Contacts of the helix formed by residues 251 - 260 (chain C) in PDB entry 5YL4
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 ASP 251 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B GLU* 5.2 7.1 - - - +
133C GLN* 6.1 0.7 - - - +
241C SER* 4.3 11.1 - - - +
242C LEU* 5.5 4.0 - - + -
249C ASN* 4.4 6.9 - - - +
250C VAL* 1.3 80.4 - - - +
252C LEU* 1.3 65.7 + - - +
253C THR* 3.3 20.6 + - + +
254C GLU* 3.3 23.8 + - + +
255C PHE* 3.4 10.0 - - - -
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Residues in contact with LEU 252 (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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136C LEU* 5.7 0.7 - - + -
167C LEU* 3.9 23.8 - - + -
169C PHE* 6.5 0.2 - - + -
202C PHE* 4.5 12.8 - - + -
238C ILE* 3.7 40.6 - - + +
239C THR* 5.1 2.9 - - + -
241C SER* 3.6 17.0 + - - +
242C LEU* 4.1 28.8 - - + +
251C ASP* 1.3 73.1 - - - +
253C THR* 1.3 58.5 + - + +
255C PHE* 3.2 15.0 + - + -
256C GLN* 3.0 38.4 + - + +
259C LEU* 5.6 0.7 - - + -
318C LEU* 5.3 1.1 - - + -
378C LEU* 4.5 12.8 - - + -
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Residues in contact with THR 253 (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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98B GLY* 5.8 4.1 - - - -
397B TRP* 5.8 0.5 - - - -
133C GLN* 3.2 35.2 + - + +
165C SER* 6.0 1.8 - - - +
242C LEU* 5.7 1.6 - - + -
251C ASP* 3.7 15.5 + - + +
252C LEU* 1.3 78.6 - - + +
254C GLU* 1.3 59.8 + - - +
256C GLN* 3.4 22.4 + - - +
257C THR* 3.1 27.0 + - - -
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Residues in contact with GLU 254 (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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99B ASN* 3.6 27.9 + - - +
177B ASP* 4.1 13.7 - - - +
178B THR* 3.7 11.6 - - + +
250C VAL* 3.6 15.3 - - + +
251C ASP* 3.3 25.0 + - + +
252C LEU 3.2 0.6 - - - -
253C THR* 1.3 79.6 + - - +
255C PHE* 1.3 64.5 + - - +
257C THR* 3.5 18.9 - - - -
258C ASN* 3.8 2.9 + - - +
352C LYS* 3.1 29.4 + - - +
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Residues in contact with PHE 255 (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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241C SER* 5.2 2.2 - - - -
250C VAL* 3.5 35.9 - - + -
251C ASP 3.4 16.5 + - - -
252C LEU* 3.2 17.8 + - + +
254C GLU* 1.3 75.1 - - - +
256C GLN* 1.3 59.3 + - - +
258C ASN* 2.9 7.4 + - - +
259C LEU* 2.8 44.7 + - + +
316C CYS* 3.4 26.2 - - + -
318C LEU* 3.7 35.0 - - + -
352C LYS* 3.7 42.6 - - + +
354C GLY* 3.9 16.6 - - - -
378C LEU* 5.0 0.9 - - + -
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Residues in contact with GLN 256 (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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397B TRP* 3.5 21.5 - - + -
165C SER* 5.3 4.9 + - - -
167C LEU* 3.7 32.2 - - + +
199C ASP* 4.5 10.6 - - - +
200C CYS* 4.0 25.3 - - - +
202C PHE* 5.8 0.2 - - + -
252C LEU* 3.0 27.1 + - + +
253C THR* 3.4 34.5 - - - +
255C PHE* 1.3 76.9 - - - +
257C THR* 1.3 62.2 + - - +
259C LEU* 3.0 17.2 + - + +
260C VAL* 3.1 16.6 + - + +
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Residues in contact with THR 257 (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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98B GLY* 4.2 17.4 + - - +
99B ASN* 5.1 0.5 + - - -
178B THR* 4.3 13.9 - - + +
179B VAL* 4.4 0.3 - - - +
180B VAL* 3.9 31.6 - - + -
394B PHE* 3.4 13.7 - - - -
397B TRP* 3.2 40.3 + - + +
253C THR 3.1 14.4 + - - -
254C GLU* 3.5 13.2 + - - -
256C GLN* 1.3 77.2 - - - +
258C ASN* 1.3 62.9 - - - +
260C VAL 4.0 0.7 - - - +
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Residues in contact with ASN 258 (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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177B ASP 4.5 0.2 + - - -
178B THR* 3.4 14.6 - - - +
179B VAL* 3.0 46.4 + - + +
394B PHE* 3.4 21.4 - - - -
254C GLU 3.8 1.1 + - - -
255C PHE 2.9 9.8 + - - +
257C THR* 1.3 78.7 - - - +
259C LEU* 1.3 61.6 + - - +
261C PRO* 4.7 1.0 - - - +
313C MET 4.4 0.3 - - - +
314C ALA* 3.5 19.9 - - + +
315C CYS 5.9 0.2 + - - -
316C CYS* 4.7 11.2 - - - -
350C GLY 5.6 3.2 + - - -
352C LYS* 3.6 31.1 - - + +
380C ASN* 5.2 0.2 + - - -
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Residues in contact with LEU 259 (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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200C CYS* 5.3 2.7 - - - -
202C PHE* 5.0 4.0 - - + -
252C LEU* 5.6 0.9 - - + -
255C PHE* 2.8 33.4 + - + +
256C GLN* 3.0 9.8 + - + +
258C ASN* 1.3 73.0 - - - +
260C VAL* 1.3 62.8 + - + +
261C PRO* 3.4 9.7 - - - +
265C ILE 3.8 4.9 - - - +
266C HIS* 5.1 1.2 - - - -
267C PHE 5.6 0.2 + - - -
268C PRO* 4.1 27.1 - - + +
314C ALA* 4.2 7.2 - - + -
316C CYS* 4.1 11.0 - - - -
378C LEU* 3.7 55.9 - - + +
379C SER 4.1 1.6 - - - -
380C ASN* 3.4 32.5 + - + +
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Residues in contact with VAL 260 (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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394B PHE* 3.7 5.3 - - - -
396B HIS* 2.9 33.6 + - + +
397B TRP* 3.5 20.0 + - + -
199C ASP 3.9 19.7 - - - +
200C CYS* 4.8 10.5 - - + -
256C GLN* 3.1 17.5 + - + +
258C ASN 3.4 1.2 - - - -
259C LEU* 1.3 85.0 - - + +
261C PRO* 1.3 58.8 - - - +
262C TYR 3.3 22.0 - - - +
263C PRO* 4.2 3.8 - - + +
265C ILE 3.8 4.3 - - - +
266C HIS* 4.0 18.4 - - + -
268C PRO* 6.0 0.2 - - + -
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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