Contacts of the strand formed by residues 20 - 27 (chain D) in PDB entry 3C5C
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 GLU 20 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141C TYR* 5.4 10.5 - - - +
19D LEU* 1.3 83.8 + - - +
21D VAL* 1.3 64.5 + - - +
22D ASN* 3.3 18.9 + - - +
69D HIS* 3.2 20.6 - - + +
71D ARG* 2.9 36.9 + - + +
90D TRP* 5.5 1.2 + - - -
92D HIS* 3.7 14.5 - - + -
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Residues in contact with VAL 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 4.0 6.5 - - - +
20D GLU* 1.3 76.6 - - - +
22D ASN* 1.3 63.4 + - - +
23D LEU* 3.8 26.0 - - + -
68D VAL* 3.5 28.5 - - + -
69D HIS 3.0 7.1 + - - +
70D LEU* 3.5 6.4 - - + +
71D ARG* 2.9 28.2 + - - -
92D HIS* 3.7 7.0 - - + +
180D VAL* 4.2 20.6 - - + -
183D ALA* 3.9 23.6 - - + -
184D ARG* 6.4 1.8 - - + -
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Residues in contact with ASN 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C MET* 5.2 4.0 - - - +
20D GLU* 3.3 26.7 + - - +
21D VAL* 1.3 73.9 - - - +
23D LEU* 1.3 63.1 + - - +
71D ARG* 3.5 6.0 - - - +
90D TRP* 3.0 65.4 + - + +
91D ALA* 3.5 1.6 - - - -
92D HIS* 2.7 53.3 + - - +
93D ALA 3.3 6.9 + - - -
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D VAL* 3.8 19.7 - - + -
22D ASN* 1.3 73.7 - - - +
24D ALA* 1.3 59.7 + - - +
25D ILE* 4.3 10.8 - - + -
70D LEU* 3.7 25.4 - - + -
71D ARG 2.7 13.0 + - - +
72D VAL* 3.3 5.8 - - + +
73D MET 2.8 26.2 + - - -
90D TRP* 3.4 3.5 - - - -
93D ALA* 3.4 32.3 - - + +
95D LEU* 5.1 3.4 - - + -
176D PHE* 3.8 34.3 - - + +
179D ALA* 3.7 26.2 - - + -
180D VAL* 4.5 0.7 - - + +
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Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 1.3 72.3 - - - +
25D ILE* 1.3 63.7 + - - +
26D LEU* 4.0 5.8 + - + -
73D MET* 3.6 9.2 - - + +
87D TYR* 3.9 17.3 - - + -
90D TRP* 4.2 5.8 - - + -
91D ALA* 3.8 12.0 - - + +
93D ALA 3.1 7.9 + - - -
94D PHE* 3.4 28.6 - - + +
95D LEU 3.0 24.9 + - - +
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Residues in contact with ILE 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D LEU* 4.3 4.7 - - + -
24D ALA* 1.3 84.2 - - - +
26D LEU* 1.3 56.1 + - - +
33D LYS* 3.7 23.3 - - + +
36D LEU* 6.0 1.6 - - + -
37D THR* 4.0 10.8 - - - +
72D VAL* 3.5 33.2 - - + -
73D MET 2.8 13.8 + - - +
74D ASP* 4.5 5.2 - - - -
75D THR* 2.7 34.7 + - - +
95D LEU* 3.4 36.1 - - + +
97D VAL* 3.6 28.5 - - + -
176D PHE* 4.2 4.9 - - + -
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Residues in contact with LEU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ALA* 4.4 5.2 - - + +
25D ILE* 1.3 80.2 - - - +
27D GLY* 1.3 60.2 + - - +
33D LYS* 3.3 14.6 - - - +
75D THR* 3.7 14.1 - - + +
87D TYR* 3.7 50.0 - - + +
94D PHE* 3.9 24.9 - - + -
95D LEU 2.8 12.6 + - - +
96D VAL* 4.3 10.5 - - + -
97D VAL* 2.9 24.3 + - - +
112D TYR* 4.0 21.3 - - + -
115D LEU* 5.7 0.2 - - + -
116D LEU* 4.0 20.2 - - + -
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Residues in contact with GLY 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D LEU* 1.3 79.2 - - - +
28D ARG* 1.3 69.0 + - - -
29D ARG 3.5 0.9 + - - -
33D LYS* 3.1 16.3 + - - -
75D THR* 4.8 0.9 + - - -
77D ASP* 4.9 4.3 - - - +
96D VAL* 5.0 2.0 - - - -
97D VAL 3.5 13.9 - - - -
109D SER* 5.6 1.1 - - - -
112D TYR* 3.5 34.3 + - - -
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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