Contacts of the strand formed by residues 145 - 150 (chain O) in PDB entry 3KYM
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 LYS 145 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136O LEU* 5.7 0.2 - - - -
143O GLU* 5.6 1.0 - - + +
144O ALA* 1.3 72.7 - - - +
146O VAL* 1.3 60.4 + - - +
147O GLN* 2.9 44.8 + - + +
195O GLU* 3.9 19.4 + - - -
196O VAL* 3.3 9.5 - - - +
197O THR* 2.9 73.5 + - - +
204O PRO* 5.3 0.2 - - - +
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Residues in contact with VAL 146 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136O LEU* 4.1 25.1 - - + -
144O ALA 3.8 4.2 + - - +
145O LYS* 1.3 74.1 - - - +
147O GLN* 1.3 66.6 + - - +
148O TRP* 4.3 4.4 + - + +
161O GLU* 3.4 25.8 - - - +
175O LEU* 4.8 5.2 - - + -
177O SER* 3.7 25.6 - - - +
194O CYS* 3.8 28.7 - - - -
195O GLU 3.6 1.3 - - - +
196O VAL* 4.3 6.3 - - + -
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Residues in contact with GLN 147 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145O LYS* 2.9 40.7 + - + +
146O VAL* 1.3 77.8 - - - +
148O TRP* 1.3 63.7 + - - +
149O LYS* 4.8 7.8 + - + +
154O LEU* 3.9 34.1 - - + +
193O ALA 4.0 0.3 - - - +
194O CYS* 3.8 2.1 - - - -
195O GLU* 2.8 60.1 + - + +
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Residues in contact with TRP 148 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117O ILE* 3.5 37.5 - - + -
132O VAL* 3.9 34.3 - - + -
134O CYS* 3.6 29.6 - - + -
146O VAL* 4.3 6.5 + - + +
147O GLN* 1.3 76.0 - - - +
149O LYS* 1.3 63.9 + - - +
150O VAL* 4.1 2.5 - - + -
154O LEU* 3.4 9.7 - - - +
155O GLN* 3.0 42.5 + - + +
159O SER* 4.0 23.2 - - - -
177O SER* 3.0 32.7 + - - -
179O LEU* 4.1 24.7 - - + -
192O TYR* 5.3 3.4 - + + -
193O ALA 3.3 25.6 - - - -
194O CYS* 4.1 7.5 - - + -
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Residues in contact with LYS 149 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147O GLN* 4.8 10.4 + - + +
148O TRP* 1.3 79.1 - - - +
150O VAL* 1.3 62.1 + - - +
151O ASP 3.4 6.1 + - - -
152O ASN* 4.1 27.2 + - - +
153O ALA 3.5 3.8 - - - +
154O LEU* 4.3 20.4 - - + -
191O VAL* 3.7 3.6 - - - +
193O ALA* 3.1 45.8 + - + +
195O GLU* 2.8 36.8 + - + +
206O THR* 5.8 2.9 - - + -
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Residues in contact with VAL 150 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148O TRP* 5.6 1.3 - - + -
149O LYS* 1.3 71.1 - - - +
151O ASP* 1.3 73.5 + - - +
152O ASN 3.3 0.2 - - - -
153O ALA* 3.0 21.5 + - - +
155O GLN* 3.2 33.5 + - + +
179O LEU* 4.2 13.2 - - + -
181O LEU* 5.2 7.4 - - + -
189O HIS* 3.7 35.8 + - + +
191O VAL 3.8 2.7 - - - +
192O TYR* 3.7 36.3 - - + -
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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