Contacts of the strand formed by residues 30 - 34 (chain Z) in PDB entry 1UL1
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 LYS 30 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Z GLY 4.1 3.1 + - - +
29Z ARG* 1.3 72.1 - - - +
31Z VAL* 1.3 70.6 + - - +
80Z LYS* 3.4 22.2 - - + +
82Z VAL* 5.4 0.4 - - + -
171Z LYS* 3.9 27.8 + - - +
172Z VAL* 3.1 19.3 - - + -
173Z TYR* 3.1 25.9 + - - +
296Z LEU* 3.5 34.3 - - + +
298Z TRP* 4.7 7.4 - - + -
342Z ASP* 5.0 1.6 + - - -
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Residues in contact with VAL 31 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Z TYR* 5.9 1.8 - - + -
29Z ARG* 4.3 6.5 - - + +
30Z LYS* 1.3 84.8 - - - +
32Z ALA* 1.3 58.1 + - - +
33Z ILE* 4.3 9.2 - - + -
79Z ILE* 3.6 27.4 - - + -
80Z LYS 3.2 3.0 + - - -
81Z PRO* 3.7 16.4 - - + -
82Z VAL* 2.7 34.8 + - - +
172Z VAL* 3.0 12.2 - - - +
173Z TYR* 4.9 1.6 - - + -
174Z ALA 3.5 6.5 - - - +
176Z ALA* 4.8 2.7 - - + -
191Z MET* 3.7 35.0 - - + -
194Z LEU* 4.4 10.1 - - + -
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Residues in contact with ALA 32 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Z VAL* 1.3 70.7 - - - +
33Z ILE* 1.3 62.9 + - - +
82Z VAL* 3.4 10.1 - - + +
84Z VAL* 4.7 0.2 - - + -
163Z CYS* 3.6 40.4 - - + +
166Z LEU* 4.1 17.5 - - + -
172Z VAL* 3.6 11.3 - - + +
174Z ALA 3.1 9.6 + - - +
175Z ALA* 3.4 4.0 - - - -
176Z ALA 2.9 23.1 + - - +
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Residues in contact with ILE 33 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Z VAL* 4.3 8.7 - - + -
32Z ALA* 1.3 74.2 - - - +
34Z ASP* 1.3 59.6 + - - +
38Z SER* 3.3 22.2 - - - +
74Z MET* 3.4 35.9 - - + -
81Z PRO* 3.5 15.3 - - + -
82Z VAL 2.9 6.6 + - - +
83Z TYR* 3.4 37.5 - - + -
84Z VAL* 2.6 37.2 + - - +
163Z CYS* 3.9 2.2 - - - -
176Z ALA* 3.6 24.7 - - + +
194Z LEU* 4.4 3.4 - - + -
195Z THR* 3.9 7.4 - - + -
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Residues in contact with ASP 34 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Z ALA 4.1 0.4 + - - -
33Z ILE* 1.3 72.4 - - - +
35Z ALA* 1.3 66.8 + - - +
36Z SER* 3.3 0.7 + - - -
37Z MET* 3.1 35.9 + - + +
38Z SER* 2.8 25.4 + - - +
84Z VAL 3.8 2.9 - - - -
86Z ASP* 3.3 20.3 - - - +
159Z ALA* 3.8 8.6 - - - +
160Z GLU* 3.8 21.0 + - - +
163Z CYS* 4.3 4.9 - - - -
176Z ALA 3.1 5.7 + - - +
177Z THR* 2.7 28.9 + - - +
179Z ASP* 5.4 0.3 - - - +
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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
------------------------------------------------------------
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