Contacts of the strand formed by residues 156 - 161 (chain A) in PDB entry 4JJE
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 LYS 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A PHE* 3.5 9.9 - - + -
143A PHE* 3.3 30.2 + - + +
145A GLY* 5.1 4.8 - - - +
151A LEU* 2.8 43.0 + - + -
152A THR* 4.3 2.4 - - - +
153A GLY 4.2 4.0 - - - +
154A LYS 2.8 23.3 + - - +
155A PRO* 1.3 76.4 - - - +
157A LEU* 1.3 61.5 + - - +
158A PHE* 4.0 11.3 - - + -
191A ALA 3.9 5.2 + - - -
192A ASP* 2.9 22.8 + - - +
193A PHE* 3.2 40.2 - - + +
194A LEU 2.9 25.6 + - - +
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Residues in contact with LEU 157 (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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78A PHE* 5.8 1.3 - - + -
83A TYR* 5.0 1.8 - - - +
113A SER* 5.7 2.5 - - - -
114A PHE* 2.8 17.4 + - - +
115A VAL* 3.3 24.9 - - + +
116A CYS* 2.9 26.9 + - - +
155A PRO* 4.0 10.8 - - + +
156A LYS* 1.3 78.5 - - - +
158A PHE* 1.3 64.6 + - - +
159A ILE* 4.1 7.2 - - + -
194A LEU* 3.4 32.1 - - + +
232A PHE* 3.7 27.8 - - + -
269A LEU* 4.5 2.0 - - + -
273A LEU* 3.9 26.7 - - + -
275A PHE* 4.4 13.9 - - + -
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Residues in contact with PHE 158 (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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114A PHE* 4.0 10.3 - + - -
116A CYS* 3.3 32.5 - - + +
118A LEU* 5.1 6.3 - - + -
139A ILE* 4.1 17.3 - - + -
140A THR* 3.9 25.6 - - + -
143A PHE* 3.9 25.6 - + - -
156A LYS* 4.0 14.8 - - + -
157A LEU* 1.3 74.4 - - - +
159A ILE* 1.3 57.8 + - - +
160A ILE* 4.0 12.7 + - + +
193A PHE* 3.7 33.9 - + - -
194A LEU 2.8 12.6 + - - +
195A TYR* 3.3 16.9 - + + -
196A ALA 2.8 31.0 + - - +
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Residues in contact with ILE 159 (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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78A PHE* 3.8 28.9 - - + -
115A VAL* 4.0 15.5 - - + -
116A CYS 2.8 10.1 + - - +
117A VAL* 3.3 22.0 - - + +
118A LEU 2.9 26.3 + - - -
157A LEU* 5.0 6.3 - - + -
158A PHE* 1.3 79.2 - - - +
160A ILE* 1.3 61.8 + - - +
194A LEU* 5.9 0.2 - - + -
196A ALA* 3.5 16.6 - - + +
215A PHE* 3.8 16.6 - - + -
216A ILE* 4.0 5.2 - - + -
219A LEU* 3.7 30.1 - - + -
232A PHE* 5.2 11.9 - - + -
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Residues in contact with ILE 160 (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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118A LEU* 3.7 15.0 - - + +
126A ILE 6.1 0.2 - - - +
127A ILE* 4.3 11.9 - - + -
136A LEU* 4.0 26.9 - - + -
140A THR* 6.3 1.6 - - + -
158A PHE* 4.2 17.3 - - + +
159A ILE* 1.3 83.7 - - - +
161A GLN* 1.3 60.7 + - - +
162A ALA* 3.7 21.7 + - + +
164A ARG* 6.4 1.1 - - + -
195A TYR* 4.8 6.7 - - + -
196A ALA 2.9 10.3 + - - +
197A TYR* 3.6 41.3 - - + +
198A SER* 3.0 29.7 + - - -
215A PHE* 4.7 2.2 - - - -
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Residues in contact with GLN 161 (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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64A ARG* 4.1 8.5 - - - +
70A ASP* 4.3 2.0 - - - +
118A LEU 2.8 10.4 + - - +
119A LEU* 3.7 20.2 - - + -
120A SER 3.1 25.5 + - - +
159A ILE 4.0 1.0 + - - -
160A ILE* 1.3 70.5 - - - +
162A ALA* 1.3 61.3 + - - +
198A SER* 3.1 21.1 - - - -
205A SER* 3.0 26.1 + - - -
206A TRP 4.1 6.1 + - - +
213A SER* 3.3 37.5 + - - +
215A PHE* 3.5 8.3 + - - +
216A ILE* 3.9 12.5 - - + +
406B 1U8 2.8 25.7 + - - +
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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