Contacts of the strand formed by residues 191 - 196 (chain A) in PDB entry 1JCZ
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 TYR 191 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A LEU* 3.4 41.3 - - + +
45A THR 2.7 28.8 + - - -
46A PRO* 4.7 2.2 - - + -
47A LEU* 4.8 9.1 - - + +
188A THR 3.4 13.5 - - - -
189A ALA* 3.3 20.9 - - - -
190A GLU* 1.3 75.0 - - - +
192A TYR* 1.3 71.7 + - - +
193A ARG* 3.6 29.5 + - + -
210A THR* 3.8 22.9 - - + -
211A VAL 3.3 13.9 - - - +
212A PHE* 4.0 5.2 - + + -
213A ARG 3.9 3.1 - - - +
258A THR* 3.3 4.3 - - - -
259A SER* 2.8 32.8 + - - -
260A PHE* 3.6 10.7 - - - -
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Residues in contact with TYR 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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33A LEU* 3.7 35.2 - - + -
38A LEU* 3.8 30.5 - - + +
109A VAL* 3.8 25.9 - - + +
147A LEU* 5.3 0.7 - - + -
191A TYR* 1.3 77.2 - - - +
193A ARG* 1.3 61.2 + - - +
194A TYR* 5.4 2.0 - - + -
209A TRP 3.7 0.3 - - - +
210A THR* 3.3 7.6 - - - -
211A VAL* 2.7 59.4 + - + +
212A PHE 4.2 2.5 - - - -
213A ARG* 3.9 27.7 + - - +
256A VAL* 3.8 9.0 - - + -
257A TYR 3.5 4.3 - - - -
258A THR* 3.6 15.9 - - + -
260A PHE* 3.8 21.5 - + - -
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Residues in contact with ARG 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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44A LEU* 3.9 27.5 - - + +
47A LEU* 4.0 10.5 - - - +
84A LEU* 3.8 30.4 - - - +
191A TYR* 3.6 31.6 + - + -
192A TYR* 1.3 74.5 - - - +
194A TYR* 1.3 70.2 + - - +
208A LEU* 3.7 26.4 - - - +
209A TRP 3.2 15.8 + - - -
210A THR* 2.9 29.5 + - - -
256A VAL* 3.7 1.5 - - - +
257A TYR* 2.7 44.4 + - + +
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Residues in contact with TYR 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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27A LEU 6.2 0.2 - - - -
28A GLN 4.9 2.2 - - - -
29A SER* 2.8 32.3 + - - -
30A PRO* 3.9 0.5 - - - +
31A ILE* 3.7 36.9 - - + +
33A LEU* 5.1 2.2 - - + -
107A HIS* 2.6 35.6 + + - -
192A TYR* 5.4 0.4 - - + -
193A ARG* 1.3 82.3 - - - +
195A ARG* 1.3 83.9 + - - +
196A GLY* 3.9 2.9 - - - -
208A LEU* 3.9 4.8 - - - +
209A TRP* 2.9 50.2 + + + +
211A VAL* 4.6 7.4 - - + -
251A PHE* 4.4 4.0 - + + -
254A ARG* 4.3 9.0 - - - +
255A LEU 4.6 4.5 - - - +
256A VAL* 4.0 22.7 - - + -
257A TYR* 6.3 0.2 - - - -
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Residues in contact with ARG 195 (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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27A LEU* 4.1 19.8 - - + +
139A GLU* 6.2 2.8 - - - +
194A TYR* 1.3 79.4 - - - +
196A GLY* 1.3 59.1 + - - +
207A VAL 3.7 5.8 - - - +
208A LEU* 4.2 18.6 - - + +
254A ARG* 2.7 37.8 + - - +
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Residues in contact with GLY 196 (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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27A LEU* 3.1 18.3 - - - +
29A SER* 3.3 12.6 - - - -
194A TYR* 3.7 4.6 + - - -
195A ARG* 1.3 75.8 - - - +
197A SER* 1.3 58.5 + - - -
205A PRO* 3.2 13.9 - - - +
207A VAL 2.8 33.8 + - - -
209A TRP* 3.7 4.6 - - - -
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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