Contacts of the strand formed by residues 48 - 54 (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 ALA 48 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47L THR* 1.3 78.5 - - - +
49L SER* 1.3 62.7 + - - +
50L VAL* 4.4 1.6 + - - +
107L SER* 3.0 34.1 + - - +
108L LEU 4.9 1.1 - - - +
109L PRO* 4.5 5.1 - - + -
210L THR 3.4 9.2 - - - +
211L GLY* 3.7 1.3 - - - -
212L ASN* 3.5 19.7 - - - +
213L ILE* 3.5 32.5 - - + -
382L PRO* 4.8 0.7 - - - -
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Residues in contact with SER 49 (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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47L THR* 4.9 2.4 + - - -
48L ALA* 1.3 73.3 + - - +
50L VAL* 1.3 63.4 + - - +
104L ILE* 3.8 15.5 - - - -
105L VAL 3.4 9.4 - - - -
106L SER* 2.7 32.0 + - - -
208L VAL 4.1 0.3 - - - +
209L GLY* 3.4 2.6 - - - -
210L THR* 2.9 36.9 + - - +
382L PRO* 4.2 17.2 - - - +
383L VAL* 3.9 7.5 - - - +
386L ALA* 5.4 2.5 - - - +
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Residues in contact with VAL 50 (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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48L ALA 5.3 2.2 - - - +
49L SER* 1.3 80.1 - - - +
51L GLY* 1.3 62.1 + - - +
104L ILE* 4.2 2.2 - - - -
105L VAL* 2.9 31.0 + - - +
107L SER* 5.8 0.2 - - - +
112L THR* 4.6 11.9 - - - +
115L SER* 4.5 19.5 + - - +
116L LEU* 4.0 26.5 - - + -
119L LEU* 3.6 10.0 - - + +
207L VAL* 4.2 8.5 - - + -
208L VAL 3.2 12.3 - - - +
209L GLY* 4.3 6.3 - - - -
213L ILE* 4.4 11.4 - - + -
218L LEU* 4.0 22.9 - - + -
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Residues in contact with GLY 51 (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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50L VAL* 1.3 77.5 - - - +
52L VAL* 1.3 60.5 + - - -
53L VAL* 3.8 1.9 + - - +
103L TYR 3.1 14.4 - - - -
104L ILE* 3.9 12.2 - - - +
119L LEU* 4.4 6.7 - - - -
207L VAL* 3.4 6.5 - - - -
208L VAL* 2.8 42.6 + - - +
386L ALA* 6.2 1.2 - - - +
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Residues in contact with VAL 52 (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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51L GLY* 1.3 71.7 - - - -
53L VAL* 1.3 61.9 + - - +
54L PHE* 3.6 31.8 + - + -
102L SER* 3.6 1.0 - - - -
103L TYR* 2.9 35.4 + - - +
119L LEU* 3.6 14.8 - - + +
123L PHE* 3.6 39.5 - - + -
205L ALA* 4.4 9.2 - - + -
206L VAL 3.6 9.0 - - - +
207L VAL* 4.2 9.2 - - + +
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Residues in contact with VAL 53 (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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51L GLY 4.3 8.1 - - - +
52L VAL* 1.3 75.8 - - - +
54L PHE* 1.3 59.3 + - - +
100L PHE* 4.1 13.2 - - + -
101L GLN 3.3 14.4 - - - +
102L SER* 3.7 19.3 - - - -
104L ILE* 4.9 10.1 - - + -
205L ALA* 3.7 0.2 - - - -
206L VAL* 2.7 41.9 + - + +
208L VAL* 4.4 13.9 - - + -
386L ALA 5.1 4.0 - - - +
387L ASN* 5.3 2.5 - - - +
390L GLY* 4.3 21.1 - - - -
391L ALA 4.5 0.4 - - - +
394L LEU* 3.6 24.7 - - + +
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Residues in contact with PHE 54 (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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52L VAL* 3.6 20.0 - - + -
53L VAL* 1.3 71.2 - - - +
55L GLY* 1.3 58.0 + - - +
56L SER* 2.9 15.1 + - - +
100L PHE* 3.4 3.1 - - - +
101L GLN* 2.8 42.5 + - + +
103L TYR* 3.9 16.6 - + - -
123L PHE* 3.6 37.2 - + - -
199L HIS 4.3 0.2 - - - -
200L PHE* 3.5 60.6 - + + -
201L LEU 4.2 0.7 - - - -
204L ASN* 3.5 9.6 - - - +
205L ALA* 3.6 27.1 - - + -
394L LEU* 3.5 2.2 - - - -
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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