Contacts of the strand formed by residues 48 - 54 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A THR* 1.3 75.6 - - - +
49A SER* 1.3 61.7 + - - +
50A VAL* 5.1 2.6 - - + +
105A VAL 4.2 0.2 - - - +
106A SER* 3.6 0.8 - - - -
107A SER* 2.9 39.6 + - - +
108A LEU 4.2 3.1 - - - +
109A PRO* 3.8 11.8 - - + -
112A THR* 5.2 3.8 - - - -
115A SER* 5.1 0.5 + - - -
210A THR 3.8 3.8 - - - -
211A GLY* 4.0 0.9 - - - -
212A ASN* 3.7 11.0 - - - +
213A ILE* 3.7 32.8 - - + -
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Residues in contact with SER 49 (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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47A THR 4.4 0.2 - - - -
48A ALA* 1.3 72.5 - - - +
50A VAL* 1.3 62.5 + - - +
104A ILE* 3.0 28.0 - - - +
105A VAL 3.2 4.8 + - - -
106A SER* 2.7 25.9 + - - -
208A VAL 3.9 0.7 - - - +
209A GLY* 3.5 1.7 - - - -
210A THR* 2.7 50.4 + - - +
213A ILE* 5.3 0.6 - - - +
382A PRO* 3.8 15.0 - - - -
383A VAL* 3.8 4.8 - - - +
386A ALA* 5.5 0.9 - - - +
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Residues in contact with VAL 50 (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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48A ALA* 5.1 2.7 - - + -
49A SER* 1.3 81.2 - - - +
51A GLY* 1.3 57.4 + - - +
104A ILE* 4.1 2.9 - - - -
105A VAL* 2.6 47.7 + - - +
112A THR* 4.1 22.9 - - - +
115A SER* 4.2 23.8 - - - +
116A LEU* 4.6 9.6 - - + -
119A LEU* 4.7 5.3 - - + +
207A VAL* 4.4 12.6 - - + -
208A VAL 3.3 11.2 - - - +
209A GLY* 4.6 0.2 - - - -
213A ILE* 4.4 11.9 - - + -
218A LEU* 3.8 23.1 - - + -
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Residues in contact with GLY 51 (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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50A VAL* 1.3 77.6 - - - +
52A VAL* 1.3 58.9 + - - -
53A VAL* 4.9 0.7 - - - -
103A TYR 3.1 15.3 - - - -
104A ILE* 3.7 12.7 - - - +
119A LEU* 4.7 7.0 - - - -
207A VAL* 3.6 5.4 - - - +
208A VAL* 2.6 45.4 + - - +
386A ALA* 6.2 0.4 - - - +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A GLY* 1.3 72.5 - - - -
53A VAL* 1.3 62.8 + - - +
54A PHE* 3.9 32.7 + - + -
102A SER* 3.6 1.7 - - - -
103A TYR* 2.9 36.1 + - + +
119A LEU* 3.7 29.3 - - + +
123A PHE* 4.1 17.0 - - + -
205A ALA* 4.2 13.7 - - + -
206A VAL 3.8 8.7 - - - +
207A VAL* 4.3 9.2 - - + +
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Residues in contact with VAL 53 (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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51A GLY 4.6 2.7 - - - +
52A VAL* 1.3 73.9 - - - +
54A PHE* 1.3 61.3 + - - +
100A PHE* 4.0 13.9 - - + -
101A GLN 3.7 11.0 - - - +
102A SER* 3.7 17.0 - - - -
104A ILE* 5.3 5.6 - - + -
205A ALA* 3.5 1.1 - - - -
206A VAL* 2.9 36.9 + - + +
208A VAL* 3.8 27.8 - - + -
386A ALA 4.8 4.9 - - - +
387A ASN* 5.8 2.5 - - - +
390A GLY* 3.9 18.2 - - - +
391A ALA 4.6 0.4 - - - +
394A LEU* 3.4 27.2 - - + +
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Residues in contact with PHE 54 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A VAL* 3.9 20.4 - - + -
53A VAL* 1.3 72.3 - - - +
55A GLY* 1.3 53.3 + - - +
56A SER* 2.8 19.5 + - - +
100A PHE* 3.2 3.1 - - - +
101A GLN* 2.9 38.5 + - + +
103A TYR* 3.8 34.3 - + - -
123A PHE* 4.0 19.1 - + + -
200A PHE* 3.7 55.6 - + + -
201A LEU 3.8 5.8 - - - -
204A ASN* 3.3 10.8 - - - +
205A ALA* 3.4 27.4 - - + -
394A LEU* 3.8 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