Contacts of the strand formed by residues 21 - 30 (chain D) in PDB entry 5CYP
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 GLY 21 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D GLN* 1.3 72.1 - - - +
22D PHE* 1.3 59.4 + - - -
23D GLU* 4.1 5.3 + - - +
80D ARG* 3.3 44.3 + - - +
82D LYS* 5.4 0.4 - - - -
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Residues in contact with PHE 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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20D GLN 3.4 3.1 + - - +
21D GLY* 1.3 73.2 - - - -
23D GLU* 1.3 65.4 + - - +
24D PHE* 3.9 0.9 + - - +
79D VAL* 6.4 0.4 - - + -
80D ARG 2.8 14.2 + - - +
81D MET* 3.2 10.8 - - + +
82D LYS 2.9 23.3 + - - -
270D MET* 5.1 17.4 - - + +
271D GLN* 5.8 2.9 - - - +
274D LYS* 5.0 6.1 - - - +
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Residues in contact with GLU 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 GLY 5.1 4.3 - - - +
22D PHE* 1.3 76.0 - - - +
24D PHE* 1.3 64.7 + - - +
25D ASN* 5.3 1.3 - - - +
80D ARG* 6.3 0.9 - - - +
82D LYS* 4.0 20.0 - - + +
128D ILE 4.5 2.3 - - - +
129D PRO* 3.6 13.2 - - - +
130D ASP* 2.6 62.0 + - + +
131D THR* 5.6 0.3 - - - +
134D HIS* 4.2 1.8 - - + -
270D MET* 4.9 0.5 - - - +
274D LYS* 2.8 36.1 + - - +
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Residues in contact with PHE 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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22D PHE 3.9 2.7 + - - +
23D GLU* 1.3 75.4 - - - +
25D ASN* 1.3 63.8 + - - +
26D ILE* 3.5 29.4 - - + -
81D MET* 5.8 4.7 - - + -
82D LYS 3.4 9.0 + - - +
83D LEU* 3.6 10.2 - - + +
84D THR 2.9 25.3 + - - +
134D HIS* 3.6 30.7 - - + -
135D CYS* 4.1 19.1 - - + -
265D LEU* 3.6 24.7 - - + -
266D ILE* 3.9 18.8 - - + -
270D MET* 3.9 27.4 - - + -
273D ILE* 3.9 17.5 - - + -
274D LYS* 3.8 11.2 - - + -
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Residues in contact with ASN 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 GLU* 5.3 0.9 - - - +
24D PHE* 1.3 78.3 + - - +
26D ILE* 1.3 63.6 + - - +
82D LYS 4.8 0.3 - - - +
84D THR* 3.3 31.0 + - - +
86D ILE* 4.4 9.6 - - + -
130D ASP 3.1 27.6 + - - +
131D THR* 3.2 12.7 - - - +
132D ARG 2.5 31.6 + - - +
133D VAL* 4.1 7.1 - - - -
134D HIS* 3.2 15.8 + - - +
135D CYS* 3.2 25.8 + - - +
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Residues in contact with ILE 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 PHE* 3.5 34.8 - - + -
25D ASN* 1.3 73.6 - - - +
27D MET* 1.3 64.2 + - - +
28D VAL* 5.1 3.8 - - + +
43D LEU* 4.2 19.3 - - + -
83D LEU* 3.9 17.3 - - + -
84D THR 2.8 11.5 + - - +
85D VAL* 3.2 14.0 - - + +
86D ILE* 2.9 25.8 + - - +
135D CYS* 3.3 13.0 - - + +
137D LEU* 4.0 31.9 - - + +
265D LEU* 4.7 13.5 - - + -
266D ILE* 4.1 9.6 - - + -
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Residues in contact with MET 27 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D ASN 4.2 0.2 - - - -
26D ILE* 1.3 73.9 - - - +
28D VAL* 1.3 64.5 + - - +
29D VAL* 3.7 25.6 - - + -
67D ILE* 5.3 0.2 - - + -
86D ILE* 3.6 28.9 - - + +
88D THR* 4.2 9.0 - - + -
104D ILE* 3.9 16.8 - - + -
107D PHE* 3.4 38.4 - - + -
108D ILE* 4.1 15.5 - - + -
133D VAL* 3.8 21.5 - - + -
135D CYS 3.0 8.4 + - - +
136D CYS* 3.2 9.3 - - - -
137D LEU 2.8 30.4 + - - +
158D LEU* 5.9 0.4 - - - -
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Residues in contact with VAL 28 (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 ILE* 4.2 2.8 + - + -
27D MET* 1.3 75.0 - - - +
29D VAL* 1.3 56.1 + - - +
36D LYS* 4.3 10.1 - - + +
39D LEU* 5.1 2.9 - - + -
40D ILE* 3.7 26.5 - - + -
85D VAL* 4.6 6.5 - - + -
86D ILE 3.2 12.9 + - - +
87D ASP* 3.3 25.6 - - - +
88D THR* 2.5 31.2 + - - +
137D LEU* 3.6 18.4 - - + -
139D PHE* 3.7 28.3 - - + -
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Residues in contact with VAL 29 (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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27D MET* 3.7 25.1 - - + -
28D VAL* 1.3 81.0 - - - +
30D GLY* 1.3 56.2 + - - +
36D LYS* 3.7 4.5 - - - -
88D THR* 3.7 9.6 - - - +
91D PHE* 3.5 20.2 - - + -
104D ILE* 3.9 15.5 - - + -
136D CYS* 3.8 13.5 - - - -
137D LEU 2.8 11.7 + - - +
138D TYR* 3.2 24.6 - - + -
139D PHE* 2.6 34.9 + - - -
154D PHE* 4.1 5.2 - - + -
158D LEU* 4.0 7.9 - - + -
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Residues in contact with GLY 30 (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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29D VAL* 1.3 80.7 - - - +
31D GLN* 1.3 62.0 + - - -
36D LYS* 2.5 32.8 + - - +
88D THR* 4.7 0.2 + - - -
90D GLY* 3.4 6.6 - - - -
91D PHE* 3.4 22.3 - - - -
138D TYR* 5.1 0.7 - - - -
139D PHE* 3.8 16.2 - - - -
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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