Contacts of the strand formed by residues 204 - 207 (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 ALA 204 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ASN 3.9 0.2 + - - -
203D PRO* 1.3 74.1 - - - +
205D ILE* 1.3 68.1 + - - +
229D ALA* 4.3 1.1 - - - -
230D PRO* 3.6 12.6 - - + +
232D TRP* 4.8 5.6 - - + -
264D LEU* 4.5 9.4 - - + -
267D HIS* 3.7 32.7 + - + +
269D VAL 3.0 6.3 + - - +
270D VAL* 3.3 12.0 - - + -
271D LEU* 2.9 24.9 + - - +
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Residues in contact with ILE 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D PRO* 6.0 0.7 - - + -
204D ALA* 1.3 77.4 - - - +
206D VAL* 1.3 69.2 + - - +
207D LEU* 3.4 31.0 - - + -
220D CYS* 5.1 1.8 - - + +
223D LEU* 4.3 17.3 - - + -
224D ALA* 3.8 36.1 - - + +
227D LEU* 4.4 10.8 - - + -
229D ALA* 4.0 15.5 - - + -
230D PRO 2.9 10.3 + - - +
231D VAL* 3.3 9.1 - - + -
232D TRP* 2.9 26.7 + - - -
271D LEU* 3.3 17.9 - - + +
273D ILE* 4.8 7.9 - - + -
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Residues in contact with VAL 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ILE* 1.3 78.8 - - - +
207D LEU* 1.3 61.0 + - - +
232D TRP* 3.3 7.9 - - + +
234D ALA* 3.8 23.6 - - + +
253D MET* 3.7 41.1 - - + -
264D LEU* 4.5 5.2 - - + -
270D VAL* 3.9 21.8 - - + -
271D LEU 2.8 7.3 + - - +
272D VAL* 3.2 16.0 - - + +
273D ILE 2.8 30.8 + - - -
278D PHE* 3.9 13.9 - - + -
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Residues in contact with LEU 207 (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* 3.4 27.8 - - + -
206D VAL* 1.3 77.4 - - - +
208D GLY* 1.3 58.9 + - - +
211D VAL* 4.3 2.9 - - + -
220D CYS* 3.8 28.0 - - + -
231D VAL* 3.8 11.7 - - + -
232D TRP 2.9 9.4 + - - +
233D VAL* 3.4 10.4 - - - +
234D ALA* 2.9 27.5 + - - -
241D PRO* 3.5 26.2 - - + +
242D PHE* 3.5 34.8 - - + -
273D ILE* 3.4 22.0 - - + +
275D ALA* 4.4 0.4 - - - -
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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