Contacts of the strand formed by residues 16 - 21 (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 PHE 16 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B LEU* 2.9 48.7 + - + +
8D LEU* 4.9 0.4 - - + -
14D TRP* 3.5 28.5 - + + -
15D GLY* 1.3 79.6 - - - +
17D ARG* 1.3 65.5 + - - +
18D LEU* 3.8 24.7 - - + -
30D ILE* 3.6 23.8 - - + -
32D SER 3.3 13.2 - - - +
33D LEU* 3.9 12.1 - - + -
39D ALA* 3.9 14.8 - - + -
70D ILE* 3.7 21.3 - - + -
77D LEU* 3.8 13.0 - - + -
79D MET* 3.7 22.9 - - + -
1090D EDO 3.6 8.8 + - - -
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Residues in contact with ARG 17 (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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45B ARG* 3.2 44.2 - - - +
85B SER* 3.5 33.7 - - - +
86B ASP* 2.8 46.6 + - - +
87B LEU* 4.9 1.1 - - - -
16D PHE* 1.3 77.6 - - - +
18D LEU* 1.3 66.1 + - - +
30D ILE* 3.5 6.9 - - - -
31D SER* 2.8 35.7 + - - +
32D SER* 3.1 37.7 + - - +
1090D EDO 3.6 11.1 - - - +
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Residues in contact with LEU 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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85B SER 5.1 1.2 + - - -
87B LEU* 4.2 10.1 - - + +
16D PHE* 3.8 19.3 - - + -
17D ARG* 1.3 76.7 - - - +
19D GLN* 1.3 62.0 + - - +
28D LEU* 4.5 11.2 - - + -
29D THR 3.3 14.1 - - - +
30D ILE* 3.9 7.0 - - + -
31D SER* 3.3 10.9 + - - -
50D VAL* 3.6 30.3 - - + -
53D ILE* 5.3 0.7 - - + -
63D HIS* 3.1 29.0 + - + +
66D ALA* 4.2 20.0 - - + -
67D GLN* 5.0 2.9 - - + +
70D ILE* 3.8 26.5 - - + -
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Residues in contact with GLN 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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18D LEU* 1.3 74.9 - - - +
20D GLY* 1.3 65.2 + - - +
27D PRO 3.6 0.3 - - - +
28D LEU* 3.4 4.2 - - - +
29D THR* 2.9 60.7 + - - +
30D ILE 5.0 1.2 + - - -
31D SER* 3.9 22.4 - - - +
47D GLY* 6.1 1.2 - - - -
63D HIS* 3.7 7.4 - - - -
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Residues in contact with GLY 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 GLN* 1.3 80.5 - - - +
21D GLY* 1.3 61.5 + - - -
24D PHE* 3.5 18.4 - - - -
26D MET* 4.2 11.9 - - - -
27D PRO 3.5 8.1 - - - -
28D LEU* 3.7 2.0 - - - +
63D HIS* 2.9 31.4 + - - +
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Residues in contact with GLY 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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20D GLY* 1.3 73.5 - - - -
22D LYS* 1.3 60.3 + - - -
23D ASP* 3.3 6.7 - - - -
24D PHE* 2.9 19.2 + - - -
25D ASN 3.1 8.1 + - - -
26D MET 3.0 24.4 + - - +
27D PRO 3.3 4.0 + - - -
28D LEU* 3.6 19.6 - - - +
61D MET 3.8 4.5 - - - -
63D HIS 4.3 1.1 - - - -
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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