Contacts of the strand formed by residues 252 - 259 (chain E) in PDB entry 3K75
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 HIS 252 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142E TYR* 3.4 45.4 + + + -
145E ASP* 2.8 46.1 + - + +
146E PHE* 3.6 8.2 - - - -
225E THR* 3.5 31.0 + - + +
238E VAL* 3.9 12.0 - - + +
239E CYS 3.8 2.7 - - - -
240E GLN* 3.7 35.0 + - + +
251E PRO* 1.3 72.4 - - - +
253E ARG* 1.3 66.8 + - - +
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Residues in contact with ARG 253 (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 ASP 4.0 3.5 + - - -
146E PHE* 3.6 6.5 - - - +
148E LYS* 3.6 22.6 + - - +
149E ARG 3.2 26.3 + - - -
150E ILE* 3.5 33.2 - - + +
151E PRO* 3.8 9.1 - - - +
154E GLU* 2.9 28.9 + - - -
158E MET* 4.4 15.0 - - + -
238E VAL* 3.5 6.1 - - - +
239E CYS* 3.0 44.9 + - - +
240E GLN* 5.7 1.1 - - - -
241E LEU* 6.2 1.6 - - + +
250E TYR* 5.9 0.2 - - - +
251E PRO* 3.5 41.2 + - - +
252E HIS* 1.3 80.2 - - - +
254E ARG* 1.3 64.1 + - - +
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Residues in contact with ARG 254 (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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104E THR* 4.9 13.5 - - + +
146E PHE* 3.7 35.1 - - + +
150E ILE* 5.2 0.4 - - - +
189E GLY 5.0 3.0 + - - +
190E ASP* 3.5 26.1 + - + +
191E MET* 2.8 27.2 + - - +
228E LEU* 3.4 25.7 - - - +
236E MET* 3.1 25.3 - - - +
237E GLY 3.1 18.9 + - - +
253E ARG* 1.3 75.5 - - - +
255E ILE* 1.3 91.7 + - - +
256E ASP* 2.6 24.1 + - - -
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Residues in contact with ILE 255 (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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162E VAL* 4.3 12.1 - - + -
191E MET* 3.3 23.1 - - + +
193E VAL* 4.6 2.5 - - + -
218E LEU* 5.1 2.2 - - + -
223E PHE* 3.9 29.2 - - + -
224E ILE* 4.7 3.6 - - + -
235E PHE* 3.7 13.6 - - + +
237E GLY* 3.0 33.3 + - - +
238E VAL 4.1 12.1 - - - +
239E CYS* 4.0 12.8 - - + -
253E ARG 3.7 0.2 + - - -
254E ARG* 1.3 91.8 + - - +
256E ASP* 1.3 69.3 + - - +
257E ILE* 4.4 15.7 - - + -
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Residues in contact with ASP 256 (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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190E ASP* 4.9 6.9 + - - +
191E MET 2.6 14.1 + - - +
192E ASP* 3.3 24.5 - - - +
193E VAL* 3.0 24.4 + - - +
234E LYS* 3.5 24.8 + - - +
235E PHE 3.6 2.2 - - - -
236E MET* 3.9 10.4 - - - +
254E ARG* 2.6 38.7 + - - -
255E ILE* 1.3 71.6 - - - +
257E ILE* 1.3 71.8 + - - +
258E ARG* 4.2 8.9 + - + +
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Residues in contact with ILE 257 (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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162E VAL* 6.0 1.8 - - + -
193E VAL* 3.5 18.4 - - + +
195E LEU* 4.4 20.6 - - + -
211E LEU* 3.4 24.8 - - + +
214E VAL* 5.1 5.8 - - + -
215E VAL* 4.1 11.2 - - + -
218E LEU* 4.0 25.8 - - + -
224E ILE* 4.7 1.1 - - + -
233E THR 3.6 1.7 - - - +
234E LYS* 3.4 3.0 - - - +
235E PHE* 2.9 56.3 + - + +
255E ILE* 4.4 14.4 - - + -
256E ASP* 1.3 83.1 - - - +
258E ARG* 1.3 60.4 + - - +
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Residues in contact with ARG 258 (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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192E ASP* 4.0 17.8 + - - +
193E VAL 3.0 6.8 + - - +
194E LEU* 3.5 19.8 - - + -
195E LEU* 2.8 29.0 + - - +
233E THR 3.5 4.7 - - - +
234E LYS* 3.3 50.1 - - + +
256E ASP* 4.2 8.3 + - - +
257E ILE* 1.3 73.0 - - - +
259E LEU* 1.3 62.2 + - - +
260E ILE* 3.9 10.3 - - + +
272E PHE* 4.0 41.6 - - - -
295E GLU* 5.4 1.2 + - - -
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Residues in contact with LEU 259 (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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173E TYR* 5.6 0.2 - - + -
195E LEU* 3.5 38.1 - - + +
196E THR* 4.2 8.7 - - - -
197E HIS 5.1 0.4 - - - +
200E PHE* 3.8 30.9 - - + -
207E GLN 3.9 24.0 - - - +
208E PRO* 5.1 0.2 - - + -
210E LEU* 4.2 16.6 - - + -
211E LEU* 4.3 18.4 - - + +
232E GLU 4.9 4.7 - - - +
233E THR* 2.6 40.5 + - + +
257E ILE 3.8 0.8 + - - -
258E ARG* 1.3 73.2 - - - +
260E ILE* 1.3 64.8 + - - +
261E PRO* 4.4 2.1 - - - +
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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