Contacts of the helix formed by residues 179 - 185 (chain D) 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 ALA 179 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D THR* 3.3 26.5 - - + -
178D VAL* 1.3 74.1 - - - +
180D ASP* 1.3 70.3 + - - +
181D TYR* 3.5 19.7 - - + -
182D ASN* 2.3 38.1 + - - +
616I A 3.2 27.1 - - + +
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Residues in contact with ASP 180 (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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8D THR* 5.6 0.6 - - - +
52D GLN* 4.8 1.6 + - - -
114D MET* 3.9 26.0 - - + +
115D ILE 4.6 2.5 - - - +
116D ARG* 2.9 40.4 + - - +
178D VAL* 4.4 1.3 + - - -
179D ALA* 1.3 70.6 - - - +
181D TYR* 1.3 60.0 + - + +
182D ASN* 2.8 7.1 + - - +
183D LYS* 2.8 54.9 + - - +
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Residues in contact with TYR 181 (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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7D TYR* 3.5 37.5 - + - -
8D THR* 2.5 39.0 + - + +
52D GLN* 4.6 7.9 - - - +
173D PRO* 3.9 16.7 - - + +
179D ALA* 2.9 14.1 + - + -
180D ASP* 1.3 77.2 + - + +
182D ASN* 1.3 58.1 + - - -
183D LYS* 3.0 16.4 + - - +
184D PHE* 3.3 24.7 + - + +
185D TRP 4.5 0.2 + - - -
302D SFG 2.7 54.0 + - + +
616I A 3.3 27.2 - - - -
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Residues in contact with ASN 182 (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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173D PRO* 3.3 18.9 - - - +
174D TYR 3.2 17.0 - - - +
175D LEU* 5.2 1.0 - - - -
177D THR 2.9 12.7 + - - +
178D VAL* 2.8 19.9 - - + +
179D ALA* 2.3 50.1 + - - +
181D TYR* 1.3 70.5 - - - +
183D LYS* 1.3 65.7 + - - +
184D PHE 3.0 1.1 - - - -
185D TRP* 2.8 28.2 + - + +
616I A 3.4 8.5 - - - +
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Residues in contact with LYS 183 (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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52D GLN* 4.1 9.2 - - - +
116D ARG* 4.5 1.8 - - - +
117D ILE* 2.9 37.9 + - - +
180D ASP* 2.8 42.2 + - - +
181D TYR* 4.0 3.4 - - - +
182D ASN* 1.3 77.9 - - - +
184D PHE* 1.3 96.9 + - + +
185D TRP 3.1 9.0 + - - +
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Residues in contact with PHE 184 (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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51D ILE* 4.1 22.0 - - + -
52D GLN* 3.9 33.0 - - + -
181D TYR* 3.3 15.5 + - + +
182D ASN 3.0 1.2 - - - -
183D LYS* 1.3 109.8 - - + +
185D TRP* 1.3 67.6 + - - +
189D GLU* 3.8 15.3 - - - +
302D SFG 3.2 35.6 + + + +
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Residues in contact with TRP 185 (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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32D PHE* 4.0 15.5 - + - -
157D PHE* 4.3 9.6 - + - -
172D PRO* 3.7 11.4 - - + -
173D PRO* 3.5 47.4 + - + -
174D TYR 5.0 0.2 - - - -
175D LEU* 3.9 20.4 - - + +
182D ASN* 2.8 22.0 + - - +
183D LYS 3.1 5.4 + - - +
184D PHE* 1.3 86.2 - - - +
186D SER* 1.3 81.1 + - - +
189D GLU* 3.7 33.9 - - + -
190D GLU* 3.0 30.4 + - - -
193D LEU* 3.5 35.2 - - + -
302D SFG 4.4 9.0 - - - -
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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