Contacts of the strand formed by residues 17 - 24 (chain D) in PDB entry 5IXG
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 TYR 17 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C TRP* 3.7 17.2 - + - -
65C GLY* 3.5 32.9 + - - -
66C SER* 3.6 9.2 + - - -
13D PRO 3.6 8.9 + - - -
14D SER* 2.8 39.6 + - - -
15D HIS* 3.9 4.3 - - - -
16D THR* 1.4 83.8 - - - +
18D PRO* 1.3 69.0 - - + +
19D SER* 3.7 2.7 + - - +
34D LYS* 3.5 31.9 - - - -
35D PHE 3.5 16.8 - - - +
36D ASP* 3.4 20.9 - - - -
166D LEU 4.0 0.7 - - - +
168D THR* 2.8 43.7 + - + +
201D OTP 4.4 3.6 - - - -
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Residues in contact with PRO 18 (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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17D TYR* 1.3 83.3 - - - +
19D SER* 1.3 62.2 + - - +
34D LYS* 3.3 2.2 - - - +
35D PHE* 3.1 42.8 + - + +
38D SER* 3.6 17.3 - - - +
57D THR* 3.9 24.9 - - + +
165D LEU* 5.1 0.9 - - + -
167D ILE* 3.6 27.1 - - + -
201D OTP 3.9 28.9 - - + -
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Residues in contact with SER 19 (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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32C ARG* 3.8 34.6 - - - +
17D TYR* 3.7 3.0 + - - +
18D PRO* 1.3 76.2 - - - +
20D PHE* 1.3 63.3 - - - +
33D GLY 3.2 12.3 - - - -
34D LYS* 3.5 18.2 - - - +
165D LEU* 3.3 9.5 - - - +
166D LEU* 2.8 42.4 + - - -
168D THR* 5.3 1.0 + - - -
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Residues in contact with PHE 20 (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 SER* 1.3 79.5 - - - +
21D GLU* 1.3 71.7 + - - +
31D TRP* 4.3 4.7 - + + -
32D ARG* 3.3 11.2 - - - +
33D GLY* 3.0 57.6 + - - +
34D LYS* 3.4 7.0 - - - -
35D PHE* 3.7 32.5 - + - -
62D ILE* 3.8 23.6 - - + -
64D THR* 4.4 6.5 - - + -
163D THR* 4.5 2.9 - - + -
164D LYS 3.1 11.9 - - - +
165D LEU* 4.4 4.0 - - + -
166D LEU* 4.4 3.0 - - - +
201D OTP 3.9 52.3 - - + -
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Residues in contact with GLU 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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166C LEU* 4.4 7.3 - - - +
20D PHE* 1.3 79.3 - - - +
22D ALA* 1.3 61.6 + - - +
30D VAL* 3.8 13.1 - - + +
31D TRP 3.2 5.6 - - - -
32D ARG* 3.5 37.6 + - + +
162D LYS 4.2 0.9 - - - +
163D THR* 3.5 7.5 - - - +
164D LYS* 2.9 72.7 + - + +
166D LEU* 3.9 24.9 - - + +
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Residues in contact with ALA 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 PHE* 4.8 0.2 - - + -
21D GLU* 1.3 76.7 - - - +
23D ASP* 1.3 63.6 + - - +
30D VAL* 3.5 6.3 - - - +
31D TRP* 2.7 43.7 + - + +
146D ARG* 5.3 4.9 - - - +
162D LYS 4.4 6.5 - - - -
163D THR* 4.8 8.5 - - + +
201D OTP 3.6 39.9 - - + -
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Residues in contact with ASP 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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22D ALA* 1.3 78.6 - - - +
24D HIS* 1.3 61.4 + - - +
26D GLY* 2.8 24.3 + - - -
27D GLY* 2.8 28.3 + - - -
29D SER 3.9 5.2 - - - +
30D VAL* 5.0 1.8 - - - +
31D TRP* 4.3 6.5 - - - -
146D ARG* 5.0 3.1 + - - -
159D PHE* 3.5 19.4 - - - -
160D LYS* 2.8 62.1 + - + +
162D LYS 4.4 7.0 + - - +
201D OTP 5.1 2.3 - - - +
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Residues in contact with HIS 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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15C HIS* 3.3 21.6 + + - -
128C HIS* 5.2 3.6 - - - -
170C GLU* 2.6 37.1 + - - -
23D ASP* 1.3 73.7 - - - +
25D PHE* 1.3 97.7 + + - +
26D GLY 3.3 1.7 + - - -
27D GLY 3.6 0.5 + - - -
28D LEU* 3.0 23.0 + - + +
29D SER* 3.0 23.4 + - - +
31D TRP* 3.9 13.0 - - + +
159D PHE* 3.6 20.2 - + - -
201D OTP 3.2 29.1 + - - -
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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