Contacts of the strand formed by residues 205 - 210 (chain B) in PDB entry 5H15
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 LEU 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B PHE* 3.6 5.2 - - - -
199B HIS* 3.0 60.5 + - + +
202B ASP* 3.3 29.4 + - + +
203B PRO 3.5 0.2 - - - -
204B ASN* 1.3 74.1 - - - +
206B LEU* 1.3 60.4 + - - +
217B LEU* 4.1 14.8 - - + -
218B TRP 3.3 10.3 - - - +
219B ASN* 4.4 19.3 - - + +
226B VAL* 4.4 10.5 - - + -
244B TYR* 3.3 3.8 + - - -
274B ILE* 4.1 39.5 - - + -
278B TYR* 4.9 1.3 - - + -
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Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ALA* 4.2 9.9 - - + -
172B ILE* 3.7 40.6 - - + -
174B ILE* 4.3 6.3 - - + -
196B LEU* 4.2 13.9 - - + -
197B LYS 3.6 26.0 - - - +
198B PHE* 3.6 37.0 - - + -
204B ASN 3.4 0.8 + - - -
205B LEU* 1.3 74.4 - - - +
207B LEU* 1.3 64.2 + - - +
217B LEU* 3.6 1.0 - - - -
218B TRP* 2.8 47.5 + - + +
220B ILE* 4.2 14.6 - - + -
244B TYR* 3.9 1.3 - - - -
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Residues in contact with LEU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLU 3.8 0.7 - - - +
196B LEU* 3.3 6.8 - - - +
197B LYS* 2.8 46.4 + - + +
206B LEU* 1.3 73.6 - - - +
208B SER* 1.3 60.3 + - - +
209B VAL* 4.5 3.7 - - + +
215B LEU* 4.0 24.7 - - + -
216B ARG 3.4 17.0 - - - +
217B LEU* 4.6 5.8 - - + +
229B PHE* 4.7 5.4 - - + -
242B ALA* 3.8 17.5 - - + -
243B ASP 5.0 1.3 - - - +
244B TYR* 3.5 22.4 + - + +
251B ILE* 3.7 48.7 - - + -
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Residues in contact with SER 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ILE* 3.9 11.2 - - - -
189B HIS* 2.7 33.6 + - - -
193B ILE* 4.2 4.7 - - - -
195B GLU 3.5 5.2 - - - -
196B LEU* 3.7 18.2 - - - -
206B LEU 4.1 0.6 + - - -
207B LEU* 1.3 71.9 - - - +
209B VAL* 1.3 64.1 + - - +
215B LEU* 3.2 5.5 - - - +
216B ARG* 2.8 30.5 + - - +
218B TRP* 3.0 18.1 + - - -
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ILE* 3.4 4.0 - - - -
194B ASN 2.9 26.2 + - - -
195B GLU* 3.1 27.5 + - + +
197B LYS* 6.4 1.3 - - + -
207B LEU* 4.5 6.3 - - + -
208B SER* 1.3 79.4 - - - +
210B SER* 1.3 60.9 + - - +
214B ALA 3.8 2.9 - - - -
215B LEU* 3.8 11.9 - - + +
239B VAL* 3.5 30.7 - - + +
240B LEU 3.8 19.3 - - - -
241B SER* 3.9 3.1 - - - +
242B ALA* 3.6 30.1 - - + +
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Residues in contact with SER 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B HIS* 3.0 35.6 + - - -
191B ASN 3.5 9.0 + - - -
192B ALA 3.0 12.9 + - - -
193B ILE* 4.6 0.2 - - - -
194B ASN* 4.6 0.4 - - - +
209B VAL* 1.3 75.9 - - - +
211B LYS* 1.3 70.8 + - - +
212B ASP* 3.1 24.6 + - - +
213B HIS* 3.1 10.0 + - - -
214B ALA 2.9 9.7 + - - -
239B VAL* 3.0 27.3 + - - +
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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