Contacts of the helix formed by residues 302 - 306 (chain D) in PDB entry 4RYD
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 SER 302 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D ASP* 1.3 80.6 + - - +
303D CYS* 1.3 58.1 + - - +
304D ASN* 3.0 26.3 + - - +
305D CYS* 3.1 19.9 + - - +
306D ASP* 4.3 0.9 + - - +
331D GLU* 3.2 6.2 - - - +
332D ALA 3.7 12.8 + - - -
333D CYS* 4.0 1.7 - - - +
515D LEU 4.4 2.4 + - - -
516D LEU* 4.2 19.4 - - - +
517D ALA* 4.8 9.1 + - - -
519D ARG* 3.8 17.9 - - - +
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Residues in contact with CYS 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D SER* 3.4 28.3 - - - +
302D SER* 1.3 72.1 + - - +
304D ASN* 1.3 57.3 - - - +
305D CYS 3.2 2.2 - - - -
306D ASP* 3.5 10.9 + - - +
309D THR* 2.7 31.5 + - - +
310D ASN 4.2 0.2 + - - -
331D GLU* 3.2 34.8 + - - +
332D ALA 3.7 1.1 + - - -
333D CYS* 2.0 44.1 - - - +
335D SER* 3.8 4.2 + - - -
336D THR* 3.7 9.2 - - - -
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Residues in contact with ASN 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D SER* 3.0 8.2 + - - +
303D CYS* 1.3 75.5 - - - +
305D CYS* 1.3 57.7 + - - +
306D ASP 3.2 8.2 + - - -
310D ASN* 3.8 17.6 - - - +
333D CYS* 2.8 27.6 - - - +
334D SER* 3.1 23.2 + - - +
335D SER* 2.9 18.9 + - - -
515D LEU* 3.1 32.6 + - - +
531D TRP* 2.8 25.5 + - - -
533D PHE* 4.2 7.2 - - + -
534D MET 3.3 15.2 + - - +
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Residues in contact with CYS 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D PRO* 5.6 1.2 - - - +
262D THR* 3.6 17.5 + - - +
263D VAL* 3.4 12.5 - - + -
264D ASP 3.2 24.6 + - - -
301D ASP* 4.8 0.9 - - - +
302D SER* 3.1 15.6 + - - +
304D ASN* 1.3 77.9 - - - +
306D ASP* 1.3 58.7 + - - +
516D LEU* 3.7 28.5 - - - -
519D ARG* 3.6 28.3 - - - +
528D PHE* 4.6 7.9 - - - -
531D TRP* 3.8 10.1 - - - +
533D PHE* 5.2 1.8 - - - -
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Residues in contact with ASP 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D PRO* 3.5 13.0 - - + +
264D ASP 3.4 3.6 - - - -
293D SER 4.6 1.3 - - - +
302D SER 4.9 0.7 - - - +
303D CYS* 3.5 9.8 - - - +
304D ASN 3.2 0.4 - - - -
305D CYS* 1.3 79.5 - - - +
307D GLY* 1.3 58.7 + - - +
308D TYR* 2.8 27.5 + - - +
309D THR* 3.1 22.0 + - + +
310D ASN* 2.9 30.2 + - - +
331D GLU* 5.8 0.7 - - - +
531D TRP* 4.2 0.7 - - - -
5K 00S 2.8 41.2 + - - +
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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