Contacts of the strand formed by residues 145 - 150 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E LEU* 6.2 0.4 - - - -
144E ALA* 1.3 71.1 - - - +
146E VAL* 1.3 61.9 + - - +
147E GLN* 3.6 40.4 - - + +
195E GLU 3.5 0.9 - - - +
196E VAL* 3.2 8.3 - - - +
197E THR* 2.8 58.5 + - + +
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Residues in contact with VAL 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E CYS* 4.3 3.1 - - - -
136E LEU* 4.7 13.7 - - + -
144E ALA 3.9 2.5 + - - +
145E LYS* 1.3 75.3 - - - +
147E GLN* 1.3 67.6 + - - +
148E TRP* 4.3 5.9 + - + +
161E GLU* 4.3 18.4 - - + +
175E LEU* 4.7 6.3 - - + -
177E SER* 3.8 35.2 - - - +
194E CYS* 3.4 33.2 - - - -
195E GLU 3.3 4.0 - - - +
196E VAL* 4.7 1.1 - - + +
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Residues in contact with GLN 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E LYS* 3.6 33.1 - - + +
146E VAL* 1.3 74.5 - - - +
148E TRP* 1.3 65.0 + - - +
149E LYS* 3.9 8.3 + - - +
154E LEU* 3.5 42.7 - - + +
194E CYS* 3.8 2.4 - - - -
195E GLU* 2.9 61.1 + - + +
197E THR* 5.3 1.4 + - - -
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Residues in contact with TRP 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E ILE* 3.8 23.8 - - + -
132E VAL* 3.1 52.3 - - + -
133E VAL 4.0 3.1 - - - -
134E CYS* 3.8 15.0 - - + -
146E VAL* 4.8 5.8 - - + +
147E GLN* 1.3 74.9 - - - +
149E LYS* 1.3 66.2 - - - +
154E LEU* 3.6 4.3 - - - +
155E GLN* 3.0 45.2 + - + +
159E SER* 3.9 20.4 - - - +
177E SER* 3.3 39.7 + - - -
179E LEU* 3.8 31.2 - - + +
192E TYR* 4.8 2.7 - - + -
193E ALA 3.3 25.1 - - - -
194E CYS* 4.4 3.4 - - + -
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Residues in contact with LYS 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E GLN* 3.9 11.6 + - - +
148E TRP* 1.3 80.2 - - - +
150E VAL* 1.3 67.4 + - - +
151E ASP 4.0 0.7 - - - -
152E ASN* 4.3 22.6 + - - +
153E ALA 3.3 18.8 - - - +
154E LEU* 4.2 10.1 - - + +
191E VAL 3.9 0.7 - - - +
192E TYR* 3.7 1.0 - - - +
193E ALA* 3.0 44.6 + - + +
195E GLU* 3.0 37.8 + - + -
206E THR* 5.4 0.8 + - - -
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Residues in contact with VAL 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E TRP* 5.8 0.4 - - + -
149E LYS* 1.3 78.0 - - - +
151E ASP* 1.3 86.8 + - - +
153E ALA* 3.2 20.4 + - - +
155E GLN* 3.3 31.1 + - + +
179E LEU* 4.6 8.7 - - + -
181E LEU* 5.0 4.3 - - + -
189E HIS* 3.3 37.3 + - + +
191E VAL 3.5 4.5 - - - +
192E TYR* 3.5 31.6 - - + -
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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