Contacts of the helix formed by residues 305 - 309 (chain A) in PDB entry 3R5J
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 CYS 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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259A ALA* 3.5 25.8 - - - +
260A GLN* 4.5 1.3 - - - +
264A HIS* 4.9 0.4 - - - -
299A LEU 3.5 15.3 - - - +
300A PHE* 3.7 10.7 - - - +
301A ASP 2.8 20.8 + - - +
302A ASN* 4.4 0.4 - - - -
304A ASN* 1.3 80.0 - - - +
306A PRO* 1.3 66.0 - - - +
307A SER* 3.1 8.5 - - - -
308A LEU* 3.1 48.5 + - - +
309A GLN* 3.7 6.4 + - - +
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Residues in contact with PRO 306 (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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260A GLN* 5.5 2.5 - - - +
302A ASN 4.0 1.5 - - - +
303A ALA 3.9 10.1 - - - +
304A ASN 3.4 9.4 - - - +
305A CYS* 1.3 87.4 - - - +
307A SER* 1.3 64.9 + - - +
309A GLN* 3.1 37.5 + - + +
332C GLN* 3.3 46.6 - - + +
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Residues in contact with SER 307 (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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259A ALA 5.8 0.7 - - - -
261A LEU 5.2 4.5 + - - -
262A PRO* 5.4 1.2 + - - +
264A HIS* 3.5 13.2 - - - +
265A ARG* 3.4 44.5 + - - +
305A CYS* 3.1 4.8 + - - -
306A PRO* 1.3 82.2 - - - +
308A LEU* 1.3 58.8 + - - +
309A GLN 3.5 0.4 + - - -
311A LYS* 3.0 28.9 + - - -
332C GLN* 5.9 0.2 - - - -
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Residues in contact with LEU 308 (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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264A HIS* 3.7 39.0 - - + +
267A THR* 4.6 1.1 - - - +
269A SER 4.3 8.7 - - - +
270A CYS* 3.6 38.1 - - + -
300A PHE* 4.2 10.1 - - + +
302A ASN* 5.0 0.2 - - - -
305A CYS* 3.1 32.7 + - + +
307A SER* 1.3 75.2 - - - +
309A GLN* 1.3 66.4 + - - +
311A LYS* 3.0 26.6 + - + +
313A LYS* 2.8 44.5 + - + +
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Residues in contact with GLN 309 (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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302A ASN* 2.9 39.5 + - - +
305A CYS 3.7 1.2 + - - -
306A PRO* 3.1 33.1 + - + +
307A SER 3.5 1.0 - - - +
308A LEU* 1.3 77.4 - - - +
310A ASN* 1.3 69.9 + - - +
311A LYS* 3.1 14.4 + - - +
358B LEU* 3.6 25.0 - - + +
329C VAL* 4.2 2.0 - - - +
330C ASP 3.4 17.2 + - - -
331C GLN* 3.4 7.8 - - - +
332C GLN* 2.9 29.0 + - - +
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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