Contacts of the strand formed by residues 190 - 198 (chain D) in PDB entry 2BS3
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 190 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186D HIS* 3.0 6.1 - - - +
187D GLN 3.0 31.5 + - - +
188D ASP* 3.9 11.0 - - + +
189D GLY* 1.3 83.1 - - - +
191D CYS* 1.3 61.0 + - - +
192D TYR* 3.8 31.1 + - + +
385D LEU* 3.7 4.7 - - - +
386D LYS* 3.4 21.1 - - + +
427D HIS* 6.3 2.2 - - - -
431D THR* 4.5 8.0 + - - -
432D GLN 3.6 22.0 + - - -
433D VAL* 4.3 10.6 - - - +
434D ASP 5.4 1.0 - - - +
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Residues in contact with CYS 191 (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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184D LEU* 4.5 6.7 - - - -
185D ILE 3.5 7.0 - - - -
186D HIS* 4.2 1.8 - - - -
190D LYS* 1.3 73.7 - - - +
192D TYR* 1.3 68.9 + - - +
193D GLY 3.7 23.7 + - - -
209D ALA 4.4 4.0 - - - +
210D LYS 4.6 5.9 - - - +
211D GLY* 5.2 0.3 - - - -
212D THR* 3.9 22.1 + - - -
385D LEU* 3.8 20.1 - - + +
386D LYS 2.7 18.0 + - - +
387D GLY* 4.1 8.7 - - - +
388D LEU* 4.0 22.4 - - + +
433D VAL* 5.3 0.5 - - - +
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Residues in contact with TYR 192 (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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185D ILE* 2.8 25.1 + - + +
186D HIS* 4.6 2.9 - - - -
187D GLN* 3.6 48.2 + - + +
188D ASP* 4.9 5.4 + - - +
190D LYS* 3.8 37.6 + - + +
191D CYS* 1.3 77.5 - - - +
193D GLY* 1.3 56.7 + - - +
208D VAL* 3.1 11.6 - - + +
209D ALA 2.9 29.6 + - - +
212D THR* 4.4 0.7 - - - -
433D VAL* 3.2 41.7 - - + -
434D ASP* 4.1 21.8 + - - +
435D LEU* 3.9 15.4 - - + +
436D GLU 6.1 0.4 - - - -
439D THR* 5.3 2.5 - - + -
440D LEU* 5.5 1.8 - - + -
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Residues in contact with GLY 193 (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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9D LEU* 4.2 3.8 - - - -
184D LEU* 3.5 11.2 - - - +
185D ILE* 2.8 23.9 + - - +
191D CYS* 3.6 5.5 - - - -
192D TYR* 1.3 81.6 - - - +
194D ALA* 1.3 62.4 + - - +
207D TYR 3.1 10.5 - - - -
208D VAL* 4.3 1.1 - - - -
209D ALA 4.4 0.7 - - - -
212D THR* 3.4 21.7 + - - -
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Residues in contact with ALA 194 (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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9D LEU* 4.0 7.9 - - + +
11D ILE* 3.9 27.4 - - + -
181D ALA* 4.3 7.9 - - + -
183D ALA 3.2 13.2 - - - +
184D LEU* 4.1 3.6 - - + -
185D ILE* 3.7 8.8 - - - +
193D GLY* 1.3 75.6 - - - +
195D VAL* 1.3 66.7 + - - +
196D VAL* 3.7 5.4 + - + -
206D ALA* 3.7 1.4 - - - -
207D TYR* 2.8 34.6 + - - +
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Residues in contact with VAL 195 (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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181D ALA* 3.6 2.6 - - - -
182D ILE* 3.0 30.1 + - + +
183D ALA* 2.8 23.9 + - + +
185D ILE* 3.9 13.2 - - + -
194D ALA* 1.3 72.6 - - - +
196D VAL* 1.3 61.9 + - - +
204D ILE* 3.5 30.1 - - + -
205D ILE 3.5 6.1 - - - +
206D ALA* 4.6 0.4 - - - +
443D PHE* 3.7 38.6 - - + +
444D VAL* 4.3 6.1 - - + +
447D GLN* 3.6 21.8 - - + -
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Residues in contact with VAL 196 (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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34D LEU* 3.5 21.5 - - + -
179D LYS* 3.1 39.3 - - + -
180D GLU 3.4 12.3 - - - +
181D ALA* 4.2 6.7 - - - -
182D ILE* 4.8 0.7 - - - -
194D ALA* 4.0 9.2 - - + +
195D VAL* 1.3 82.6 - - - +
197D ARG* 1.3 63.9 + - - +
198D ASP 4.0 0.2 + - - -
203D ASP 3.5 1.0 - - - +
204D ILE* 3.4 4.2 - - - +
205D ILE* 2.6 40.8 + - + +
207D TYR* 3.4 32.8 - - + -
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Residues in contact with ARG 197 (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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179D LYS* 3.7 0.5 - - - -
180D GLU* 2.8 40.2 + - + +
182D ILE* 4.1 13.9 - - + +
195D VAL 4.4 0.4 + - - -
196D VAL* 1.3 76.5 - - - +
198D ASP* 1.3 69.3 + - - +
199D LEU* 3.2 23.5 + - - +
202D GLY* 4.1 9.6 + - - +
203D ASP 3.4 4.0 - - - +
204D ILE* 4.0 17.0 - - + -
451D MET* 3.8 28.6 - - - +
511D LEU* 2.8 29.7 + - - +
513D ALA 4.5 3.0 - - - +
514D ASN* 4.3 15.2 + - - +
517D LEU* 3.7 18.4 - - - +
518D GLU* 3.7 11.9 + - - +
521D TYR* 3.0 29.4 + - - +
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Residues in contact with ASP 198 (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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178D ARG 3.9 2.5 - - - +
179D LYS* 3.0 38.5 + - + +
196D VAL* 4.0 0.8 + - - +
197D ARG* 1.3 72.3 - - - +
199D LEU* 1.3 57.4 + - - +
200D VAL* 2.8 34.7 + - - +
201D THR* 3.0 33.1 + - - +
202D GLY* 2.7 32.9 + - - -
203D ASP* 2.8 20.6 + - + +
205D ILE* 4.5 8.2 - - + +
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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