Contacts of the helix formed by residues 322 - 333 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A ASP* 4.4 15.3 - - + +
289A LEU* 4.0 19.1 - - + -
309A VAL* 3.8 28.7 - - + -
310A GLY 4.0 17.0 - - - +
311A SER* 4.1 11.0 - - - +
318A ILE* 4.4 5.6 - - + -
319A LEU* 2.9 20.4 + - + +
321A VAL* 1.3 79.8 - - - +
323A SER* 1.3 64.4 + - - +
324A PRO* 3.5 0.7 - - - -
325A LEU* 3.5 5.2 + - + +
326A LEU* 3.4 27.2 + - + +
355A LEU* 4.3 7.4 - - + -
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Residues in contact with SER 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ILE* 3.4 18.4 - - - +
319A LEU 3.8 0.2 + - - -
320A PRO* 3.2 11.4 + - - +
322A VAL* 1.3 76.1 - - - +
324A PRO* 1.3 72.7 - - - +
326A LEU* 3.1 6.5 + - - +
327A ASP* 3.0 26.1 + - - +
358A ARG* 5.1 1.6 - - - +
323B SER* 3.5 21.8 - - - -
327B ASP* 2.7 34.9 + - - +
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Residues in contact with PRO 324 (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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294A ARG* 4.0 20.9 - - + +
320A PRO 3.3 9.9 - - - +
321A VAL* 3.3 20.0 - - + +
322A VAL 3.5 0.4 - - - -
323A SER* 1.3 91.1 - - - +
325A LEU* 1.3 62.2 + - - +
327A ASP* 3.6 0.5 + - - -
328A ASP* 3.1 25.6 + - - +
320B PRO* 3.6 33.1 - - + +
321B VAL* 5.4 1.3 - - - -
323B SER* 4.0 1.8 - - - +
324B PRO* 3.7 14.6 - - + -
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Residues in contact with LEU 325 (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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258A ALA* 4.1 20.6 - - + -
289A LEU* 4.2 28.9 - - + -
294A ARG* 4.1 13.6 - - + +
297A VAL* 4.3 15.7 - - + -
298A ILE* 3.6 30.7 - - + -
301A ILE* 4.7 3.8 - - + -
307A VAL* 5.6 0.2 - - + -
309A VAL* 4.3 15.7 - - + -
321A VAL 4.9 0.6 + - - +
322A VAL 3.5 7.9 + - - +
323A SER 3.3 0.4 - - - -
324A PRO* 1.3 80.0 - - - +
326A LEU* 1.3 59.4 + - + +
328A ASP* 3.4 1.5 + - - +
329A LEU* 2.9 58.4 + - + +
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Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A VAL* 4.3 25.4 - - + -
318A ILE* 4.0 15.9 - - + -
322A VAL* 3.4 21.1 + - + +
323A SER 3.1 6.3 + - - +
325A LEU* 1.3 74.7 - - + +
327A ASP* 1.3 66.8 + - - +
328A ASP 3.0 1.8 - - - -
329A LEU* 3.0 12.7 + - + +
330A VAL* 3.0 27.8 + - - +
354A ILE 5.3 0.2 - - - +
355A LEU* 3.5 29.2 - - + +
358A ARG* 4.1 37.4 - - + +
359A LEU* 4.5 14.8 - - + -
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Residues in contact with ASP 327 (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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323A SER 3.0 12.5 + - - +
324A PRO 4.3 1.6 - - - +
326A LEU* 1.3 74.9 - - - +
328A ASP* 1.3 60.1 + - - +
330A VAL* 4.4 3.4 - - - +
331A GLY* 3.3 10.6 + - - -
358A ARG* 3.7 15.6 + - - -
317B ASP* 3.1 42.5 - - - +
318B ILE* 4.7 5.2 - - + +
320B PRO* 5.2 5.4 - - + -
323B SER* 2.7 27.3 + - - +
354B ILE* 5.6 0.2 - - - +
358B ARG* 2.6 41.0 + - - -
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Residues in contact with ASP 328 (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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198A ASN* 4.8 3.1 - - - +
294A ARG* 3.3 23.0 + - - -
298A ILE* 3.7 20.1 - - + +
324A PRO 3.1 19.8 + - - +
325A LEU* 3.6 6.3 - - - +
326A LEU 3.0 0.6 - - - -
327A ASP* 1.3 76.9 - - - +
329A LEU* 1.3 59.6 + - - +
331A GLY* 4.1 0.8 - - - -
332A LEU* 3.0 50.8 + - - +
315B ASN* 4.8 6.6 + - - -
320B PRO* 3.9 22.1 - - + +
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Residues in contact with LEU 329 (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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201A MET* 5.9 0.9 - - - -
298A ILE* 3.6 25.1 - - + -
301A ILE* 4.0 14.6 - - + -
307A VAL* 4.5 18.4 - - + -
309A VAL* 4.8 2.5 - - + -
325A LEU* 2.9 45.8 + - + +
326A LEU* 3.0 14.8 + - + +
328A ASP* 1.3 76.5 - - - +
330A VAL* 1.3 64.8 + - - +
332A LEU* 4.4 3.1 - - + -
333A ARG 3.0 19.1 + - - -
334A PRO* 3.2 29.8 - - + +
359A LEU* 5.0 2.5 - - + -
362A ALA* 3.4 14.5 - - + +
364A ILE* 4.6 8.7 - - + -
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Residues in contact with VAL 330 (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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326A LEU 3.0 18.9 + - - +
327A ASP* 3.9 4.0 - - - +
329A LEU* 1.3 76.4 - - - +
331A GLY* 1.3 61.0 + - - +
333A ARG* 2.5 51.6 + - - +
358A ARG* 3.6 34.3 - - + +
361A ALA* 3.6 20.2 - - + +
362A ALA* 3.6 7.2 - - - -
317B ASP* 3.8 16.2 - - - +
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Residues in contact with GLY 331 (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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202A PRO* 3.8 8.3 - - - +
327A ASP 3.3 12.7 + - - -
328A ASP 4.1 1.6 - - - -
330A VAL* 1.3 82.6 - - - +
332A LEU* 1.3 59.7 + - - +
333A ARG* 3.4 5.8 + - - +
315B ASN* 3.5 42.3 - - - +
317B ASP* 4.0 5.1 + - - -
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Residues in contact with LEU 332 (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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197A ALA 3.4 21.3 - - - +
198A ASN* 3.6 22.4 - - - +
199A ILE 5.0 0.2 - - - +
201A MET* 3.4 14.6 - - - +
202A PRO* 3.2 44.9 - - + +
298A ILE* 3.6 28.7 - - + -
328A ASP* 3.0 35.6 + - - +
329A LEU* 3.4 5.1 + - + +
331A GLY* 1.3 75.3 - - - +
333A ARG* 1.3 68.4 + - - +
334A PRO* 4.7 1.8 - - + -
315B ASN* 3.5 19.5 - - - +
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Residues in contact with ARG 333 (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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201A MET 4.2 7.8 - - - +
202A PRO* 4.7 10.4 - - + +
204A SER* 5.2 0.7 + - - -
329A LEU 3.0 8.7 + - - -
330A VAL* 2.5 33.3 + - - +
331A GLY* 4.1 6.0 - - - +
332A LEU* 1.3 79.4 - - - +
334A PRO* 1.4 71.5 - - - +
335A LYS* 3.3 4.5 + - - +
361A ALA* 3.1 23.6 + - - +
362A ALA 3.9 3.6 - - - -
363A LYS* 2.7 75.2 - - - +
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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