Contacts of the strand formed by residues 189 - 192 (chain Y) 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 VAL 189 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167Y VAL* 4.0 0.2 - - - +
173Y TYR* 3.7 28.3 - - + +
174Y ALA* 3.3 24.0 - - + -
175Y ALA 3.0 21.0 + - - -
187Y SER* 3.1 11.8 + - - -
188Y PRO* 1.3 95.1 - - + +
190Y LEU* 1.3 61.9 + - - +
206Y GLU* 3.2 31.9 - - + +
207Y PHE 3.3 7.2 - - - +
208Y HIS* 3.9 12.6 - - + +
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Residues in contact with LEU 190 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175Y ALA 2.9 28.3 - - - +
177Y THR* 3.7 28.3 - - - +
179Y ASP 4.1 5.4 - - - +
180Y MET* 3.9 42.4 - - - -
182Y CYS* 4.4 15.5 - - + -
183Y LEU* 4.0 25.7 - - + +
187Y SER* 5.1 0.2 - - - +
188Y PRO 4.4 0.2 - - - -
189Y VAL* 1.3 73.7 - - - +
191Y MET* 1.3 68.7 + - - +
192Y ARG* 4.2 10.5 - - + -
205Y GLN 3.4 1.7 - - - +
206Y GLU* 3.4 3.6 - - - -
207Y PHE* 2.9 36.3 + - + +
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Residues in contact with MET 191 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Y TYR* 3.5 37.9 - - + -
31Y VAL* 3.6 27.4 - - + -
79Y ILE* 5.1 0.9 - - + -
173Y TYR* 4.4 1.6 - - - -
174Y ALA* 3.6 19.7 - - + -
175Y ALA 2.7 12.2 + - - +
176Y ALA* 3.2 27.6 - - + +
177Y THR 3.5 4.2 + - - -
190Y LEU* 1.3 71.7 - - - +
192Y ARG* 1.3 62.6 + - - +
193Y HIS 4.2 0.5 + - - -
194Y LEU* 3.7 36.0 + - + -
204Y ILE* 3.6 21.1 - - + -
205Y GLN 3.5 4.0 - - - -
206Y GLU* 3.8 12.8 - - + -
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Residues in contact with ARG 192 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Y ALA* 3.6 21.8 - - - +
177Y THR 3.6 14.8 - - - +
178Y GLU* 2.8 36.9 + - - +
180Y MET* 4.0 25.8 - - - +
190Y LEU* 4.2 13.9 - - + -
191Y MET* 1.3 73.9 - - - +
193Y HIS* 1.3 86.4 + - + +
194Y LEU 3.3 5.7 + - - -
204Y ILE* 3.3 5.2 - - - +
205Y GLN* 2.8 63.5 + - + +
207Y PHE* 3.8 6.0 - - + -
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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