Contacts of the strand formed by residues 91 - 95 (chain A) in PDB entry 5WN0
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 ILE 91 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 4.5 9.2 - - + -
63A LYS 3.4 2.6 + - - -
64A ILE* 3.9 15.9 - - + -
65A CYS 2.8 26.7 + - - -
89A PRO* 3.3 7.7 - - - +
90A ASP* 1.3 88.4 - - + +
92A LEU* 1.3 63.2 + - - +
93A CYS* 4.0 13.9 - - - -
114A LEU* 4.4 0.2 - - - -
133A LEU* 4.5 10.1 - - + -
134A LEU 3.2 9.6 - - - +
135A SER* 3.6 13.5 - - - -
162A PHE* 3.7 32.1 - - + -
165A PHE* 4.0 13.0 - - + -
167A LEU* 3.6 28.9 - - + -
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Residues in contact with LEU 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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65A CYS* 3.1 37.2 - - + +
67A TRP* 4.9 4.5 - - + -
75A TRP* 4.4 5.4 - - + -
81A LEU* 5.3 3.1 - - + -
84A VAL* 3.7 39.0 - - + -
89A PRO* 4.3 7.9 - - + -
91A ILE* 1.3 73.9 - - - +
93A CYS* 1.3 61.2 - - - +
94A LEU* 3.5 38.4 - - + -
108A LEU* 6.1 0.2 - - + -
111A LEU* 5.4 0.4 - - + -
114A LEU* 4.2 9.3 - - + +
132A GLY 3.9 0.3 - - - +
133A LEU* 3.5 2.8 - - - -
134A LEU* 2.7 57.5 + - + +
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Residues in contact with CYS 93 (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 ILE* 4.4 2.5 - - - -
65A CYS 2.7 14.4 + - - +
66A SER* 3.2 2.1 - - - +
67A TRP 2.8 31.5 + - - -
91A ILE* 4.0 18.4 - - - -
92A LEU* 1.3 75.1 - - - +
94A LEU* 1.3 60.3 - - - +
95A GLN* 3.5 4.3 - - - +
132A GLY 3.3 5.6 - - - +
133A LEU* 4.2 7.9 - - - -
167A LEU* 4.1 10.5 - - - -
169A THR* 3.1 29.6 - - - +
208A CYS* 3.4 26.2 - - - -
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Residues in contact with LEU 94 (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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67A TRP* 3.2 12.3 - - + +
69A VAL* 4.1 16.8 - - + -
72A LEU* 4.2 16.8 - - + -
75A TRP* 4.4 8.7 - - + -
92A LEU* 3.5 35.0 - - + -
93A CYS* 1.3 81.6 - - - +
95A GLN* 1.3 66.7 + - - +
97A THR* 4.2 13.9 - - + -
108A LEU* 5.3 1.3 - - + -
119A TRP* 4.1 16.6 - - + -
131A VAL* 3.3 5.5 - - - +
132A GLY 2.8 34.0 + - - +
134A LEU* 4.0 24.9 - - + -
169A THR* 5.0 0.3 - - - +
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Residues in contact with GLN 95 (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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66A SER* 3.1 20.5 + - - -
67A TRP 2.8 10.2 + - - -
68A ASN* 3.2 31.8 + - + +
69A VAL* 2.9 27.2 + - - +
93A CYS 3.5 18.6 - - - -
94A LEU* 1.3 76.8 - - - +
96A GLU* 1.3 67.6 + - - +
97A THR* 3.4 2.6 + - - -
130A GLY 4.0 2.7 - - - -
131A VAL* 4.0 9.9 - - + -
169A THR* 3.0 24.9 + - - +
170A ALA 3.3 21.1 - - - +
171A TYR* 4.1 11.7 - - + -
209A GLY* 3.6 14.4 - - - -
210A ASP* 3.8 4.8 + - + +
283A ASP* 4.4 1.6 - - - +
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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