Contacts of the strand formed by residues 178 - 183 (chain A) in PDB entry 4J2X
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 ASP 178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A LYS* 5.4 4.0 - - - +
171A MET 2.9 19.2 + - - +
172A PHE* 4.1 7.7 - - - +
173A TYR* 4.5 5.0 - - - -
176A SER 3.2 6.6 + - - +
177A ASP* 1.3 76.7 - - - +
179A ILE* 1.3 64.2 + - - +
180A GLY* 3.3 11.9 + - - -
181A VAL* 6.1 0.2 - - - +
374A LEU 5.7 4.5 - - - +
376A PRO* 3.4 29.5 - - + +
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Residues in contact with ILE 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TRP* 4.3 8.5 - - + -
125A PRO* 4.4 1.3 - - + -
171A MET* 2.9 32.1 + - + +
172A PHE* 3.5 31.6 - - - +
173A TYR* 3.6 41.7 - - + +
178A ASP* 1.3 72.4 - - - +
180A GLY* 1.3 59.9 + - - +
182A PHE* 3.7 26.5 - - + -
366A PHE* 3.7 23.3 - - + -
376A PRO* 3.4 6.8 - - - +
377A VAL* 3.1 33.8 + - + +
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Residues in contact with GLY 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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169A VAL 3.3 2.6 - - - +
170A LYS* 3.7 0.4 - - - -
171A MET* 2.8 32.8 + - - -
178A ASP* 3.3 9.8 + - - -
179A ILE* 1.3 80.9 - - - +
181A VAL* 1.3 62.2 + - - -
182A PHE* 3.7 5.1 - - - -
376A PRO* 4.0 6.5 - - - -
378A THR* 3.3 17.0 - - - -
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Residues in contact with VAL 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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138A MET* 5.9 1.1 - - + -
168A SER* 3.2 29.4 - - - +
169A VAL 3.2 2.0 - - - +
170A LYS* 3.9 34.1 - - + -
180A GLY* 1.3 76.0 - - - +
182A PHE* 1.4 60.4 + - - +
183A LEU* 4.2 12.7 + - + +
378A THR* 3.1 25.3 + - - +
379A PRO* 5.3 1.6 - - - +
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Residues in contact with PHE 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 3.9 16.2 - - + -
76A ILE* 3.7 17.9 - - + +
167A LEU 3.6 0.7 - - - +
168A SER* 3.4 1.9 - - - -
169A VAL* 2.7 51.8 + - + +
171A MET* 4.0 18.8 - - + -
179A ILE* 3.7 30.3 - - + -
180A GLY 3.7 14.1 - - - -
181A VAL* 1.4 72.1 - - - +
183A LEU* 1.3 62.1 + - - +
364A TYR* 3.6 34.1 - + + -
366A PHE* 3.7 24.0 - + - -
377A VAL* 4.2 0.9 - - + -
378A THR* 3.5 23.3 - - + -
380A VAL* 4.3 4.7 - - + -
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Residues in contact with LEU 183 (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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76A ILE* 3.9 2.7 - - - -
132A GLY* 6.4 1.1 - - - -
166A MET* 3.8 27.6 - - + +
167A LEU 3.3 12.8 - - - +
168A SER* 3.9 19.1 - - - -
181A VAL* 4.2 11.2 + - + +
182A PHE* 1.3 74.6 - - - +
184A SER* 1.3 68.0 + - - +
362A ALA* 3.6 1.7 - - - +
364A TYR* 2.5 39.7 + - - +
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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