Contacts of the strand formed by residues 21 - 26 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LYS* 4.7 6.5 - - - +
19B VAL* 3.5 5.2 - - - +
20B ASP* 1.3 80.3 - - - +
22B ILE* 1.3 66.3 + - - +
73B ILE* 3.3 3.3 - - - -
74B ALA* 2.8 43.5 + - + -
148B GLY 4.0 13.0 + - - -
149B ILE* 3.0 42.6 + - + +
160B THR* 4.6 7.2 - - + -
161B PRO* 3.6 13.9 - - - +
162B GLU* 3.2 39.3 + - - +
163B TYR* 4.5 8.3 - - + -
184B ILE* 4.5 3.4 - - - +
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 4.3 11.9 - - + -
11B ILE* 4.0 34.8 - - + -
14B ALA* 3.7 25.8 - - + -
15B LYS* 4.7 11.8 - - + +
19B VAL* 4.2 8.7 - - + -
21B LYS* 1.3 79.8 - - - +
23B GLY* 1.3 61.3 + - - +
24B PHE* 4.1 17.4 - - + -
71B VAL* 3.6 26.2 - - + -
72B ALA 3.2 9.4 - - - +
73B ILE* 4.2 7.2 - - + -
116B LEU* 4.8 2.2 - - + -
149B ILE* 3.7 5.8 - - - +
181B ASP* 4.6 2.6 - - - +
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Residues in contact with GLY 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ILE* 1.3 76.2 - - - +
24B PHE* 1.3 68.8 + - - -
71B VAL* 3.4 7.6 - - - +
72B ALA 2.7 33.5 + - - +
147B ALA* 3.5 22.4 - - - -
148B GLY 5.7 0.2 - - - -
149B ILE* 3.6 7.6 - - - +
181B ASP* 3.6 4.7 - - - -
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Residues in contact with PHE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LYS* 3.6 24.0 - - + -
10B LEU* 3.8 30.3 - - + -
11B ILE* 3.7 37.9 - - + -
22B ILE* 4.1 15.3 - - + -
23B GLY* 1.3 79.4 - - - -
25B THR* 1.3 62.3 + - - +
69B SER* 5.9 0.2 - - - -
70B ILE 3.7 2.5 - - - -
71B VAL* 3.8 14.8 - - + -
146B ARG 4.2 0.5 - - - +
147B ALA* 3.4 13.2 - - - +
178B PHE* 3.8 32.3 - + + -
179B GLU 3.6 18.4 - - - +
180B PRO* 3.9 1.3 - - + -
181B ASP* 2.7 43.4 + - - +
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Residues in contact with THR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B PHE* 1.3 78.2 - - - +
26B THR* 1.3 71.5 + - - +
30B PHE* 5.1 1.1 - - + -
69B SER* 3.2 9.0 - - - -
70B ILE* 2.6 59.7 + - + +
143B VAL* 4.3 12.1 - - + +
146B ARG* 2.9 45.6 + - + +
147B ALA* 3.9 11.0 - - + -
178B PHE* 5.3 1.7 - - - +
180B PRO* 3.7 11.7 - - - +
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Residues in contact with THR 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B THR* 1.3 87.4 + - - +
27B ALA* 1.3 59.5 - - - +
28B ASP* 3.0 38.9 + - - +
68B LYS 3.8 10.3 - - - +
69B SER* 3.9 2.9 - - - -
70B ILE* 3.6 6.2 - - - +
146B ARG* 2.9 22.9 + - - -
178B PHE 5.7 1.6 - - - +
180B PRO* 3.9 26.5 - - + -
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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