Contacts of the strand formed by residues 214 - 222 (chain D) in PDB entry 6VSU
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 214 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178D PRO* 4.0 5.3 - - - +
179D VAL 3.1 10.1 - - - +
181D ILE* 3.8 26.7 - - + -
208D ILE* 4.2 4.1 + - + -
209D MET* 3.8 31.4 - - + +
212D GLY* 3.2 8.7 - - - +
213D TYR* 1.3 80.2 - - - +
215D ARG* 1.3 62.8 + - - +
216D ARG 4.1 8.3 - - - +
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Residues in contact with ARG 215 (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 PRO* 4.0 9.7 - - + +
179D VAL 2.9 9.4 + - - +
180D ASP* 2.9 38.5 + - - +
209D MET* 4.1 10.6 - - - +
214D ALA* 1.3 75.2 - - - +
216D ARG* 1.3 74.8 + - + +
217D LEU 4.0 0.7 + - - -
236D PHE 5.3 0.7 - - - +
237D GLY 5.5 2.4 - - - +
260D GLU* 2.9 32.9 + - - +
261D GLY* 4.6 3.0 + - - -
262D VAL* 3.6 32.5 - - + +
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Residues in contact with ARG 216 (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 VAL 4.1 1.9 - - - +
180D ASP* 2.9 35.0 + - + +
181D ILE* 2.8 31.2 + - - +
214D ALA* 4.1 3.6 - - - +
215D ARG* 1.3 91.0 - - + +
217D LEU* 1.3 58.1 + - - +
218D LEU* 3.7 19.9 - - + +
237D GLY 5.7 2.2 - - - -
239D GLU* 2.8 42.7 + - - +
252D MET* 5.0 8.7 - - - +
256D LEU* 5.9 0.6 - - - +
257D LYS 4.1 8.5 + - - -
258D LEU* 3.7 20.4 - - - +
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Residues in contact with LEU 217 (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 ILE* 3.4 22.0 - - + -
183D HIS* 3.6 31.0 - - + -
190D ILE* 4.7 0.9 - - + -
205D PHE* 4.0 21.1 - - + -
209D MET* 3.9 38.7 - - + +
214D ALA* 5.2 0.2 - - + -
215D ARG 4.0 1.4 + - - -
216D ARG* 1.3 74.8 - - - +
218D LEU* 1.3 59.1 - - - +
219D GLN* 3.9 13.5 - - + +
237D GLY 5.2 3.2 + - - -
238D VAL* 3.5 30.0 - - + +
239D GLU* 2.9 28.3 + - - +
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Residues in contact with LEU 218 (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 ILE 2.8 13.6 + - - +
182D LEU* 3.6 11.2 - - + +
183D HIS* 2.8 30.7 + - - +
216D ARG* 3.7 31.0 - - + +
217D LEU* 1.3 73.2 - - - +
219D GLN* 1.3 57.3 + - - +
220D VAL* 4.0 6.2 + - + -
239D GLU* 3.3 38.6 - - + +
241D TYR* 4.1 13.9 - - + +
252D MET* 5.1 0.2 - - + -
256D LEU* 3.8 35.2 - - + -
258D LEU* 4.0 19.1 - - + -
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Residues in contact with GLN 219 (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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183D HIS* 2.8 35.6 + - - +
188D PRO* 2.8 31.7 + - - +
190D ILE* 4.8 3.2 - - - +
205D PHE* 4.4 1.6 - - - +
217D LEU* 3.9 16.0 - - + +
218D LEU* 1.3 71.2 - - - +
220D VAL* 1.3 61.6 + - - +
222D ILE* 3.9 17.7 - - + +
238D VAL* 3.4 21.1 - - + +
239D GLU 2.8 11.0 + - - +
240D GLN* 3.0 33.7 + - + +
241D TYR* 2.8 34.3 + - - +
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Residues in contact with VAL 220 (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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182D LEU* 3.8 22.7 - - + -
183D HIS 2.7 9.8 + - - +
184D LEU* 3.4 28.2 - - + +
185D ASP 3.0 25.9 + - - +
218D LEU* 4.4 4.7 - - + +
219D GLN* 1.3 79.2 - - - +
221D GLY* 1.3 63.9 + - - +
222D ILE* 3.5 2.4 - - - +
241D TYR* 3.9 9.9 - - + -
246D PHE* 5.3 1.1 - - + -
253D LEU* 3.8 41.7 - - + -
256D LEU* 5.2 0.9 - - + -
273D CYS* 4.6 0.9 - - - +
290D LEU* 4.5 6.1 - - + -
298D ILE* 4.2 13.7 - - + -
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Residues in contact with GLY 221 (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 ASP 3.2 11.0 - - - +
186D ALA* 3.5 0.3 - - - -
220D VAL* 1.3 74.2 - - - +
222D ILE* 1.3 65.2 + - - +
223D ARG* 3.1 26.9 + - - -
241D TYR* 3.3 6.0 + - - +
243D MET* 3.4 28.2 - - - +
273D CYS 5.0 0.4 - - - -
290D LEU* 4.2 12.6 - - - -
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Residues in contact with ILE 222 (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 ASP* 3.5 11.9 - - + +
186D ALA 3.5 5.4 - - - +
187D HIS 3.4 33.4 - - - +
188D PRO* 3.5 11.9 - - + -
219D GLN* 3.9 30.3 - - + +
221D GLY* 1.3 75.9 - - - +
223D ARG* 1.3 61.9 + - - +
225D ILE* 4.0 37.5 - - + -
240D GLN* 5.1 4.3 - - + -
241D TYR 3.3 18.5 + - - +
242D GLU* 3.2 17.0 - - + +
243D MET 2.8 26.5 + - - -
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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