Contacts of the strand formed by residues 87 - 92 (chain A) in PDB entry 4EJX
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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2A GLU* 4.5 6.4 + - - -
3A LYS 2.6 17.5 + - - +
4A HIS* 3.3 45.3 - + + +
5A TYR* 3.6 15.1 + - - -
85A LYS* 3.3 54.3 + - + -
86A VAL* 1.3 78.1 - - - +
88A VAL* 1.3 66.5 + - - +
89A HIS* 4.2 5.2 - - - +
137A THR* 3.7 24.5 - - + -
138A TYR 3.5 2.7 - - - -
139A MET* 4.1 33.3 - - + -
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Residues in contact with VAL 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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5A TYR* 3.9 4.7 - - + -
7A ILE* 3.6 28.5 - - + -
78A ILE* 4.7 8.5 - - + -
86A VAL* 4.6 4.7 - - + +
87A TYR* 1.3 80.2 - - - +
89A HIS* 1.3 61.5 + - - +
90A LEU* 3.5 4.7 + - + +
100A PHE* 3.7 43.3 - - + -
136A TYR 3.0 7.3 - - - +
137A THR* 3.4 1.0 - - - -
138A TYR* 2.8 46.6 + - + +
140A LEU* 3.8 17.7 - - + -
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Residues in contact with HIS 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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4A HIS* 3.2 33.1 + + + -
5A TYR 3.2 19.3 + - - +
6A TYR* 3.2 39.5 + + + -
7A ILE 2.7 34.4 + - - +
59A GLU* 4.8 9.6 - - + +
61A PHE* 3.4 11.8 - - + -
87A TYR* 4.3 4.0 - - + +
88A VAL* 1.3 72.5 - - - +
90A LEU* 1.3 53.5 + - - +
135A GLN* 4.8 15.1 + - + +
136A TYR 3.4 6.2 - - - -
137A THR* 3.6 30.0 + - + +
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Residues in contact with LEU 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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7A ILE* 3.2 34.5 - - + +
9A ILE* 3.7 29.2 - - + -
53A TYR* 4.1 4.5 - - + -
88A VAL* 3.5 3.0 + - + -
89A HIS* 1.3 72.9 - - - +
91A LYS* 1.3 69.4 + - - +
92A ASN* 5.9 0.2 - - + -
99A THR* 3.6 35.9 - - - +
100A PHE* 3.7 11.0 - - + +
130A VAL* 4.6 15.4 - - + +
134A GLU 3.8 0.3 - - - +
135A GLN* 3.3 8.3 - - - +
136A TYR* 3.0 29.9 + - + +
138A TYR* 4.2 22.7 - - + +
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Residues in contact with LYS 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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7A ILE 2.9 8.1 + - - +
8A GLY* 3.4 2.4 - - - -
9A ILE* 2.9 27.0 + - - +
61A PHE* 3.7 54.3 + - + +
90A LEU* 1.3 78.8 - - - +
92A ASN* 1.3 71.5 + - - +
93A LEU* 4.0 31.5 - - + +
130A VAL* 5.6 0.2 - - - -
133A GLY* 5.0 6.3 - - - -
134A GLU 3.4 21.8 - - - +
135A GLN* 3.8 13.6 + - - +
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Residues in contact with ASN 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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9A ILE* 3.7 14.9 - - + +
90A LEU* 5.7 0.7 - - + -
91A LYS* 1.3 77.1 - - - +
93A LEU* 1.3 60.7 + - - +
94A ALA* 3.3 25.6 - - - +
96A ARG 3.0 18.7 - - - +
98A TYR* 3.5 20.7 - - + +
130A VAL* 4.0 15.9 - - + +
131A TYR 3.2 15.3 - - - +
132A PRO* 3.1 23.7 - - - +
133A GLY 2.8 28.3 + - - -
134A GLU 3.4 7.9 + - - +
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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