Contacts of the strand formed by residues 29 - 35 (chain C) 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 SER 29 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C ASP* 3.9 6.1 - - - +
24C HIS* 3.0 31.5 + - - +
27C GLY* 3.4 2.5 - - - -
28C LEU* 1.3 80.0 - - - +
30C VAL* 1.4 69.0 + - - +
15D HIS* 4.7 2.9 - - - -
122D SER* 5.7 2.0 - - - -
138D VAL 4.2 14.6 - - - -
139D ASP* 5.7 0.2 - - - -
168D THR* 3.8 20.8 - - - +
169D ALA 4.3 0.7 - - - -
170D GLU* 2.4 34.7 + - - +
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Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLU* 3.8 25.1 - - + +
22C ALA 3.5 8.5 - - - +
23C ASP* 5.7 1.8 - - - +
29C SER* 1.4 81.3 - - - +
31C TRP* 1.4 72.7 + - - +
32C ARG* 3.6 15.6 + - - +
139D ASP* 3.8 35.4 + - + +
168D THR* 2.6 35.0 + - - +
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Residues in contact with TRP 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C PHE* 3.8 2.2 - - - +
21C GLU* 3.2 5.5 - - - -
22C ALA* 2.7 44.9 + - + +
23C ASP 4.4 4.3 - - - -
24C HIS* 4.0 18.3 - - + -
29C SER* 4.2 1.2 - - - -
30C VAL* 1.4 70.4 - - - +
32C ARG* 1.3 64.1 + - - +
64C THR* 3.3 35.4 - - + -
66C SER* 4.1 7.6 - - - -
69C LEU* 3.4 26.9 - - + -
201C OTP 3.1 60.8 + - + +
14D SER 3.3 17.9 - - - -
15D HIS* 3.5 22.8 + + - -
17D TYR* 3.7 20.0 - + - -
34D LYS* 4.5 0.7 - - - -
168D THR* 5.2 2.9 - - + -
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Residues in contact with ARG 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C PHE* 3.3 8.7 - - - +
21C GLU* 3.2 40.1 + - + -
30C VAL* 3.6 14.1 + - + +
31C TRP* 1.3 78.8 - - - +
33C GLY* 1.3 57.1 + - - +
64C THR* 3.4 6.9 - - - +
19D SER* 3.8 34.1 - - - +
34D LYS* 2.7 33.4 + - - +
139D ASP* 2.7 41.8 + - - -
141D VAL* 6.1 1.2 - - - +
166D LEU* 3.7 37.4 - - - +
168D THR* 3.4 19.5 + - - +
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Residues in contact with GLY 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C SER* 3.2 8.5 - - - -
20C PHE* 2.8 42.5 + - - +
32C ARG* 1.3 76.1 - - - +
34C LYS* 1.3 61.7 + - - +
63C HIS 3.2 15.5 - - - -
64C THR* 4.4 0.2 - - - -
34D LYS* 4.8 6.5 - - - -
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Residues in contact with LYS 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C TYR* 3.4 39.0 - - - +
18C PRO 3.4 14.4 - - - +
19C SER* 3.6 13.0 + - - +
20C PHE* 3.4 4.1 - - - -
33C GLY* 1.3 76.4 - - - +
35C PHE* 1.3 63.2 + - - +
36C ASP* 3.7 18.4 - - - +
62C ILE* 3.6 3.1 - - - +
63C HIS* 2.8 35.6 + - - +
168C THR* 5.7 1.2 + - - -
31D TRP* 4.4 1.4 - - - -
32D ARG* 2.7 29.2 + - - +
33D GLY* 5.0 3.4 - - - -
63D HIS* 4.5 9.9 - - + +
64D THR 2.7 32.8 + - - +
65D GLY* 4.2 0.4 - - - +
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Residues in contact with PHE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C TYR* 3.5 15.4 - - - +
18C PRO* 3.1 32.2 + - + +
20C PHE* 3.8 19.7 - + - -
34C LYS* 1.3 76.9 - - - +
36C ASP* 1.3 65.5 + - - +
37C LYS 3.6 0.3 + - - -
38C SER* 4.7 0.2 + - - -
57C THR* 3.4 26.0 - - + -
58C ASP 3.6 17.7 - - - -
59C ILE* 3.8 20.6 - - + -
61C SER* 3.7 5.2 - - - +
62C ILE* 3.5 39.0 - - + -
79C PHE* 4.0 7.6 - + - -
201C OTP 3.5 46.2 - - + -
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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