Contacts of the helix formed by residues 298 - 304 (chain A) in PDB entry 5I2S
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 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A ILE* 1.3 74.0 - - - +
299A PRO* 1.3 72.2 - - - +
300A VAL* 3.1 19.8 + - - +
301A ASP* 2.8 31.7 + - - +
302A LEU* 3.0 13.5 + - - +
318A ILE* 6.0 0.7 - - - -
363A TYR* 4.0 1.1 - - - -
396A LEU 3.6 11.5 + - - -
397A HIS 5.0 1.3 - - - -
398A LEU 3.2 18.2 - - - -
399A SER* 4.2 4.2 - - - -
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Residues in contact with PRO 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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298A SER* 1.3 84.6 - - - +
300A VAL* 1.3 61.4 + - - +
302A LEU* 3.1 9.7 + - + +
303A SER* 3.0 20.8 + - - -
363A TYR* 3.2 23.1 - - + +
368A ILE* 4.8 1.8 - - + -
372A GLY* 3.6 30.6 - - - +
374A LEU* 3.8 26.0 - - + -
383A PRO* 3.7 15.2 - - + +
395A ASP 4.1 5.6 - - - +
396A LEU* 4.1 10.3 - - + +
398A LEU 3.2 15.3 - - - +
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Residues in contact with VAL 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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298A SER* 3.1 10.9 - - - +
299A PRO* 1.3 72.4 - - - +
301A ASP* 1.3 66.5 + - - +
303A SER* 2.7 23.2 + - - +
304A TYR* 3.4 40.3 + - + +
383A PRO* 4.0 5.6 - - + +
387A ILE* 3.7 34.3 - - + -
392A LEU* 5.0 3.8 - - + -
396A LEU* 3.8 31.2 - - + +
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Residues in contact with ASP 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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287A THR* 3.0 44.6 + - + +
290A LYS* 3.3 36.5 + - - +
296A PRO 4.3 0.9 - - - +
297A ILE* 3.4 19.3 - - + -
298A SER* 2.8 36.1 + - - +
300A VAL* 1.3 78.1 - - - +
302A LEU* 1.3 62.2 + - - +
304A TYR* 3.6 12.7 + - - +
305A LEU 4.1 0.3 + - - -
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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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297A ILE* 3.8 26.0 - - + -
298A SER 3.0 10.4 + - - +
299A PRO* 3.1 9.4 + - + +
301A ASP* 1.3 75.6 - - - +
303A SER* 1.3 60.3 + - - +
305A LEU* 2.8 44.2 + - + +
306A ALA* 3.6 2.8 + - - +
316A PHE* 4.3 10.6 - - + +
317A THR* 4.2 11.7 - - - -
318A ILE* 4.0 15.3 - - + -
323A LEU* 4.0 19.7 - - + -
368A ILE* 3.8 29.6 - - + -
371A ASN* 4.0 5.6 - - - +
372A GLY* 3.8 16.8 - - - +
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Residues in contact with SER 303 (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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299A PRO 3.0 11.4 + - - -
300A VAL* 2.7 22.7 + - - +
302A LEU* 1.3 74.4 - - - +
304A TYR* 1.3 56.9 + - - +
306A ALA* 2.9 29.8 + - - +
308A LYS* 4.9 1.2 + - - -
371A ASN 3.4 17.5 + - - -
383A PRO* 3.9 2.6 - - - +
384A LEU* 3.7 48.4 + - - +
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Residues in contact with TYR 304 (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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25A PRO* 3.5 11.7 - - - +
280A ASP 4.7 2.0 - - - +
283A LEU* 3.5 62.3 - - + +
284A CYS* 3.5 18.1 - - - +
286A GLU* 6.5 0.2 - - + -
287A THR* 3.4 25.1 - - + -
300A VAL* 3.4 37.9 - - + +
301A ASP* 3.7 11.0 - - - +
302A LEU 3.1 1.0 + - - -
303A SER* 1.3 77.2 - - - +
305A LEU* 1.3 59.1 + - - +
306A ALA 3.3 0.2 - - - -
308A LYS* 5.1 7.6 + - - +
384A LEU* 4.0 24.5 - - + -
387A ILE* 4.1 11.2 - - + +
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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