Contacts of the strand formed by residues 246 - 251 (chain L) in PDB entry 1KYO
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 246 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166L THR* 2.7 39.9 + - - -
167L ALA* 4.2 0.3 + - - -
169L GLN* 3.9 11.8 + - - -
244L LEU* 2.9 11.7 + - - +
245L GLY* 1.3 75.9 - - - -
247L GLU* 1.3 63.6 + - - +
430L ILE 3.2 6.8 + - - +
431L ALA* 3.1 8.1 - - - +
432L ILE 3.1 19.9 + - - -
444L TYR* 3.8 6.0 + - - -
28S ALA 3.2 15.7 - - - -
29S VAL* 4.1 6.5 - - - +
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Residues in contact with GLU 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166L THR* 3.6 7.0 + - - -
246L SER* 1.3 77.7 - - - +
248L VAL* 1.3 60.9 + - - +
249L ARG* 2.6 48.9 + - + +
432L ILE* 3.2 24.9 - - + +
444L TYR* 3.2 33.9 + - + +
298O ARG* 5.7 3.6 - - - +
26S SER* 4.8 2.9 + - - -
27S TYR* 3.3 7.4 - - - +
28S ALA* 2.9 46.5 + - + +
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Residues in contact with VAL 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162L HIS* 3.7 21.3 - - + +
165L SER* 6.0 0.2 - - - +
166L THR* 3.6 21.1 - - + -
247L GLU* 1.3 75.1 - - - +
249L ARG* 1.3 64.5 + - - +
250L LEU* 3.7 27.1 + - + -
432L ILE 2.8 10.8 + - - +
433L ALA* 3.1 30.9 - - + -
434L GLY 3.1 5.0 + - - +
25S THR* 4.0 3.1 - - + -
26S SER 3.5 4.0 - - - -
27S TYR* 3.7 29.4 - - + -
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Residues in contact with ARG 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247L GLU* 2.6 52.4 + - + +
248L VAL* 1.3 78.1 - - - +
250L LEU* 1.3 60.8 + - - +
251L ARG* 3.2 8.4 + - + +
432L ILE* 5.2 4.9 - - + +
434L GLY 3.7 4.3 - - - +
438L ILE* 3.9 18.3 + - + +
441L LEU* 2.6 58.4 + - + +
442L LEU 2.8 20.4 + - - -
443L ASP* 4.3 3.1 - - - +
444L TYR* 4.1 4.4 - - - +
24S ILE 3.8 1.6 - - - +
25S THR* 3.6 4.7 - - - -
26S SER* 3.0 43.4 + - - +
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Residues in contact with LEU 250 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158L ARG* 4.1 22.3 + - + +
159L VAL* 5.0 4.7 - - + -
162L HIS* 3.7 46.9 - - + +
248L VAL* 3.7 16.6 - - + +
249L ARG* 1.3 69.4 - - - +
251L ARG* 1.3 63.1 + - - +
252L ASP* 3.3 1.2 + - - +
434L GLY 2.7 22.8 + - - +
435L THR* 2.8 32.2 + - - +
33P THR* 4.1 9.4 - - + +
24S ILE 4.5 3.4 - - - -
25S THR* 3.4 33.0 - - + +
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Residues in contact with ARG 251 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249L ARG* 3.2 8.5 + - + +
250L LEU* 1.3 72.4 - - - +
252L ASP* 1.3 61.4 + - - +
253L ASP* 2.6 49.5 + - - +
436L GLY 3.6 12.6 - - - +
438L ILE* 3.7 21.7 - - + +
439L GLU* 2.8 53.8 + - - +
215N ASN 5.1 0.2 + - - -
216N LEU 4.6 5.7 + - - -
19S PRO 4.7 0.8 + - - -
21S GLN* 3.4 58.3 + - + +
22S LYS* 3.9 9.0 - - - -
23S GLY 4.3 2.3 + - - -
24S ILE* 4.0 14.1 + - + +
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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