Contacts of the strand formed by residues 269 - 273 (chain D) in PDB entry 4K9N
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 VAL 269 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196D ALA* 4.5 8.5 - - + +
197D LEU* 4.1 25.8 - - + -
200D ALA* 3.9 26.0 - - + -
202D ASN 4.3 0.7 - - - +
203D PRO* 3.1 6.3 - - + +
204D ALA 3.0 24.1 + - - +
267D HIS* 4.6 0.2 - - - +
268D ASP* 1.3 91.6 + - + +
270D VAL* 1.3 71.3 + - - +
271D LEU 4.7 0.4 - - - +
294D ARG* 3.4 22.7 - - + +
296D ILE* 4.1 20.4 - - + -
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Residues in contact with VAL 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D ALA* 3.3 9.0 - - + +
206D VAL* 3.9 28.0 - - + -
264D LEU* 3.9 31.9 - - + -
267D HIS* 4.1 12.3 - - + -
269D VAL* 1.3 78.1 - - - +
271D LEU* 1.3 60.2 + - - +
272D VAL* 4.1 11.9 - - + -
293D THR* 3.7 24.5 - - + -
294D ARG 2.9 10.5 + - - +
295D LEU* 3.4 9.8 - - + +
296D ILE* 2.8 28.9 + - - +
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Residues in contact with LEU 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D LEU* 4.8 6.1 - - + -
197D LEU* 4.2 35.2 - - + -
204D ALA 2.9 11.2 + - - +
205D ILE* 3.3 15.2 - - + +
206D VAL 2.8 25.9 + - - +
223D LEU* 4.0 17.0 - - + -
227D LEU* 5.3 1.8 - - + -
269D VAL* 4.1 1.6 - - + +
270D VAL* 1.3 70.9 - - - +
272D VAL* 1.3 62.4 + - - +
273D ILE* 3.8 25.8 - - + -
296D ILE* 3.4 31.4 - - + +
298D VAL* 4.2 18.6 - - + -
325D LEU* 4.3 7.2 - - + -
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Residues in contact with VAL 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D VAL* 3.2 17.7 - - + +
270D VAL* 4.1 4.7 - - + -
271D LEU* 1.3 77.2 - - - +
273D ILE* 1.3 60.1 + - - +
275D ALA* 3.9 28.0 - - + +
277D VAL* 4.2 14.1 - - + -
278D PHE* 4.0 19.7 - - + -
295D LEU* 3.8 34.8 - - + -
296D ILE 2.8 10.3 + - - +
297D SER* 3.3 8.4 - - - +
298D VAL* 2.7 33.8 + - - +
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Residues in contact with ILE 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D ILE* 4.8 2.0 - - + -
206D VAL 2.8 10.0 + - - +
207D LEU* 3.4 22.9 - - + -
208D GLY 2.9 23.7 + - - -
211D VAL* 3.5 19.6 - - + +
220D CYS* 4.4 9.2 - - - -
223D LEU* 3.8 18.8 - - + -
271D LEU* 3.8 33.2 - - + +
272D VAL* 1.3 77.9 - - - +
274D GLY* 1.3 62.7 + - - +
275D ALA 3.4 2.0 - - - -
298D VAL* 3.6 12.6 - - + +
318D ILE* 3.9 20.6 - - + +
321D MET* 6.1 0.4 - - + -
322D ALA* 5.1 8.3 - - + +
325D LEU* 4.7 7.4 - - + -
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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