Contacts of the helix formed by residues 171 - 175 (chain A) in PDB entry 2Y60
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 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A LEU* 3.8 38.1 - - + +
160A TYR* 4.0 6.3 - - + -
161A ALA* 3.7 24.2 - - - +
164A LEU* 3.5 29.2 - - + -
168A GLU 4.8 0.2 + - - -
170A PHE* 1.3 95.3 - + - +
172A ALA* 1.3 62.6 + - - +
173A ARG 3.2 2.0 - - - -
174A HIS* 2.9 27.9 + - - +
175A PHE* 3.6 4.9 + - - +
219A LEU* 4.1 15.7 - - + -
257A MET* 3.6 21.3 - - + -
260A LEU* 3.7 25.4 - - + -
288A LEU* 4.3 3.1 - - - +
294A ILE* 3.7 19.3 - - + -
297A PHE* 4.8 1.8 - + - -
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A SER* 4.4 23.6 - - - +
157A LEU* 4.4 9.9 - - + +
158A LYS* 4.7 6.5 - - + -
168A GLU 4.5 4.8 + - - +
169A ASN* 3.4 24.5 + - - +
171A PHE* 1.3 79.5 - - - +
173A ARG* 1.3 57.5 + - - +
174A HIS 3.0 0.4 - - - -
175A PHE* 3.0 35.7 + - + +
176A LYS* 4.3 2.9 - - - +
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Residues in contact with ARG 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLU* 4.3 13.8 + - - +
169A ASN* 2.9 26.3 + - + +
170A PHE* 2.9 51.1 + - - -
172A ALA* 1.3 75.7 - - - +
174A HIS* 1.4 86.3 + - + +
175A PHE 3.4 0.4 - - - -
176A LYS* 3.7 21.0 - - - +
294A ILE* 4.3 6.9 - - - +
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Residues in contact with HIS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A PHE 3.4 11.9 - - - -
171A PHE 2.9 8.6 + - - +
173A ARG* 1.4 118.5 + - + +
175A PHE* 1.3 58.5 + - - +
176A LYS* 3.8 5.8 + - - -
179A ASP* 4.7 2.6 - - - +
288A LEU* 3.5 16.9 - - + +
289A GLY* 3.4 23.4 + - - -
292A SER* 3.6 24.9 + - - +
293A VAL 4.0 19.9 + - - -
294A ILE* 3.6 20.1 - - + +
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Residues in contact with PHE 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A PHE* 3.3 57.7 - + - -
153A SER* 3.9 11.2 - - - -
154A SER* 3.5 16.1 + - - -
157A LEU* 3.9 26.2 - - + -
171A PHE 4.1 2.2 - - - +
172A ALA* 3.0 18.6 + - - +
173A ARG 3.4 0.4 - - - -
174A HIS* 1.3 77.6 - - - +
176A LYS* 1.3 60.6 + - - +
177A PRO* 4.4 0.5 - - - +
180A THR* 3.4 21.3 - - - -
182A ALA* 4.1 6.5 - - + -
284A PHE* 4.0 18.6 - + - -
286A VAL* 3.7 15.7 - - + -
287A ASN 3.5 20.0 - - - -
288A LEU* 4.1 3.1 - - + -
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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