Contacts of the strand formed by residues 29 - 35 (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 SER 29 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C HIS* 4.7 2.4 + - - +
122C SER* 5.7 1.3 - - - -
138C VAL 4.1 15.0 - - - -
139C ASP* 5.4 0.7 - - - +
168C THR* 3.7 21.0 - - - +
169C ALA 4.3 0.4 - - - -
170C GLU* 2.4 33.7 + - - +
23D ASP* 3.9 6.2 - - - +
24D HIS* 3.0 31.6 + - - +
27D GLY* 3.3 2.7 - - - -
28D LEU* 1.3 80.8 + - - +
30D VAL* 1.4 67.2 + - - +
31D TRP* 4.1 0.6 - - - -
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Residues in contact with VAL 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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122C SER* 5.6 1.1 - - - +
139C ASP* 3.8 35.0 + - + +
168C THR* 2.7 34.4 + - - +
21D GLU* 3.8 32.8 - - + +
22D ALA 3.5 8.3 - - - +
23D ASP* 5.8 1.1 - - - -
29D SER* 1.4 79.1 - - - +
31D TRP* 1.4 64.4 + - - +
32D ARG* 3.6 16.2 + - - +
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Residues in contact with TRP 31 (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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14C SER 3.3 17.5 - - - -
15C HIS* 3.6 22.2 - + - -
17C TYR* 3.8 18.4 - + - -
34C LYS* 4.5 1.3 - - - -
168C THR* 5.2 3.4 - - + -
20D PHE* 3.8 3.0 - + + +
21D GLU* 3.2 5.9 - - - -
22D ALA* 2.7 49.4 + - + +
23D ASP 4.3 8.5 - - - -
24D HIS* 3.9 19.5 - + + -
29D SER* 4.1 1.4 + - - -
30D VAL* 1.4 71.9 - - - +
32D ARG* 1.4 64.5 + - - +
64D THR* 3.3 39.5 - - + -
66D SER* 4.4 5.8 - - - -
69D LEU* 3.3 26.2 - - + +
201D OTP 2.9 59.3 + - + -
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Residues in contact with ARG 32 (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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19C SER* 3.8 32.5 - - - +
34C LYS* 2.7 31.9 + - - +
139C ASP* 2.8 42.4 + - - -
140C ALA 5.6 0.2 + - - -
141C VAL* 5.7 1.0 - - - +
166C LEU* 3.8 38.2 - - - +
168C THR* 3.5 17.9 + - - +
20D PHE* 3.3 9.6 - - - +
21D GLU* 3.5 38.7 + - + -
30D VAL* 3.6 13.2 + - + +
31D TRP* 1.4 81.9 - - - +
33D GLY* 1.3 58.7 + - - +
64D THR* 3.6 6.2 - - - +
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Residues in contact with GLY 33 (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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34C LYS* 5.0 5.8 - - - -
19D SER* 3.2 7.4 - - - -
20D PHE* 3.0 42.6 + - - +
32D ARG* 1.3 77.8 - - - +
34D LYS* 1.3 62.1 + - - +
63D HIS 3.3 13.5 - - - -
64D THR* 4.5 0.4 - - - -
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Residues in contact with LYS 34 (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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31C TRP* 4.5 1.2 - - - -
32C ARG* 2.7 28.5 + - - +
33C GLY* 4.8 4.3 - - - -
63C HIS* 4.5 8.7 - - + +
64C THR 2.6 36.1 + - - +
65C GLY 4.3 0.7 - - - +
17D TYR* 3.5 40.4 - - - +
18D PRO 3.3 14.6 - - - +
19D SER* 3.5 14.4 - - - +
20D PHE* 3.4 5.2 - - - -
33D GLY* 1.3 75.9 - - - +
35D PHE* 1.3 66.6 + - - +
36D ASP* 3.8 15.7 - - - +
62D ILE* 3.5 2.9 - - - +
63D HIS* 2.8 34.0 + - - +
168D THR* 5.9 0.6 + - - -
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Residues in contact with PHE 35 (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* 3.5 15.8 - - - +
18D PRO* 3.1 34.0 + - + +
20D PHE* 3.7 22.9 - + - -
34D LYS* 1.3 77.1 - - - +
36D ASP* 1.3 65.7 + - - +
37D LYS 3.4 1.0 + - - -
38D SER* 4.7 0.3 + - - -
57D THR* 3.3 26.0 - - + -
58D ASP 3.6 17.5 - - - -
59D ILE* 3.8 22.2 - - + -
61D SER* 3.6 5.6 - - - +
62D ILE* 3.5 37.9 - - + -
79D PHE* 4.0 13.5 - + - -
201D OTP 3.4 35.7 - - + -
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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