Contacts of the helix formed by residues 292 - 301 (chain B) in PDB entry 5YDJ
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 292 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B PRO* 4.8 15.1 - - + +
288B LEU 4.7 2.0 - - - -
289B ASP* 3.4 29.1 + - - +
290B VAL 3.2 4.9 + - - -
291B TYR* 1.3 71.9 - - - +
293B HIS* 1.3 67.1 + - - +
294B ARG* 3.4 34.8 + - - +
295B ALA* 4.0 5.6 + - + +
296B LEU 4.3 0.2 + - - -
608B PHE* 3.3 27.6 - - + +
610B GLU* 6.5 1.6 - - + -
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Residues in contact with HIS 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LEU* 6.0 1.3 - - + -
259B ASN* 4.3 11.6 + - + -
261B VAL* 3.7 30.3 - - + -
275B TRP* 4.7 2.0 - + + -
286B ALA 4.0 13.5 + - - -
291B TYR* 3.0 25.6 + - + -
292B ASP* 1.3 73.2 + - - +
294B ARG* 1.3 65.2 + - - +
295B ALA 3.4 0.4 - - - -
296B LEU* 3.4 2.0 + - - +
297B ALA* 3.0 26.3 + - - +
304B VAL* 3.5 31.4 - - + +
306B SER* 2.7 39.8 + - - -
608B PHE* 3.6 14.1 - + - -
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Residues in contact with ARG 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B VAL* 3.6 31.5 - - - +
181B ASP 2.8 35.6 + - - +
182B ALA* 3.8 17.5 - - + +
183B PRO* 4.0 10.1 - - + +
188B VAL* 3.9 16.5 - - + +
190B VAL* 4.7 9.9 - - + +
192B LEU* 6.0 3.8 - - - +
261B VAL* 4.1 10.5 - - + -
292B ASP* 3.3 22.4 + - - +
293B HIS* 1.3 77.1 - - - +
295B ALA* 1.3 56.8 + - - +
298B SER* 2.7 37.3 + - - -
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ALA* 4.5 4.5 - - - -
183B PRO* 4.8 13.0 - - + +
184B SER* 5.8 3.8 - - - +
292B ASP* 4.0 6.3 + - + +
293B HIS 3.4 0.4 - - - -
294B ARG* 1.3 79.2 - - - +
296B LEU* 1.3 63.2 + - - +
298B SER* 3.0 16.7 + - - -
299B GLU* 3.0 20.5 + - - +
608B PHE 3.4 17.7 - - - +
609B GLY* 3.5 21.3 - - - +
612B LEU* 5.3 7.9 - - + -
630B MET* 4.4 2.0 - - + -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B MET* 4.4 19.5 - - + -
293B HIS 3.4 6.5 + - - +
295B ALA* 1.3 79.1 - - - +
297B ALA* 1.3 63.9 + - - +
300B GLU* 3.2 44.0 + - + +
302B VAL* 4.4 3.3 - - + +
304B VAL* 3.7 22.0 - - + -
357B PHE* 3.9 29.6 - - + -
607B VAL 3.6 22.9 - - - +
608B PHE* 3.7 23.4 + - + +
630B MET* 4.0 19.1 - - + +
633B TRP* 5.8 0.9 - - + -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B VAL* 4.9 0.7 - - + -
261B VAL* 3.9 22.4 - - + +
262B ALA 4.8 0.4 - - - -
263B PRO* 3.4 12.6 - - - +
293B HIS 3.0 17.6 + - - +
294B ARG 3.9 2.0 - - - +
296B LEU* 1.3 75.5 - - - +
298B SER* 1.3 58.6 + - - +
301B ASN* 3.0 32.6 + - - -
302B VAL* 3.4 23.1 + - - +
304B VAL* 3.5 12.5 - - + +
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Residues in contact with SER 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B ALA* 3.8 7.8 - - - +
184B SER* 4.7 1.2 + - - -
186B LYS* 4.3 32.9 + - - +
187B LYS 4.9 1.8 - - - -
188B VAL* 3.7 16.6 - - - -
263B PRO* 4.0 11.7 - - - +
294B ARG 2.7 20.7 + - - -
295B ALA* 3.0 12.5 + - - -
297B ALA* 1.3 79.4 - - - +
299B GLU* 1.3 64.2 + - - +
300B GLU 3.5 0.2 - - - -
301B ASN* 4.4 10.6 + - - +
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B SER* 4.6 7.1 + - - -
186B LYS* 3.4 31.3 + - - +
295B ALA* 3.0 19.3 + - - +
297B ALA 3.3 0.2 - - - -
298B SER* 1.3 78.9 + - - +
300B GLU* 1.3 72.8 + - - +
301B ASN* 3.7 3.5 + - - -
612B LEU* 3.2 27.9 - - + +
627B ARG* 4.2 18.8 - - + -
630B MET* 3.4 22.0 - - + -
631B ARG* 4.6 11.4 + - - +
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Residues in contact with GLU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B LEU* 3.2 28.0 + - + +
299B GLU* 1.3 98.8 - - + +
301B ASN* 1.3 70.9 + - - +
302B VAL* 4.3 8.1 - - + -
627B ARG* 4.6 4.5 - - - +
630B MET* 3.4 38.6 - - + +
631B ARG* 3.5 28.6 + - - +
634B SER* 3.0 29.2 + - - +
638B LYS* 3.0 24.2 + - - +
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Residues in contact with ASN 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B PRO* 3.9 23.8 - - + +
264B ARG 5.1 4.2 - - - +
265B PRO* 4.6 11.3 - - - +
267B PRO* 5.7 4.8 - - + +
270B ALA* 4.2 12.7 - - - +
271B ALA 5.2 0.3 + - - -
297B ALA 3.0 12.1 + - - -
298B SER 4.4 7.7 + - - +
299B GLU 3.7 4.4 + - - -
300B GLU* 1.3 82.4 - - - +
302B VAL* 1.3 60.4 + - - +
638B LYS* 4.3 5.0 - - - -
803B SO4 4.9 3.6 + - - -
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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