Contacts of the helix formed by residues 16 - 27 (chain B) in PDB entry 1U5U
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 GLY 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B GLY* 2.6 26.3 + - - +
13B GLU 4.6 0.6 + - - -
14B LYS 3.7 0.6 - - - -
15B TYR* 1.3 74.1 - - - +
17B GLN* 1.3 65.9 + - - -
18B GLU* 3.2 3.6 - - - -
19B GLU 3.3 2.9 + - - -
20B LEU* 3.0 22.3 + - - +
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Residues in contact with GLN 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLY* 3.9 5.5 + - - -
16B GLY* 1.3 71.6 - - - -
18B GLU* 1.3 62.1 + - - +
20B LEU* 3.3 26.1 + - - +
21B GLU* 2.8 59.2 + - - +
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLY* 3.2 1.3 - - - -
17B GLN* 1.3 79.1 - - - +
19B GLU* 1.3 58.5 + - - +
21B GLU* 3.4 9.2 + - - +
22B LYS* 3.0 27.3 + - + +
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 4.6 2.7 - - + -
15B TYR* 3.5 42.4 + - + +
16B GLY 3.3 3.0 + - - +
18B GLU* 1.3 77.1 - - - +
20B LEU* 1.3 67.2 + - - +
22B LYS* 3.2 21.7 + - - +
23B ARG* 2.9 48.5 + - + +
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PHE* 3.5 37.0 - - + +
9B GLU* 4.8 2.7 - - + +
11B PHE* 3.8 21.3 - - + -
12B GLY* 4.2 7.0 - - - -
16B GLY 3.0 13.6 + - - +
17B GLN* 3.4 35.2 - - - +
19B GLU* 1.3 77.3 - - - +
21B GLU* 1.3 62.9 + - - +
23B ARG* 3.4 2.6 + - - +
24B ILE* 3.1 42.4 + - + +
170B PRO* 3.8 26.0 - - + -
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLN* 2.8 48.8 + - - +
18B GLU* 3.7 7.9 - - - +
20B LEU* 1.3 75.3 - - + +
22B LYS* 1.3 61.1 + - - +
24B ILE* 3.3 12.7 + - + +
25B LYS* 2.9 30.7 + - - +
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Residues in contact with LYS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLU* 3.0 16.1 + - + +
19B GLU* 3.4 30.3 + - - +
21B GLU* 1.3 76.3 - - - +
23B ARG* 1.3 63.0 + - - +
25B LYS* 3.2 19.8 + - - +
26B ASP* 2.7 64.4 + - - +
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Residues in contact with ARG 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 3.8 24.9 - - + -
19B GLU* 2.9 39.4 + - - +
20B LEU 3.8 1.6 - - - +
22B LYS* 1.3 76.0 - - - +
24B ILE* 1.3 65.8 + - - +
26B ASP* 3.1 23.2 + - - +
27B GLU* 3.0 29.6 + - - +
167B TYR 5.1 0.6 + - - -
168B LYS 2.9 30.5 + - - -
169B ASN* 3.2 25.1 - - - +
170B PRO* 3.6 24.9 - - + -
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Residues in contact with ILE 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PHE* 4.2 22.4 - - + -
20B LEU* 3.1 40.3 + - + +
21B GLU* 3.7 13.7 - - + +
23B ARG* 1.3 75.1 - - - +
25B LYS* 1.3 63.4 + - - +
27B GLU* 3.3 8.3 + - - +
28B HIS* 2.7 33.2 - - + +
170B PRO* 4.5 4.7 - - + -
171B TYR* 3.5 34.3 - - + +
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Residues in contact with LYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLU 2.9 14.2 + - - +
22B LYS* 3.4 21.0 - - - +
24B ILE* 1.3 79.5 - - - +
26B ASP* 1.3 68.0 + - - +
28B HIS* 2.9 21.1 + - + +
29B THR* 3.3 14.4 + - - +
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Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LYS* 2.7 52.3 + - - +
23B ARG* 3.2 26.5 + - - +
25B LYS* 1.3 80.3 - - - +
27B GLU* 1.3 62.1 + - + +
29B THR* 2.8 35.8 + - - +
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ARG* 3.0 17.2 + - - +
24B ILE 3.3 8.0 + - - +
26B ASP* 1.3 78.2 - - - +
28B HIS* 1.3 58.7 + - - +
29B THR 3.2 3.1 + - - -
145B TRP* 3.4 20.9 + - - -
169B ASN* 3.0 24.1 + - - +
170B PRO* 5.7 0.2 - - + -
171B TYR* 3.7 33.4 - - + -
285B THR* 4.7 2.9 + - - +
288B HIS* 2.9 47.1 + - + -
291B ILE* 4.4 5.6 - - + +
342B TYR* 4.1 8.9 + - - -
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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