Contacts of the strand formed by residues 178 - 181 (chain A) in PDB entry 4JA1
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 178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ILE* 4.9 0.6 - - + +
143A MET 3.2 5.7 + - - +
144A ILE* 3.4 15.2 - - + -
145A SER 3.2 23.0 + - - +
166A HIS 3.5 5.4 - - - +
167A ALA* 3.9 14.6 - - + -
176A GLY 3.9 0.6 + - - +
177A ASP* 1.3 74.6 - - - +
179A HIS* 1.3 64.2 + - - +
180A PHE* 3.9 19.3 - - + -
202A GLU* 4.4 8.7 - - + -
203A ILE* 4.9 7.4 - - + -
206A SER* 4.3 6.5 - - - +
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Residues in contact with HIS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A MET 4.7 1.8 + - - -
145A SER* 3.3 26.6 + - - +
147A ALA* 5.1 1.8 - - + -
151A HIS* 3.2 14.9 + + + +
152A GLY 5.9 0.7 - - - -
153A ASP* 3.3 9.4 - - - -
157A PHE* 3.7 10.3 - - + -
165A ALA* 3.2 5.2 - - - +
166A HIS* 2.9 40.0 + + + +
168A TYR* 4.0 7.0 - + - -
174A ILE* 3.8 20.4 - - + +
177A ASP* 4.3 14.0 + - + +
178A ALA* 1.3 83.2 - - - +
180A PHE* 1.3 62.3 + - - +
302A ZN 2.0 39.1 - - - -
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Residues in contact with PHE 180 (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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117A VAL* 6.1 2.0 - - + -
144A ILE* 3.9 24.7 - - + -
145A SER 2.9 15.6 + - - +
146A PHE* 3.4 30.0 - + + +
147A ALA 2.9 23.8 + - - +
157A PHE* 3.7 2.7 - - - -
164A LEU 3.9 2.5 - - - -
165A ALA* 3.7 12.3 - - + -
178A ALA* 3.9 19.5 - - + -
179A HIS* 1.3 77.1 - - - +
181A ASP* 1.3 61.9 + - - +
182A ASP 3.2 0.7 + - - -
186A TRP* 3.8 18.2 - + + -
195A LEU* 3.9 16.4 - - + -
198A VAL* 3.7 20.0 - - + -
199A ALA* 3.7 31.2 - - + -
202A GLU* 4.4 10.3 - - + -
203A ILE* 6.1 2.2 - - + -
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Residues in contact with ASP 181 (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 ALA 3.3 9.6 - - - +
148A VAL* 4.2 2.1 - - - -
149A ARG 4.8 0.2 + - - -
157A PHE* 3.4 34.9 - - + +
158A ASP* 3.3 7.3 + - - +
159A GLY 3.2 6.9 + - - +
163A VAL 3.4 0.7 - - - +
164A LEU 2.7 26.2 + - - +
180A PHE* 1.3 69.4 - - - +
182A ASP* 1.3 57.8 + - - +
183A ASP* 3.1 21.6 + - - +
184A GLU* 3.0 21.4 + - - +
186A TRP* 2.8 17.1 + - - -
303A CA 2.3 28.9 - - - -
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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