Contacts of the helix formed by residues 293 - 302 (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 ASP 293 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A SER* 3.0 23.3 + - - -
32A HIS* 3.1 12.4 + - + -
194A LYS* 3.5 2.6 + - - -
292A SER* 1.3 72.3 - - - +
294A ARG* 1.3 59.6 + - - +
295A ASN* 3.1 23.2 + - - -
296A ASP* 2.8 60.2 + - - +
297A VAL* 2.9 13.0 + - - +
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Residues in contact with ARG 294 (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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27A PRO 4.7 2.0 + - - -
28A ALA* 2.7 38.4 + - - +
289A LEU* 5.5 5.4 - - + +
292A SER 3.6 5.1 + - - -
293A ASP* 1.3 73.6 + - - +
295A ASN* 1.3 65.4 + - - +
297A VAL* 3.3 9.3 + - - +
298A ILE* 3.0 31.9 + - - +
324A PRO* 4.0 29.2 - - + +
325A LEU* 4.3 22.0 - - + +
328A ASP* 3.3 26.4 + - - +
320B PRO* 2.7 36.8 - - - +
321B VAL* 4.6 4.6 - - - +
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Residues in contact with ASN 295 (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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23A TYR* 5.5 0.2 - - - -
27A PRO 5.1 1.8 + - - -
28A ALA 3.0 23.0 + - - +
29A PHE* 3.8 5.4 - - + -
30A SER* 2.9 33.2 - - - +
194A LYS* 3.6 22.0 - - - +
198A ASN* 3.4 35.4 + - - +
293A ASP* 3.1 18.5 + - - +
294A ARG* 1.3 84.6 + - - +
296A ASP* 1.3 60.9 + - - +
298A ILE* 3.5 0.3 + - - +
299A LYS* 3.0 25.5 + - - +
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Residues in contact with ASP 296 (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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32A HIS* 2.8 26.3 + - - -
194A LYS* 3.3 22.6 + - - +
287A PHE* 4.3 10.0 - - + -
293A ASP* 2.8 32.1 + - + +
295A ASN* 1.3 78.0 - - - +
297A VAL* 1.3 63.4 + - - +
299A LYS* 3.5 19.2 + - - +
300A GLU* 3.5 22.2 + - - +
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Residues in contact with VAL 297 (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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256A VAL* 4.4 9.9 - - + -
258A ALA* 4.5 8.7 - - + -
287A PHE* 3.6 48.9 - - + -
289A LEU* 4.3 9.6 - - + -
292A SER* 4.3 3.6 - - - -
293A ASP 2.9 21.2 + - - +
294A ARG* 3.5 11.0 - - - +
295A ASN 3.2 0.2 - - - -
296A ASP* 1.3 74.3 - - - +
298A ILE* 1.3 65.5 + - - +
300A GLU* 3.0 15.1 + - - +
301A ILE* 3.3 15.8 + - + +
325A LEU* 4.3 23.3 - - + -
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Residues in contact with ILE 298 (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 30.1 - - + +
198A ASN* 3.3 23.8 - - - +
201A MET* 4.7 4.8 - - - +
294A ARG 3.0 20.7 + - - +
295A ASN* 3.8 0.7 - - - +
297A VAL* 1.3 74.3 - - - +
299A LYS* 1.3 63.8 + - - +
301A ILE* 3.0 18.6 + - + +
302A LEU 3.4 8.0 + - - -
325A LEU* 3.6 16.4 - - + -
328A ASP* 3.7 24.5 - - - +
329A LEU* 3.6 31.4 - - + -
332A LEU* 3.6 12.1 - - + -
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Residues in contact with LYS 299 (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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190A ASP* 2.8 53.8 + - - +
193A ALA* 4.3 8.2 - - + +
194A LYS* 3.8 27.1 - - + +
197A ALA* 3.7 11.7 - - + -
254A LYS* 5.0 1.0 + - - -
295A ASN 3.0 14.6 + - - +
296A ASP* 3.6 26.0 - - - +
297A VAL 3.2 0.2 - - - -
298A ILE* 1.3 77.0 - - - +
300A GLU* 1.3 85.0 + - - +
302A LEU* 3.4 18.7 - - - +
303A ASP* 4.4 1.7 + - - +
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Residues in contact with GLU 300 (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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254A LYS* 2.9 42.3 + - - +
256A VAL* 3.7 18.0 - - + +
285A LYS* 3.2 30.2 + - + +
287A PHE* 3.7 21.5 - - + -
296A ASP 3.7 12.3 - - - +
297A VAL 3.0 10.1 + - - +
299A LYS* 1.3 105.1 + - - +
301A ILE* 1.3 62.7 + - - +
302A LEU 3.4 0.2 + - - -
303A ASP 3.6 0.5 + - - -
304A ALA* 3.5 9.2 + - - +
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Residues in contact with ILE 301 (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* 4.9 4.7 - - + -
256A VAL* 4.0 21.1 - - + -
297A VAL* 3.5 22.9 - - + +
298A ILE* 3.0 14.3 + - + +
300A GLU* 1.3 75.2 - - - +
302A LEU* 1.3 65.3 + - - +
304A ALA* 3.1 11.8 + - - +
307A VAL* 3.7 38.1 - - + -
325A LEU* 4.7 3.4 - - + -
329A LEU* 4.0 25.4 - - + -
334A PRO* 4.7 16.2 - - + -
337A LYS* 3.0 24.6 - - - -
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Residues in contact with LEU 302 (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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193A ALA* 3.9 26.2 - - + +
196A TYR* 3.8 28.0 - - + -
197A ALA* 4.0 11.7 - - + -
201A MET* 3.4 26.6 - - + +
246A TRP* 3.5 54.8 - - + +
249A GLY* 5.7 2.6 - - - -
251A GLY* 5.1 2.9 - - - -
298A ILE 3.4 4.0 + - - -
299A LYS 3.4 13.2 - - - +
300A GLU 3.2 0.4 - - - -
301A ILE* 1.3 78.8 - - - +
303A ASP* 1.3 58.9 + - - +
337A LYS* 3.4 15.4 + - - -
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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