Contacts of the strand formed by residues 117 - 120 (chain D) in PDB entry 5U1R
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 117 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ASP 4.0 6.5 - - - +
116D PRO* 1.3 76.0 - - - +
118D VAL* 1.3 64.2 + - - +
119D TYR* 3.7 33.9 - - + +
133D LEU 3.3 2.3 - - - +
134D PHE* 3.4 3.6 - - - -
135D THR* 2.9 34.5 + - - +
136D ASP* 6.0 0.2 - - - +
195D THR* 3.7 5.1 - - - +
196D PHE* 3.2 23.3 - - + +
138E HIS* 5.3 0.7 - - + -
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Residues in contact with VAL 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ALA* 1.3 75.8 - - - +
119D TYR* 1.3 62.8 + - - +
120D GLN 4.1 0.7 + - - -
132D CYS* 4.1 1.6 - - + -
133D LEU 3.2 5.8 - - - +
134D PHE* 3.7 20.6 - - + -
182D CYS* 3.7 38.9 - - + +
186D PHE* 4.1 27.6 - - + -
191D ILE* 5.2 2.2 - - + -
195D THR* 4.2 3.3 - - + +
196D PHE 3.1 7.7 + - - +
197D PHE* 3.5 34.3 - - + -
198D PRO* 3.6 19.6 - - - +
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Residues in contact with TYR 119 (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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115D ASP 5.3 0.3 + - - -
117D ALA* 3.7 19.0 - - + +
118D VAL* 1.3 75.3 - - - +
120D GLN* 1.3 61.4 + - - +
121D LEU* 3.5 9.4 + - + +
132D CYS* 3.4 4.0 - - - -
133D LEU* 2.9 40.6 + - + +
135D THR* 3.6 31.0 - - + -
136D ASP* 4.9 0.7 + - - -
182D CYS* 3.8 3.1 - - - -
196D PHE* 4.2 11.9 - + - -
198D PRO* 3.9 14.6 - - + -
132E SER* 3.6 17.9 - - - -
134E ALA* 4.0 6.3 - - + -
135E GLU* 3.5 54.0 - - + +
138E HIS* 3.5 26.3 - - - +
139E THR* 3.5 12.4 - - + +
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Residues in contact with GLN 120 (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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118D VAL 4.1 1.2 + - - -
119D TYR* 1.3 71.8 - - - +
121D LEU* 1.3 82.0 + - - +
122D ARG 4.1 0.2 + - - -
123D ASP* 4.3 3.8 - - - +
130D SER* 2.8 29.4 + - - -
131D VAL 3.4 7.7 + - - +
132D CYS* 3.4 24.5 - - - -
180D PHE* 4.9 2.2 + - - -
181D ALA* 5.2 1.2 - - - +
182D CYS* 3.4 21.9 - - + +
198D PRO* 5.4 3.6 - - - +
132E SER* 3.3 20.9 + - - -
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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