Contacts of the strand formed by residues 191 - 194 (chain A) in PDB entry 4Y1W
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 GLU 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A PHE* 4.5 9.7 - - - -
68A SER* 2.8 30.6 + - - -
142A SER* 2.6 34.6 + - - +
143A THR 3.3 7.6 - - - +
179A THR* 3.7 6.9 + - - -
180A ILE* 3.1 49.9 + - + +
181A ALA* 3.8 7.7 + - + +
184A SER* 4.9 2.4 + - - +
188A LYS* 3.6 32.7 + - - +
189A GLU 4.0 1.8 - - - +
190A ALA* 1.3 74.5 - - - +
192A VAL* 1.3 65.6 + - - +
193A LEU* 4.8 1.0 - - + +
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PHE* 3.8 16.4 - - + -
111A TYR* 3.8 35.2 - - + -
115A ALA* 5.2 0.7 - - + -
141A THR 3.8 1.0 - - - +
142A SER 3.8 0.3 - - - -
143A THR* 2.9 50.2 + - - +
145A THR* 4.3 6.3 - - + +
173A ILE* 4.0 12.3 - - + -
177A GLY* 3.9 13.7 - - - -
178A HIS 3.4 22.7 - - - +
179A THR* 4.4 2.7 - - - -
190A ALA 4.2 4.9 - - - +
191A GLU* 1.3 78.6 - - - +
193A LEU* 1.3 60.2 + - - +
194A PHE* 4.5 1.8 - - + -
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Residues in contact with LEU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL* 6.0 0.7 - - + -
67A PHE* 3.5 47.1 - - + -
101A VAL* 4.3 12.8 - - + -
105A LEU* 3.9 33.1 - - + +
140A PHE* 4.0 8.1 - - + -
141A THR 3.3 23.3 - - - +
142A SER* 4.0 8.5 - - - +
176A GLY 3.8 1.2 - - - +
177A GLY* 3.6 1.7 - - - -
178A HIS* 2.9 33.6 + - - +
180A ILE* 4.2 18.8 - - + -
191A GLU* 4.2 2.2 + - + +
192A VAL* 1.3 73.3 - - - +
194A PHE* 1.3 68.2 + - - +
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Residues in contact with PHE 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU* 4.0 4.9 - - - -
140A PHE* 3.3 11.6 - - - +
141A THR* 2.9 50.0 + - + +
143A THR* 4.2 17.0 - - + -
171A VAL* 5.1 0.4 - - + -
173A ILE* 3.7 28.3 - - + -
175A GLN 3.5 11.9 - - - -
176A GLY* 3.5 18.4 - - - -
177A GLY* 3.4 22.7 - - - -
192A VAL* 4.5 1.8 - - + -
193A LEU* 1.3 77.8 - - - +
195A ALA* 1.3 70.7 + - - +
198A ALA* 4.0 17.0 - - + -
200A PHE* 4.1 9.2 - + - -
218A THR* 3.5 24.2 - - + -
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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