Contacts of the helix formed by residues 245 - 251 (chain A) in PDB entry 3KYS
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 ARG 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A ASP* 2.7 37.0 + - - +
244A ILE* 1.3 81.4 - - + +
246A GLN* 1.3 61.3 + - + +
247A ILE 3.4 0.5 + - - -
248A TYR* 3.4 28.9 + - + +
249A ASP* 4.6 1.9 + - - +
410A LYS* 3.7 35.1 - - + +
411A ASP* 3.9 30.7 + - - -
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Residues in contact with GLN 246 (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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242A VAL* 4.8 0.7 - - + -
243A ASP* 2.9 28.5 + - + +
245A ARG* 1.3 77.4 - - + +
247A ILE* 1.3 59.2 + - + +
248A TYR 3.4 0.4 - - - -
249A ASP 4.5 0.6 + - - -
89B ARG* 2.7 50.3 + - + +
90B LYS* 3.0 63.4 + - + +
91B LEU* 4.5 7.2 - - + -
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Residues in contact with ILE 247 (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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242A VAL* 4.2 13.7 - - + -
244A ILE* 3.1 18.1 + - - +
246A GLN* 1.3 79.5 - - - +
248A TYR* 1.3 63.0 + - - +
249A ASP 3.2 2.9 + - - +
250A LYS* 3.5 9.4 + - + +
251A PHE* 3.4 34.6 + - + +
258A LEU* 3.9 22.3 - - + +
272A LEU* 3.8 38.4 - - + -
389A ALA* 4.1 1.8 - - + -
391A VAL* 6.2 0.9 - - + -
408A LEU* 3.9 25.1 - - + -
86B MET* 4.8 11.0 - - + -
89B ARG* 4.4 2.7 - - - +
91B LEU* 4.2 10.3 - - + -
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Residues in contact with TYR 248 (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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244A ILE* 3.2 46.3 + - + +
245A ARG* 3.4 30.1 + - + +
247A ILE* 1.3 76.9 - - - +
249A ASP* 1.3 56.6 + - - +
250A LYS 3.1 7.0 + - - -
251A PHE 3.4 7.8 - - - +
253A GLU* 3.3 36.8 - - + +
258A LEU* 3.9 8.7 - - + -
259A LYS* 3.5 53.7 + - + +
262A PHE* 3.9 10.9 - - - +
410A LYS* 3.9 23.1 + - - -
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Residues in contact with ASP 249 (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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245A ARG 4.6 1.9 + - - +
246A GLN 4.5 0.2 + - - -
247A ILE 3.2 1.4 - - - -
248A TYR* 1.3 77.8 - - - +
250A LYS* 1.3 61.3 + - - +
251A PHE 5.2 0.2 - - - -
314A PHE 5.9 1.0 - - - -
315A GLY* 6.3 1.1 - - - -
82B GLN 5.1 1.7 - - - +
83B THR* 2.6 30.8 + - - -
84B VAL* 4.1 9.7 + - - +
89B ARG* 3.4 26.4 + - - +
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Residues in contact with LYS 250 (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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247A ILE* 3.7 13.5 - - + +
248A TYR 3.1 0.6 - - - -
249A ASP* 1.3 79.5 - - - +
251A PHE* 1.3 73.4 + - + +
314A PHE* 3.3 22.1 - - - +
315A GLY* 5.2 0.2 - - - -
368A GLU* 3.5 35.9 + - - +
369A ASN* 4.6 5.8 - - - +
371A THR* 3.0 35.4 + - + +
391A VAL* 5.8 1.6 - - + -
83B THR* 3.8 20.7 - - - +
84B VAL 3.7 5.3 + - - -
86B MET* 3.6 38.9 - - + +
89B ARG* 3.4 26.7 - - - +
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Residues in contact with PHE 251 (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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247A ILE* 3.4 30.7 + - + -
248A TYR 3.4 8.1 + - - +
249A ASP 5.2 0.2 - - - -
250A LYS* 1.3 85.8 + - + +
252A PRO* 1.4 70.2 - - + +
253A GLU* 3.1 25.3 + - - +
258A LEU* 3.9 13.2 - - + -
312A CYS* 4.5 1.1 - - - -
314A PHE 4.8 0.2 - - - -
315A GLY* 4.3 9.4 - - - +
371A THR* 3.6 33.2 - - + -
372A ILE 3.4 23.6 - - - -
373A LEU* 4.0 20.9 - - + -
389A ALA* 3.4 26.0 - - + -
390A CYS 3.5 14.6 - - - -
391A VAL* 4.3 8.3 - - + -
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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