Contacts of the strand formed by residues 185 - 190 (chain D) in PDB entry 2YVL
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 PRO 185 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59C THR* 4.3 12.8 - - + -
86D LYS 4.7 2.2 - - - +
87D LEU* 3.7 39.7 - - + +
88D ASN* 4.5 4.5 - - + +
160D HIS 3.3 18.4 - - - +
161D ALA* 3.3 6.6 - - + +
162D ALA 3.3 19.8 + - - -
180D LEU* 4.3 1.6 - - - +
183D GLY 3.6 3.8 - - - +
184D ALA* 1.4 85.6 - - - +
186D VAL* 1.3 61.2 + - - +
242D PHE* 6.2 0.4 - - + -
243D GLY 3.3 11.9 - - - +
244D ARG* 3.8 18.2 - - - +
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Residues in contact with VAL 186 (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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87D LEU* 3.7 5.1 - - - +
162D ALA* 3.2 13.7 - - + +
164D VAL* 5.7 0.9 - - + -
176D VAL* 3.8 16.4 - - + -
180D LEU* 3.4 31.0 - - + -
185D PRO* 1.3 73.2 - - - +
187D GLY* 1.3 58.9 + - - +
188D PHE* 3.9 20.9 - - + -
207D PHE* 3.3 39.3 - - + -
241D VAL 4.4 0.4 - - - -
242D PHE* 3.4 8.8 - - - -
243D GLY* 3.0 35.7 + - - +
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Residues in contact with GLY 187 (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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87D LEU* 3.7 1.6 - - - +
162D ALA 2.9 9.1 + - - +
163D PHE* 3.3 22.8 - - - -
164D VAL* 2.8 31.9 + - - +
186D VAL* 1.3 74.9 - - - +
188D PHE* 1.3 61.9 + - - -
241D VAL 3.1 9.2 - - - -
242D PHE* 3.8 8.7 - - - -
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Residues in contact with PHE 188 (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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163D PHE* 3.6 7.4 - - - -
164D VAL* 3.3 30.5 - - + +
169D PRO* 3.7 25.8 - - + -
173D LEU* 3.7 31.6 - - + -
176D VAL* 5.5 1.8 - - + -
186D VAL* 3.9 25.8 - - + -
187D GLY* 1.3 73.0 - - - -
189D LEU* 1.3 59.3 + - - +
190D LEU* 4.0 7.1 + - + -
199D LEU* 3.6 23.6 - - + -
203D ILE* 3.8 22.2 - - + -
207D PHE* 4.3 10.3 - + - -
239D TYR 3.8 0.7 - - - +
240D LEU* 3.6 6.1 - - - -
241D VAL* 2.8 50.9 + - + +
243D GLY 5.6 0.9 - - - -
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Residues in contact with LEU 189 (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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73D GLN* 6.3 3.4 - - + -
74D ILE 5.9 0.7 - - - +
75D ILE* 3.7 32.8 - - + -
79D ASP* 4.5 5.4 - - - +
83D ILE* 4.8 0.4 - - + -
163D PHE* 3.5 18.1 - - + -
164D VAL 3.0 10.3 + - - +
165D ASP* 3.6 35.7 - - - +
166D VAL 4.3 4.7 + - - +
188D PHE* 1.3 72.1 - - - +
190D LEU* 1.3 70.6 + - - +
191D PRO* 4.1 10.8 - - + +
237D THR* 6.1 0.2 - - - -
238D ALA* 3.5 28.7 - - + -
239D TYR 3.9 1.8 - - - -
240D LEU* 3.9 16.8 - - + -
603D SAM 5.9 0.9 - - + -
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Residues in contact with LEU 190 (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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166D VAL 4.0 3.4 - - - +
169D PRO* 3.7 30.1 - - + -
188D PHE* 4.6 5.6 - - + -
189D LEU* 1.3 83.6 - - - +
191D PRO* 1.3 67.1 - - - +
192D THR 3.2 1.0 + - - +
195D GLN* 3.5 53.6 - - + +
196D VAL* 3.7 19.7 - - + +
199D LEU* 3.7 27.4 - - + -
238D ALA* 3.8 2.9 - - - -
239D TYR* 2.9 37.8 + - - +
241D VAL* 4.4 5.6 - - + -
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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