Contacts of the strand formed by residues 172 - 176 (chain A) in PDB entry 1Y57
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 172 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A TRP* 3.6 28.9 - + + -
162A LEU* 3.8 5.4 - - - -
170A GLY 3.8 4.3 - - - -
171A THR* 1.3 78.7 - - - +
173A LEU* 1.3 68.1 + - - +
174A VAL* 4.9 0.4 - - + -
186A LEU* 3.8 17.3 - - + -
187A SER 3.2 12.6 - - - +
188A VAL* 4.4 1.1 - - + -
227A VAL* 3.7 34.1 - - + -
231A SER* 4.7 3.6 - - - -
241A LEU* 3.7 41.3 - - + -
242A THR 4.3 4.7 - - - -
243A THR 2.9 42.2 + - - -
244A VAL* 3.8 15.0 - - + +
245A CYS 2.9 22.3 + - - -
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TRP 3.4 5.8 - - - -
150A PHE* 3.5 37.2 - - + -
153A ILE* 4.1 13.7 - - + -
158A SER* 4.0 12.6 - - - +
161A LEU* 4.5 2.5 - - + -
162A LEU* 4.0 27.4 - - + -
172A PHE* 1.3 80.0 - - - +
174A VAL* 1.3 75.7 + - - +
175A ARG* 4.0 25.4 - - + -
186A LEU* 3.6 5.9 - - - +
187A SER* 3.0 33.3 + - - +
245A CYS* 4.2 11.4 - - + -
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TRP* 2.8 35.1 + - + +
149A TYR* 3.6 16.7 - - + -
150A PHE* 2.8 27.7 + - - +
172A PHE* 4.9 1.6 - - + -
173A LEU* 1.3 79.4 - - - +
175A ARG* 1.3 69.0 + - - +
184A TYR* 4.3 9.0 - - + -
185A CYS 3.3 10.3 - - - +
186A LEU* 4.1 13.9 - - + -
204A ILE* 4.5 10.8 - - + -
223A LEU* 4.3 18.4 - - + -
227A VAL* 4.1 15.7 - - + -
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Residues in contact with ARG 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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149A TYR* 4.6 1.6 - - - -
150A PHE* 4.8 0.2 - - + -
151A GLY 3.3 17.3 - - - +
153A ILE* 3.7 25.1 + - + +
154A THR 4.2 0.2 - - - -
155A ARG* 3.7 25.4 - - - +
158A SER* 3.5 22.9 + - - -
173A LEU* 4.0 6.5 - - + -
174A VAL* 1.3 76.2 - - - +
176A GLU* 1.3 76.1 + - - +
178A GLU* 4.3 1.2 - - - +
184A TYR* 3.3 13.2 - - - +
185A CYS* 2.8 44.1 + - + +
187A SER* 3.1 13.7 + - - -
201A HIS* 3.2 23.4 + - - -
535A SO4 2.8 43.4 + - - -
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Residues in contact with GLU 176 (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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149A TYR* 3.6 21.7 + - - +
151A GLY* 2.8 19.8 + - - +
152A LYS* 4.1 31.8 + - + +
153A ILE 4.2 4.7 - - - +
175A ARG* 1.3 94.9 + - - +
177A SER* 1.3 65.9 + - - +
178A GLU* 3.7 1.2 + - - +
183A ALA 4.0 7.2 - - - +
184A TYR* 4.1 8.0 - - + -
185A CYS 4.5 0.4 - - - -
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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