Contacts of the strand formed by residues 185 - 188 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D ILE* 3.6 33.2 - - + -
120D ALA* 4.5 2.9 - - + -
125D LYS 3.4 2.8 + - - +
126D VAL* 3.2 11.3 - - + +
127D ILE 2.9 24.4 + - - -
183D VAL* 3.5 4.0 - - - +
184D GLN* 1.3 82.9 - - - +
186D VAL* 1.3 65.6 + - - +
209D VAL* 4.0 1.3 - - - -
210D MET* 3.3 25.4 - - + +
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Residues in contact with VAL 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D ILE* 4.1 5.5 - - - +
126D VAL* 5.9 0.2 - - - -
127D ILE* 3.2 11.9 - - + +
129D LEU* 4.3 15.0 - - + -
173D MET* 3.7 40.8 - - + -
183D VAL* 4.3 4.0 - - + -
185D ALA* 1.3 80.3 - - - +
187D PHE* 1.3 70.9 - - - +
188D ALA* 4.3 3.4 - - + +
197D ALA* 4.6 2.2 - - + -
201D LEU* 4.5 6.3 - - + -
209D VAL* 4.1 15.0 - - + -
210D MET 2.8 11.0 + - - +
211D VAL* 3.5 15.2 - - + -
212D VAL* 3.0 27.9 + - - +
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Residues in contact with PHE 187 (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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109D GLY* 4.1 16.2 - - - -
112D ALA* 3.5 26.0 - - + -
116D ILE* 4.0 7.2 - - + -
126D VAL* 5.8 0.2 - - - +
127D ILE 3.0 8.4 + - - +
128D GLU* 3.3 33.6 - - + +
129D LEU 2.8 23.3 + - - -
141D ARG* 4.1 7.6 - - + -
145D PHE* 3.5 46.4 - + + -
186D VAL* 1.3 73.9 - - - +
188D ALA* 1.3 75.3 + - - +
189D GLN* 3.8 20.0 - - + -
212D VAL* 3.6 10.3 - - + -
213D GLY 3.9 9.2 - - - -
214D PHE* 4.2 11.7 - + - -
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Residues in contact with ALA 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D LEU* 3.6 15.3 - - + -
186D VAL* 4.0 5.1 - - + -
187D PHE* 1.3 87.9 - - - +
189D GLN* 1.3 60.0 + - - +
190D ASN 3.0 10.0 + - - +
193D MET* 3.9 9.4 - - + +
194D ALA* 3.4 42.2 - - + +
211D VAL* 4.9 0.2 - - + -
212D VAL 3.0 11.4 + - - +
213D GLY 3.5 8.0 - - - -
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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