Contacts of the strand formed by residues 87 - 92 (chain A) in PDB entry 5JJ2
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 TYR 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A PRO 3.9 0.2 - - - -
86A ASN* 1.3 112.9 - - - +
88A PHE* 1.3 66.5 + - - +
132A VAL* 3.6 1.4 - - - -
133A MET* 3.0 36.0 + - + +
135A LEU* 3.7 40.4 - - + -
141A VAL* 3.8 16.1 - - + +
262A LEU* 4.2 7.2 - - + -
263A CYS 3.2 23.3 - - - +
264A SER* 3.6 16.4 - - - -
265A MET* 3.6 5.5 - - - +
267A LYS* 3.5 27.2 + - - -
278A GLU* 3.5 32.4 + - + -
304A MLI 4.4 10.9 + - - +
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Residues in contact with PHE 88 (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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87A TYR* 1.3 76.5 - - - +
89A LEU* 1.3 74.5 + - - +
90A SER* 3.6 21.5 - - - -
127A HIS* 3.6 17.3 - + - -
129A THR* 3.9 18.2 - - + -
131A LEU 3.1 14.6 - - - +
132A VAL* 4.2 6.7 - - + -
133A MET* 4.2 5.2 - - - -
261A ASP 3.6 0.3 - - - +
262A LEU* 3.6 1.5 - - - -
263A CYS* 2.8 56.2 + - + -
264A SER 4.2 2.0 - - - -
265A MET* 3.6 31.0 - - + -
275A TYR* 3.7 36.3 - + - -
302A MLI 3.9 9.6 - - - -
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Residues in contact with LEU 89 (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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88A PHE* 1.3 75.5 - - - +
90A SER* 1.3 58.8 + - - +
129A THR* 3.5 5.7 - - - +
130A LEU* 2.9 41.9 + - + -
131A LEU* 2.9 17.5 + - + +
133A MET* 3.9 9.6 - - + +
148A LEU* 4.0 19.7 - - + -
151A LEU* 4.3 10.8 - - + -
199A ALA* 3.9 25.8 - - + -
203A PHE* 3.9 25.8 - - + -
260A ILE* 4.4 7.2 - - + -
261A ASP 3.2 10.5 - - - +
262A LEU* 4.0 22.9 - - + -
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Residues in contact with SER 90 (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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88A PHE* 3.6 11.7 - - - -
89A LEU* 1.3 75.0 - - - +
91A ILE* 1.3 59.9 + - - +
92A PRO* 3.5 4.2 - - - +
127A HIS* 3.3 25.3 - - - +
128A ILE 3.5 3.6 - - - -
260A ILE* 3.4 7.4 - - - +
261A ASP* 2.9 36.1 + - - +
263A CYS* 3.6 21.1 - - - -
274A TYR* 2.8 25.8 + - - -
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Residues in contact with ILE 91 (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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90A SER* 1.3 73.4 - - - +
92A PRO* 1.3 75.5 - - + +
93A ILE* 5.4 0.2 - - + -
127A HIS* 3.2 2.6 - - - -
128A ILE* 2.9 56.2 + - + +
130A LEU* 3.6 43.7 - - + -
166A LEU* 4.5 12.6 - - + -
192A LEU* 4.0 10.8 - - + -
255A GLU* 4.7 13.9 - - + -
257A LEU* 3.7 34.8 - - + -
258A TYR 5.9 0.4 - - - +
259A ARG 4.1 3.8 - - - +
260A ILE* 4.4 4.3 - - + -
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Residues in contact with PRO 92 (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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90A SER 3.5 7.8 - - - +
91A ILE* 1.3 94.7 - - + +
93A ILE* 1.3 62.7 + - - +
94A THR* 3.6 18.7 + - + +
126A PHE 4.0 6.1 - - - +
127A HIS* 4.3 0.2 - - + -
255A GLU* 3.7 10.4 - - - +
259A ARG* 3.4 32.3 - - + +
261A ASP* 3.8 14.4 - - - +
274A TYR* 3.6 26.0 - - + +
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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