Contacts of the strand formed by residues 175 - 179 (chain A) in PDB entry 1A1E
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 175 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A TRP* 3.8 16.6 - - + -
165A LEU* 4.1 1.8 - - - -
173A GLY 3.7 9.2 - - - -
174A THR* 1.3 74.7 - - - +
176A LEU* 1.3 69.2 + - - +
177A VAL* 4.8 0.9 - - + -
189A LEU* 3.8 17.7 - - + -
190A SER 3.0 14.4 - - - +
191A VAL* 4.4 0.9 - - - -
230A VAL* 3.7 36.1 - - + -
234A SER* 4.9 2.9 - - - -
244A LEU* 3.8 40.2 - - + -
245A THR 4.7 2.2 - - - -
246A THR 3.0 28.2 + - - -
247A VAL* 3.8 22.8 - - + +
248A CYS* 2.9 28.7 + - - +
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A TRP 3.6 6.1 - - - -
153A PHE* 3.5 23.8 - - + -
156A ILE* 4.3 7.2 - - + -
161A SER* 4.1 8.1 - - - -
164A LEU* 4.1 20.2 - - + -
165A LEU* 4.2 11.7 - - + -
175A PHE* 1.3 80.4 - - - +
177A VAL* 1.3 69.8 + - - +
178A ARG* 4.0 28.7 - - + -
188A CYS 3.7 0.2 - - - +
189A LEU* 3.4 6.9 - - - +
190A SER* 3.0 40.2 + - - -
248A CYS* 4.0 22.9 - - - -
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Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A TRP* 3.1 33.1 + - + +
152A TYR* 3.7 16.6 - - + -
153A PHE* 2.8 27.9 + - - +
175A PHE* 4.8 2.7 - - + -
176A LEU* 1.3 78.5 - - - +
178A ARG* 1.3 68.2 + - - +
187A TYR* 4.3 2.9 - - + -
188A CYS 3.2 9.2 - - - +
189A LEU* 4.1 12.6 - - + -
207A ILE* 4.2 19.3 - - + -
226A LEU* 4.3 17.9 - - + -
230A VAL* 4.0 19.5 - - + -
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Residues in contact with ARG 178 (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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152A TYR* 4.2 4.9 - - - -
153A PHE 4.6 0.2 - - - -
154A GLY 3.3 15.3 - - - +
156A ILE* 4.0 29.0 + - + +
158A ARG* 3.8 20.5 - - - +
161A SER* 3.8 8.3 + - - -
176A LEU* 4.0 14.6 - - + -
177A VAL* 1.3 77.2 - - - +
179A GLU* 1.3 74.9 + - - +
181A GLU* 4.2 2.2 - - - +
187A TYR* 3.2 14.0 - - - -
188A CYS* 2.8 43.2 + - + +
190A SER* 3.2 13.5 + - - -
204A HIS* 3.2 25.9 + - - -
101C PTR 2.8 43.8 + - - -
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Residues in contact with GLU 179 (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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147A GLN* 5.9 0.5 + - - -
152A TYR* 3.6 20.2 + - - +
154A GLY* 2.8 15.1 + - - +
155A LYS* 2.7 49.2 + - - +
156A ILE 4.4 4.2 - - - +
178A ARG* 1.3 97.7 + - - +
180A SER* 1.3 68.5 + - - +
181A GLU* 3.4 0.9 + - - +
186A ALA 4.0 5.8 - - - +
187A TYR* 3.9 12.5 + - + -
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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