Contacts of the strand formed by residues 174 - 177 (chain A) in PDB entry 1JAP
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 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A ILE* 4.7 0.8 - - + +
139A ASN 2.9 10.7 + - - +
140A ILE* 3.4 6.5 - - + -
141A ALA 3.1 23.4 + - - +
162A HIS 3.5 7.0 - - - +
163A ALA* 4.2 5.6 - - + -
172A GLY 3.8 0.4 + - - +
173A ASP* 1.3 74.0 - - - +
175A HIS* 1.3 66.4 + - - +
176A PHE* 3.9 19.8 - - + -
198A GLU* 4.3 5.8 - - + -
199A PHE* 4.1 20.9 - - + -
202A SER* 4.2 9.6 - - - +
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Residues in contact with HIS 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ASN* 4.9 2.7 - - + +
140A ILE 5.4 0.2 - - - -
141A ALA* 3.4 9.0 - - + +
143A TYR* 3.8 27.3 - + + -
147A HIS* 3.3 7.7 + + - +
149A ASP* 3.3 8.7 - - + -
153A PHE* 3.3 14.8 - - + -
161A ALA* 3.1 6.9 - - - +
162A HIS* 2.8 37.5 + + - +
164A PHE* 3.7 15.3 - + - -
170A ILE* 4.1 13.5 - - + +
173A ASP* 4.2 14.5 + - + +
174A ALA* 1.3 83.8 - - - +
176A PHE* 1.3 63.0 + - - +
998A ZN 2.1 38.7 - - - -
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Residues in contact with PHE 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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113A ILE* 5.0 2.0 - - + -
140A ILE* 3.9 19.7 - - + -
141A ALA 2.8 17.9 + - - +
142A PHE* 3.3 27.7 - + + -
143A TYR 2.9 26.2 + - - +
153A PHE* 3.5 3.4 - - - -
160A LEU 3.9 2.2 - - - -
161A ALA* 3.9 8.5 - - + -
174A ALA* 3.9 24.9 - - + -
175A HIS* 1.3 76.6 - - - +
177A ASP* 1.3 61.6 + - - +
178A ALA 2.9 2.8 + - - -
182A TRP* 3.9 14.8 - + + -
191A LEU* 3.9 21.8 - - + -
194A VAL* 4.0 8.3 - - + -
195A ALA* 3.7 40.8 - - + -
198A GLU* 4.1 13.9 - - + -
199A PHE* 4.7 4.5 - + - -
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Residues in contact with ASP 177 (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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143A TYR 3.5 5.5 - - - +
144A GLN* 4.7 1.0 - - - -
153A PHE* 3.2 34.5 - - + +
154A ASP* 3.4 3.1 + - - +
155A GLY 3.2 7.9 + - - +
159A ILE 3.3 4.4 - - - +
160A LEU 2.9 22.5 + - - +
176A PHE* 1.3 70.4 - - - +
178A ALA* 1.3 61.6 + - - +
179A GLU* 2.9 39.8 + - - +
180A GLU* 3.1 18.5 + - + +
182A TRP* 2.9 23.0 + - - -
997A CA 2.5 24.8 - - - -
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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