Contacts of the strand formed by residues 185 - 188 (chain C) in PDB entry 1URP
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 ALA 185 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C ILE* 3.6 33.2 - - + -
120C ALA* 4.4 2.9 - - + -
125C LYS 3.4 2.2 + - - -
126C VAL* 3.2 11.5 - - + +
127C ILE 2.9 24.3 + - - -
183C VAL* 3.5 4.3 - - - +
184C GLN* 1.3 83.3 - - + +
186C VAL* 1.3 66.0 + - - +
209C VAL* 4.0 1.3 - - - -
210C MET* 3.3 25.6 - - + +
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Residues in contact with VAL 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ILE* 4.1 6.0 - - - +
127C ILE* 3.2 12.3 - - + +
129C LEU* 4.3 15.9 - - + -
173C MET* 3.7 40.8 - - + -
183C VAL* 4.4 4.3 - - + -
185C ALA* 1.3 79.7 - - - +
187C PHE* 1.3 72.3 + - - +
188C ALA* 4.3 2.2 - - + +
197C ALA* 4.6 2.2 - - + -
201C LEU* 4.5 6.7 - - + -
209C VAL* 4.1 14.6 - - + -
210C MET 2.8 11.3 + - - +
211C VAL* 3.5 14.9 - - + -
212C VAL* 2.9 28.1 + - - +
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Residues in contact with PHE 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C GLY* 4.2 15.5 - - - -
112C ALA* 3.5 25.4 - - + -
116C ILE* 4.0 7.4 - - + +
126C VAL* 5.8 0.2 - - - +
127C ILE 2.9 8.6 + - - +
128C GLU* 3.2 29.8 - - + +
129C LEU 2.8 23.2 + - - -
141C ARG* 4.2 8.1 - - + -
145C PHE* 3.5 50.4 - + + -
186C VAL* 1.3 74.8 - - - +
188C ALA* 1.3 75.7 + - - +
189C GLN* 3.8 20.2 - - + -
212C VAL* 3.5 10.3 - - + -
213C GLY 3.9 9.4 - - - -
214C PHE* 4.3 11.9 - + - -
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Residues in contact with ALA 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C LEU* 3.6 14.6 - - + -
186C VAL* 4.0 4.8 - - + -
187C PHE* 1.3 87.3 - - - +
189C GLN* 1.3 59.7 + - - +
190C ASN 3.0 9.3 + - - +
193C MET* 3.9 9.6 - - + +
194C ALA* 3.4 43.1 - - + +
211C VAL* 4.9 0.2 - - + -
212C VAL 2.9 12.2 + - - +
213C GLY 3.6 7.8 - - - -
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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