Contacts of the strand formed by residues 204 - 209 (chain E) in PDB entry 2QKK
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 204 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E ASP* 3.4 35.5 + - - +
139E PHE* 3.0 49.8 - - + -
140E VAL* 3.2 6.6 + - - +
202E ILE* 3.9 2.4 - - - +
203E ASN* 1.3 98.5 - - - +
205E LEU* 1.3 59.8 + - - +
255E ASP* 3.0 22.0 - - + +
237W GLU* 4.5 6.3 + - - +
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Residues in contact with LEU 205 (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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139E PHE* 4.0 3.0 - - - -
140E VAL* 2.9 30.5 - - + +
142E VAL* 4.0 22.9 - - + -
164E TRP* 4.7 4.5 - - + -
194E ILE* 4.5 15.0 - - + +
197E ALA* 3.8 21.3 - - + -
202E ILE* 4.3 4.7 - - + -
204E LYS* 1.3 77.6 - - - +
206E VAL* 1.3 61.3 + - - +
207E LEU* 4.7 6.7 - - + -
254E MET* 4.2 15.7 - - - -
255E ASP 3.3 1.5 + - - +
256E ILE* 3.1 40.1 - - + +
257E GLN 3.2 21.5 + - - -
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Residues in contact with VAL 206 (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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136E MET 5.1 3.6 - - - +
139E PHE* 3.8 29.8 - - + -
140E VAL 3.3 5.3 + - - +
141E VAL* 3.3 17.7 - - + +
142E VAL* 2.9 27.1 + - - +
205E LEU* 1.3 72.2 - - - +
207E LEU* 1.3 59.0 + - - +
208E TYR* 3.0 37.2 - - + +
257E GLN* 3.8 27.1 - - + +
259E MET* 4.1 7.9 - - + -
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Residues in contact with LEU 207 (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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142E VAL* 3.8 15.3 - - + -
144E THR* 4.0 22.7 - - + +
190E ALA* 4.2 19.5 - - + +
193E ALA* 4.3 11.9 - - + -
194E ILE* 4.9 6.3 - - + +
205E LEU* 3.7 8.3 + - + +
206E VAL* 1.3 72.7 - - - +
208E TYR* 1.3 65.6 + - - +
209E THR* 4.0 5.1 + - + +
256E ILE* 3.9 21.1 - - + -
257E GLN 3.4 7.9 + - - -
258E TRP* 3.4 42.6 - - + +
259E MET 3.1 23.7 + - - +
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Residues in contact with TYR 208 (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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141E VAL* 3.9 25.0 - - + +
142E VAL 3.0 7.4 + - - -
143E TYR* 3.6 37.0 - + + +
144E THR* 3.1 27.0 + - - +
206E VAL* 3.0 34.1 - - + +
207E LEU* 1.3 73.8 - - - +
209E THR* 1.3 61.9 + - - +
259E MET* 3.2 26.8 - - + +
260E HIS 5.3 0.7 - - - -
261E VAL* 3.1 33.9 - - + -
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Residues in contact with THR 209 (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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144E THR* 3.2 31.5 + - - -
186E GLU* 3.8 9.8 + - - +
190E ALA* 6.0 0.7 - - + -
207E LEU* 4.4 11.4 - - + +
208E TYR* 1.3 71.0 - - - +
210E ASN* 1.3 68.9 + - - +
211E SER* 3.3 24.2 + - - +
214E THR* 5.1 4.3 - - + -
215E ILE* 4.0 26.7 - - + -
258E TRP* 5.0 3.1 - - + -
259E MET 3.1 2.6 + - - +
260E HIS* 3.2 9.4 + - - -
261E VAL* 3.2 25.9 + - - +
270E ASN* 5.4 0.9 - - - +
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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