Contacts of the strand formed by residues 26 - 33 (chain D) in PDB entry 2UZC
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 MET 26 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B ASP* 5.8 2.5 - - - +
20D GLY* 4.2 7.4 - - - -
21D GLY* 3.0 28.3 + - - +
22D LYS* 3.9 1.0 + - - -
24D PHE* 3.1 21.7 - - + +
25D ASN* 1.3 83.3 - - - +
27D PRO* 1.3 88.8 - - + +
28D LEU 3.6 0.2 + - - -
59D GLN 5.4 3.3 - - - +
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Residues in contact with PRO 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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19D GLN 3.6 0.9 - - - +
20D GLY* 3.5 8.0 - - - -
21D GLY 3.3 7.3 + - - -
25D ASN 4.9 0.4 - - - +
26D MET* 1.3 104.8 - - + +
28D LEU* 1.3 62.0 + - - +
29D THR* 3.6 10.1 + - + +
49D VAL* 3.9 35.2 - - + -
59D GLN* 5.8 9.2 - - + +
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Residues in contact with LEU 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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18D LEU* 4.5 12.6 - - + -
19D GLN 3.4 5.4 - - - +
20D GLY 3.7 9.2 - - - +
21D GLY* 3.6 24.9 - - - -
26D MET 3.6 0.4 + - - -
27D PRO* 1.3 72.5 - - - +
29D THR* 1.3 59.4 + - - +
49D VAL* 3.4 7.8 - - - +
50D VAL* 2.8 44.9 + - + +
53D ILE* 4.8 2.9 - - + -
58D ALA* 3.8 36.1 - - + +
59D GLN* 6.2 1.8 - - - +
61D MET* 4.4 6.1 - - + +
63D HIS* 4.2 17.7 - - - +
66D ALA* 3.6 27.1 - - + -
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Residues in contact with THR 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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18D LEU* 3.3 10.2 - - - -
19D GLN* 2.9 62.7 + - - +
27D PRO* 4.2 14.9 + - + +
28D LEU* 1.3 79.4 - - - +
30D ILE* 1.3 64.8 + - - +
31D SER 3.2 0.3 + - - -
47D GLY* 3.8 20.4 - - - +
48D ASP 3.2 5.6 - - - -
49D VAL* 3.8 17.5 - - + -
50D VAL 4.6 0.2 - - - +
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Residues in contact with ILE 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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16D PHE* 3.6 29.4 - - + -
17D ARG 3.5 3.1 - - - +
18D LEU* 3.9 10.1 - - + -
19D GLN* 5.0 1.2 + - - -
29D THR* 1.3 71.0 + - - +
31D SER* 1.3 60.5 + - - +
32D SER 3.6 20.0 - - - +
33D LEU* 4.0 17.0 - - + -
44D VAL* 3.6 23.1 - - + -
45D ARG 3.7 11.9 - - - +
46D ILE* 3.6 14.6 - - - +
47D GLY* 2.8 28.6 + - - -
48D ASP 2.9 18.5 + - - +
50D VAL* 4.1 10.5 - - + -
79D MET* 5.0 3.4 - - + -
81D LEU* 3.9 11.4 - - + -
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Residues in contact with SER 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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17D ARG* 2.8 28.2 + - - +
18D LEU 3.3 13.3 + - - -
19D GLN* 3.9 35.2 - - - +
29D THR 3.2 0.6 + - - -
30D ILE* 1.3 74.0 - - - +
32D SER* 1.3 61.0 + - - +
46D ILE* 4.1 15.5 - - - +
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Residues in contact with SER 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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16D PHE* 3.3 8.0 - - - +
17D ARG* 3.1 62.7 + - - -
30D ILE* 3.6 6.4 - - - +
31D SER* 1.3 80.0 + - - +
33D LEU* 1.3 66.9 + - - +
46D ILE* 4.0 7.4 - - - -
1090D EDO 3.3 19.1 - - - -
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Residues in contact with LEU 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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15D GLY 3.4 13.5 - - - +
16D PHE* 3.9 6.1 - - + -
30D ILE* 4.0 9.9 - - + -
32D SER* 1.3 83.8 + - - +
34D LYS* 1.3 67.0 + - - +
35D ASP* 3.5 2.3 + - - -
39D ALA* 3.8 21.8 - - + -
40D ALA* 4.1 15.5 - - + +
44D VAL* 3.3 29.6 - - + +
45D ARG* 4.1 0.7 - - - -
46D ILE* 3.9 35.0 - - + +
1090D EDO 3.7 8.1 - - - -
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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