Contacts of the strand formed by residues 28 - 31 (chain M) 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 ILE 28 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370L LYS 4.6 0.7 - - - +
371L LEU* 3.9 28.5 - - + +
374L GLY* 3.8 29.4 - - - -
375L GLN* 4.0 8.3 - - + +
378L GLU* 2.9 20.0 + - + +
406L PHE* 5.7 0.4 - - + -
26M THR* 3.2 16.3 + - - -
27M LYS* 1.3 81.0 - - + +
29M SER* 1.3 72.9 + - - +
30M THR* 5.4 3.6 - - + +
92M THR* 3.8 17.5 - - + -
93M PHE 3.6 10.8 - - - +
94M LEU* 3.9 21.5 - - + -
191M ASN* 3.5 8.8 + - - +
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Residues in contact with SER 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28M ILE* 1.3 78.2 - - - +
30M THR* 1.3 67.0 + - - +
92M THR* 3.7 0.2 - - - -
93M PHE* 2.9 57.2 + - - -
95M LYS* 3.1 27.7 + - - +
98M LEU* 5.7 0.4 - - - +
190M GLU 4.1 5.2 - - - -
191M ASN* 2.9 25.7 + - - -
192M VAL* 4.4 4.2 - - - +
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Residues in contact with THR 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28M ILE* 5.4 4.0 - - + +
29M SER* 1.3 82.3 - - - +
31M LEU* 1.3 60.9 + - - +
32M ALA* 3.8 1.9 + - - +
90M LYS* 3.0 39.2 - - - +
91M ALA 3.4 7.6 + - - -
92M THR* 4.2 8.2 + - - -
93M PHE* 4.1 0.4 - - - -
188M SER 4.1 1.4 - - - +
190M GLU* 3.2 52.2 + - + +
191M ASN* 5.1 2.0 - - + -
192M VAL* 4.9 0.6 - - - +
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Residues in contact with LEU 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M THR* 1.3 75.8 - - - +
32M ALA* 1.3 75.7 + - - +
33M VAL* 4.5 3.4 - - + -
90M LYS* 3.3 4.9 - - - +
91M ALA* 2.9 33.6 + - + +
93M PHE* 3.4 23.3 - - + -
98M LEU* 3.7 31.2 - - + +
101M TYR 4.3 7.9 - - - +
102M VAL* 4.2 7.2 - - + -
105M LEU* 3.9 26.5 - - + -
187M VAL* 4.2 17.9 - - + -
188M SER 4.5 1.8 - - - -
189M GLY* 4.8 3.4 - - - -
192M VAL* 4.5 7.6 - - + -
197M LEU* 3.8 15.9 - - + -
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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