Contacts of the strand formed by residues 299 - 304 (chain A) in PDB entry 5KIY
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 ALA 299 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A LEU* 3.9 5.8 - - - +
264A ALA* 4.1 1.5 - - - +
265A PHE* 3.1 29.4 - - + +
293A ALA* 3.4 34.5 - - + +
296A ASN 4.1 0.9 - - - +
297A ALA* 4.1 0.2 - - - -
298A PRO* 1.3 75.2 - - - +
300A ILE* 1.3 65.4 + - - +
340A HIS 3.1 7.3 + - - +
341A VAL* 3.4 8.0 - - + +
342A ILE 3.1 23.2 + - - -
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Residues in contact with ILE 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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220A VAL* 3.7 22.0 - - + -
221A GLU* 4.9 2.0 - - - +
224A LEU* 3.7 15.9 - - + -
258A VAL* 4.0 17.9 - - + -
262A THR* 3.7 25.6 - - + +
264A ALA* 4.2 4.5 - - + -
265A PHE* 2.6 9.9 + - - +
266A PHE* 3.3 25.9 - - + -
267A PHE* 2.8 32.2 + - - +
299A ALA* 1.3 77.9 - - - +
301A ILE* 1.3 73.1 + - - +
302A PHE 4.2 0.4 - - - +
342A ILE 3.4 7.6 - - - +
344A MET* 4.3 17.3 - - + -
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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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267A PHE* 3.4 14.4 - - + +
269A ILE* 3.7 30.3 - - + -
289A ALA* 4.2 3.8 - - + +
290A PHE* 3.8 42.4 - - + -
293A ALA* 3.8 28.3 - - + -
299A ALA 4.2 0.2 - - - -
300A ILE* 1.3 77.1 - - - +
302A PHE* 1.3 60.6 + - - +
303A ILE* 4.3 10.1 - - + -
341A VAL* 3.9 13.7 - - + -
342A ILE 2.9 9.1 + - - +
343A VAL* 3.2 8.3 - - + -
344A MET 2.8 28.8 + - - +
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Residues in contact with PHE 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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243A LEU* 4.6 7.9 - - + -
251A LYS 4.3 7.2 - - - -
254A ILE* 5.8 0.2 - - + -
255A ALA* 3.4 40.6 - - + -
266A PHE* 3.4 24.9 - + + -
267A PHE 2.9 7.7 + - - +
268A LEU* 3.6 12.1 - - + +
269A ILE* 2.8 29.6 + - - +
300A ILE* 4.0 0.8 - - - +
301A ILE* 1.3 74.2 - - - +
303A ILE* 1.3 62.9 + - - +
304A ASP* 3.6 33.4 - - + -
344A MET* 3.3 44.4 - - + -
345A ALA 4.3 3.4 - - - -
346A ALA* 3.8 20.4 - - + -
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Residues in contact with ILE 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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269A ILE* 3.4 24.2 - - + +
271A GLY 5.3 0.4 - - - +
286A LEU* 5.6 0.7 - - + -
290A PHE* 4.7 3.8 - - + -
301A ILE* 4.3 8.3 - - + -
302A PHE* 1.3 74.6 - - - +
304A ASP* 1.3 65.2 + - - +
305A GLU 3.8 0.3 + - - -
306A LEU* 4.1 13.5 + - + -
309A ILE* 3.9 25.8 - - + -
328A LEU* 4.1 32.5 - - + -
343A VAL* 3.9 21.3 - - + -
344A MET 2.8 15.2 + - - +
345A ALA* 3.1 9.6 - - + +
346A ALA 3.1 22.7 + - - +
363A PHE* 4.5 7.0 - - + -
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Residues in contact with ASP 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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252A THR* 2.6 40.0 + - - +
255A ALA* 5.3 0.4 - - - +
256A ARG* 4.5 4.9 + - - -
268A LEU* 4.2 8.5 - - + -
269A ILE 2.8 11.8 + - - +
270A ASN* 4.5 12.9 + - - +
271A GLY* 2.8 29.1 + - - -
302A PHE* 3.6 21.6 + - + -
303A ILE* 1.3 73.8 - - - +
305A GLU* 1.3 77.6 + - - +
346A ALA* 3.6 17.8 - - - +
801A MG 4.0 4.4 - - - -
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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