Contacts of the helix formed by residues 322 - 333 (chain B) in PDB entry 1YCH
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 VAL 322 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260B ASP* 4.3 13.7 - - + -
289B LEU* 3.8 21.5 - - + -
309B VAL* 3.9 28.5 - - + -
310B GLY 4.1 7.0 - - - +
311B SER* 4.0 21.1 - - - +
318B ILE* 4.5 4.9 - - + -
319B LEU* 3.0 19.6 + - + +
321B VAL* 1.3 79.0 - - - +
323B SER* 1.3 64.7 + - - +
324B PRO 3.5 0.2 - - - -
325B LEU* 3.6 5.5 + - + +
326B LEU* 3.5 26.4 + - + +
355B LEU* 4.2 8.1 - - + -
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Residues in contact with SER 323 (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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323A SER* 3.5 20.8 + - - -
327A ASP* 2.7 36.1 + - - +
318B ILE* 3.6 15.7 - - - +
319B LEU 3.8 0.8 + - - -
320B PRO* 3.2 13.0 + - - +
322B VAL* 1.3 75.7 - - - +
324B PRO* 1.3 75.0 - - - +
326B LEU* 3.0 5.7 + - - +
327B ASP* 3.0 24.8 + - - +
358B ARG* 4.5 2.0 + - - +
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Residues in contact with PRO 324 (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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320A PRO* 3.6 34.0 - - + +
321A VAL* 5.3 1.8 - - - -
323A SER* 4.1 1.3 - - - +
324A PRO* 3.7 13.5 - - + -
294B ARG* 3.8 21.1 - - + -
320B PRO 3.3 7.6 - - - +
321B VAL* 3.3 17.5 - - - +
323B SER* 1.3 93.7 - - - +
325B LEU* 1.3 62.1 + - - +
327B ASP* 3.5 0.3 + - - -
328B ASP* 3.0 26.3 + - - +
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Residues in contact with LEU 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B ALA* 4.3 13.5 - - + -
289B LEU* 4.2 28.0 - - + -
294B ARG* 4.3 11.8 - - + +
297B VAL* 4.3 13.9 - - + -
298B ILE* 3.6 28.7 - - + -
301B ILE* 4.5 5.4 - - + -
307B VAL* 5.7 0.2 - - + -
309B VAL* 4.0 27.8 - - + -
321B VAL 4.9 0.6 + - - +
322B VAL 3.6 7.9 + - - +
323B SER 3.2 0.8 - - - -
324B PRO* 1.3 78.9 - - - +
326B LEU* 1.3 60.4 + - + +
328B ASP* 3.4 4.9 + - - +
329B LEU* 3.0 53.2 + - + +
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B VAL* 4.4 15.0 - - + -
318B ILE* 4.0 17.9 - - + -
322B VAL* 3.5 16.8 + - + +
323B SER* 3.0 6.8 + - - +
325B LEU* 1.3 79.9 - - + +
327B ASP* 1.3 66.9 + - - +
328B ASP 3.1 0.9 - - - -
329B LEU* 3.0 8.7 + - + +
330B VAL* 3.0 28.4 + - - +
355B LEU* 3.6 28.9 - - + +
358B ARG* 4.0 37.9 - - + +
359B LEU* 4.5 23.8 - - + +
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Residues in contact with ASP 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ASP* 3.1 46.8 - - - +
318A ILE* 4.6 6.5 - - + +
320A PRO* 5.0 6.1 - - + -
323A SER* 2.7 28.8 + - - +
354A ILE* 5.0 1.2 - - - +
358A ARG* 2.6 35.1 + - - -
323B SER 3.0 9.3 + - - +
324B PRO 4.2 2.2 - - - +
326B LEU* 1.3 77.6 - - - +
328B ASP* 1.3 60.6 + - - +
330B VAL* 3.5 4.7 + - - +
331B GLY* 3.2 10.2 + - - -
358B ARG* 3.4 14.9 + - - -
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Residues in contact with ASP 328 (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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315A ASN* 4.9 5.2 + - - -
320A PRO* 3.7 9.0 - - + +
198B ASN* 4.4 2.4 - - - +
294B ARG* 3.0 40.2 + - - +
298B ILE* 3.7 20.8 - - + +
324B PRO 3.0 21.0 + - - +
325B LEU* 3.6 7.6 - - - +
326B LEU 3.1 0.2 - - - -
327B ASP* 1.3 75.2 - - - +
329B LEU* 1.3 58.1 + - - +
331B GLY* 4.1 1.0 - - - -
332B LEU* 2.9 53.7 + - + +
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Residues in contact with LEU 329 (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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201B MET* 5.5 2.0 - - - -
298B ILE* 3.9 22.0 - - + -
301B ILE* 4.2 13.7 - - + -
307B VAL* 4.3 14.6 - - + -
325B LEU* 3.0 43.5 + - + +
326B LEU* 3.0 10.5 + - + +
328B ASP* 1.3 76.1 - - - +
330B VAL* 1.3 65.6 + - - +
332B LEU* 4.7 3.6 - - + -
333B ARG 3.0 20.1 + - - -
334B PRO* 3.1 32.2 - - + +
358B ARG 5.8 0.2 - - - +
359B LEU* 4.5 9.0 - - + -
362B ALA* 3.5 12.8 - - + +
364B ILE* 4.2 17.3 - - + -
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Residues in contact with VAL 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ASP* 3.8 10.8 - - - +
326B LEU 3.0 17.8 + - - +
327B ASP* 3.8 8.3 - - - +
329B LEU* 1.3 78.4 - - - +
331B GLY* 1.3 61.2 + - - +
333B ARG* 3.5 19.6 + - - +
358B ARG* 3.4 34.1 - - + +
361B ALA* 3.7 30.6 - - + +
362B ALA* 3.7 8.7 - - + +
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Residues in contact with GLY 331 (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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315A ASN* 3.4 42.6 - - - +
316A ASN* 5.5 1.9 + - - -
317A ASP* 3.9 6.4 + - - -
202B PRO* 3.5 9.2 - - - +
327B ASP 3.2 13.2 + - - -
328B ASP* 4.1 1.1 - - - -
330B VAL* 1.3 82.5 - - - +
332B LEU* 1.3 58.8 + - - +
333B ARG* 3.4 7.0 + - - +
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Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ASN* 3.4 22.7 - - - +
197B ALA 4.2 3.1 - - - +
198B ASN* 3.5 25.8 - - - +
199B ILE 5.2 0.4 - - - +
201B MET* 3.4 17.4 - - - +
202B PRO* 3.0 40.8 - - + +
298B ILE* 3.9 30.7 - - + -
328B ASP* 2.9 49.5 + - - +
329B LEU* 4.2 3.8 - - + +
331B GLY* 1.3 74.6 - - - +
333B ARG* 1.3 67.8 + - - +
334B PRO* 4.9 0.7 - - + -
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Residues in contact with ARG 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ASN* 4.0 22.7 - - - +
201B MET 4.3 7.4 - - - +
202B PRO* 4.5 16.1 + - + +
329B LEU 3.0 9.9 + - - -
330B VAL 3.6 15.4 + - - +
331B GLY 4.2 5.6 + - - +
332B LEU* 1.3 80.4 - - - +
334B PRO* 1.3 71.9 - - - +
335B LYS* 3.2 5.4 + - - +
361B ALA 5.7 2.0 - - - +
362B ALA 4.4 5.8 - - - +
363B LYS* 5.5 11.0 - - + -
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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