Contacts of the strand formed by residues 184 - 192 (chain C) in PDB entry 4LXA
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 184 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ILE* 3.9 16.9 - - + +
180C ASP 3.8 3.8 - - - -
181C HIS* 3.2 62.6 + - - +
182C SER 3.4 2.4 - - - -
183C LEU* 1.3 80.8 - - - +
185C THR* 1.3 66.1 + - - +
186C GLY 3.5 22.4 - - - -
188C LEU* 3.7 28.0 - - + +
342C TYR* 3.3 35.7 - + + -
355C ALA* 3.5 16.8 - - + -
356C VAL 3.2 15.5 - - - +
358C ALA* 4.0 2.9 - - - +
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Residues in contact with THR 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C TYR* 1.3 83.3 - - - +
186C GLY* 1.3 66.7 + - - +
187C SER 3.9 0.7 + - - +
355C ALA* 4.2 0.3 - - - +
356C VAL* 3.0 43.0 + - - +
357C SER 4.9 1.0 + - - +
358C ALA* 4.9 11.4 - - + +
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Residues in contact with GLY 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C TYR* 3.5 16.6 - - - -
185C THR* 1.3 78.6 - - - +
187C SER* 1.3 60.8 + - - -
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Residues in contact with SER 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C TYR* 5.0 0.2 - - - -
185C THR 4.6 0.5 - - - +
186C GLY* 1.3 74.0 - - - -
188C LEU* 1.3 64.9 + - - +
189C TRP* 3.7 30.9 + - - -
354C PHE 3.7 1.4 - - - +
355C ALA* 3.5 17.1 - - - +
356C VAL 4.9 0.5 + - - -
370C VAL* 4.9 2.6 - - - +
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Residues in contact with LEU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ILE* 4.3 9.9 - - + -
184C TYR* 3.7 31.4 - - + +
186C GLY 4.1 0.8 + - - -
187C SER* 1.3 77.2 - - - +
189C TRP* 1.3 64.4 + - - +
190C TYR* 3.7 34.3 - - + +
342C TYR* 4.3 4.7 - - + +
344C VAL* 3.8 28.3 - - + -
353C GLY* 3.9 3.8 - - - +
354C PHE 3.4 19.5 - - - +
355C ALA* 3.7 22.4 - - + +
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Residues in contact with TRP 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C SER* 3.7 31.8 - - - -
188C LEU* 1.3 77.2 - - - +
190C TYR* 1.3 62.5 + - - +
294C GLN* 3.7 34.1 - - + -
296C PHE* 3.5 40.2 - + + -
353C GLY* 3.1 1.0 - - - -
354C PHE 2.8 36.5 + - - +
370C VAL* 3.7 22.7 + - + -
372C GLY* 3.4 41.8 - - - +
373C PRO* 3.4 21.5 - - + -
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Residues in contact with TYR 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ILE* 3.8 16.8 - - - +
188C LEU* 3.7 40.3 - - + +
189C TRP* 1.3 77.2 - - - +
191C THR* 1.3 59.1 + - - +
289C GLY* 3.8 2.9 - - - -
290C GLU* 3.6 38.5 + - + +
294C GLN 4.9 1.2 - - - +
296C PHE* 3.5 10.7 - - - -
344C VAL* 4.5 5.2 - - + +
346C ASP* 4.3 10.7 + - + -
351C ARG* 3.4 57.8 + - + -
352C ILE 3.3 2.7 - - - -
353C GLY* 3.4 27.6 - - - -
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Residues in contact with THR 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C TYR* 1.3 73.9 - - - +
192C PRO* 1.3 69.2 + - - +
201C VAL* 3.9 26.7 - - + +
202C ILE 4.5 4.5 + - - -
287C LEU* 3.9 20.1 - - + +
288C MET* 2.6 29.0 + - - +
290C GLU* 4.7 0.9 - - - -
296C PHE* 3.9 10.5 - - + -
351C ARG* 3.4 3.7 - - - -
352C ILE* 2.8 45.8 + - + +
354C PHE* 4.3 3.1 - - + -
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Residues in contact with PRO 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C THR* 1.3 90.2 + - - +
193C ILE* 1.3 69.2 + - - +
194C ARG* 3.4 6.3 + - - +
200C GLU 3.7 5.9 - - - +
201C VAL* 3.9 12.8 - - - +
202C ILE* 4.9 1.2 + - - +
288C MET* 3.2 39.7 - - + +
289C GLY 3.7 8.1 - - - +
290C GLU* 3.8 24.2 - - + +
350C LYS 3.8 8.5 - - - +
351C ARG* 4.3 2.5 - - + -
379C MET* 6.3 0.9 - - - -
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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