - - + -
11A ILE* 3.7 29.2 - - + -
22A ILE* 4.1 15.0 - - + -
23A GLY* 1.3 79.9 - - - -
25A THR* 1.3 64.9 + - - +
69A SER* 5.8 0.2 - - - -
70A ILE 3.6 3.6 - - - +
71A VAL* 3.6 28.5 - - + -
146A ARG 4.1 1.0 - - - +
147A ALA* 3.4 12.6 + - - -
178A PHE* 3.8 31.0 - + + -
179A GLU 3.7 18.8 - - - +
180A PRO* 4.1 0.7 - - + -
181A ASP* 2.9 36.3 + - - +
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Residues in contact with THR 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 1.3 78.3 - - - +
26A THR* 1.3 75.5 + - - +
30A PHE* 5.1 0.2 - - + -
69A SER* 3.3 9.2 - - - -
70A ILE* 2.8 49.1 + - + +
143A VAL* 4.2 13.0 - - + +
146A ARG* 2.8 47.0 + - + +
147A ALA* 4.1 9.4 - - + -
178A PHE 5.2 1.3 - - - +
180A PRO* 4.0 12.4 - - - +
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Residues in contact with THR 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A THR* 1.3 82.0 + - - +
27A ALA* 1.3 59.0 - - - +
28A ASP* 3.2 38.5 + - - +
68A LYS 3.8 9.9 - - - +
69A SER* 3.9 2.7 - - - -
70A ILE* 3.5 11.6 - - - +
146A ARG* 3.0 23.4 + - - -
178A PHE 5.6 1.8 - - - +
180A PRO* 4.0 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