Contacts of the strand formed by residues 167 - 170 (chain B) in PDB entry 1YFL
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 PHE 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B PHE* 2.9 36.6 - + - -
23B PRO* 3.6 33.7 - - + -
24B LYS 4.5 1.1 - - - +
25B TYR* 3.3 25.8 - + + +
27B ARG 2.7 8.9 + - - -
28B PHE* 3.6 17.2 - + - -
29B VAL* 2.7 30.1 + - - +
166B ASP* 1.3 72.8 - - - +
168B VAL* 1.3 84.3 + - - +
169B TYR* 3.8 4.8 + - + -
206B LYS* 3.2 12.1 - - + -
207B PHE* 3.2 20.9 - - - -
208B GLY* 3.5 3.8 - - - -
256B TYR* 3.4 22.2 - - - -
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 3.7 15.3 - - + -
31B LEU* 5.5 6.1 - - + -
162B ILE* 4.9 11.2 - - + -
166B ASP 4.2 1.0 + - - -
167B PHE* 1.3 82.7 - - - +
169B TYR* 1.3 61.0 + - - +
170B VAL* 4.0 8.0 - - + +
200B LEU* 4.5 18.2 - - + -
205B ILE* 5.5 0.9 - - + -
206B LYS 3.3 9.1 + - - +
207B PHE* 3.3 9.3 - - + +
208B GLY 2.8 26.7 + - - +
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Residues in contact with TYR 169 (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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11B LYS* 4.2 6.9 - - + +
18B LEU* 3.2 27.0 - - + +
22B PHE* 4.6 10.8 - + - -
28B PHE* 3.5 27.8 - + + -
29B VAL 2.7 8.9 + - - -
30B ASP* 3.8 17.1 - - - +
31B LEU* 3.4 22.2 + - - +
32B PHE 4.4 0.7 + - - -
38B VAL* 3.7 34.8 - - + -
167B PHE* 3.8 4.5 + - + -
168B VAL* 1.3 72.0 - - - +
170B VAL* 1.3 77.6 + - - +
171B ASP* 3.7 18.2 + - + +
208B GLY* 3.1 18.6 - - - -
210B SER* 3.3 21.7 - - - -
256B TYR* 4.3 10.3 - + - -
301B SFG 4.8 2.5 - - - -
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Residues in contact with VAL 170 (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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31B LEU* 3.6 28.7 - - + -
32B PHE* 3.6 14.8 - - + -
168B VAL* 5.2 5.6 - - + -
169B TYR* 1.3 80.8 - - - +
171B ASP* 1.3 61.2 + - - +
172B PRO* 3.1 25.4 - - + -
193B LEU* 3.9 12.6 - - + -
197B LEU* 4.4 17.0 - - + -
208B GLY 2.6 15.9 + - - +
209B LEU* 3.2 24.3 - - + -
210B SER 2.9 25.3 + - - -
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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