Contacts of the strand formed by residues 90 - 95 (chain C) in PDB entry 5T46
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 90 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47C PHE* 3.4 11.4 - - - -
48C PHE* 2.9 54.9 + - + +
56C TRP* 5.3 6.2 + - - -
85C LEU* 4.3 5.2 - - - -
89C CYS* 1.3 75.0 - - - +
91C TYR* 1.3 65.9 + - - +
92C SER* 4.7 3.8 + - - +
153C VAL* 4.4 5.9 - - + +
154C VAL 3.1 11.0 - - - +
155C ASN* 2.9 22.0 + - - +
157C ARG* 2.8 36.4 + - - -
301C MGP 4.4 4.0 + - - -
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Residues in contact with TYR 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C LEU* 4.4 9.4 - - + -
46C TRP 3.3 13.0 - - - -
47C PHE* 4.4 2.7 - + - -
63C ILE* 3.7 23.6 - - + -
79C ILE* 3.8 13.4 - - + +
80C GLN* 2.8 39.7 + - - +
82C SER* 3.5 23.8 - - - -
85C LEU* 3.7 27.0 - - + +
90C ASP* 1.3 77.1 - - - +
92C SER* 1.3 65.8 + - - +
130C TRP* 3.9 15.9 - + + -
153C VAL* 3.4 1.6 - - - +
154C VAL* 2.9 44.1 + - + +
639D VAL* 3.4 28.6 - - + +
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Residues in contact with SER 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ALA 3.6 0.7 - - - +
45C LEU* 3.3 9.3 - - - +
46C TRP* 2.8 42.1 + - - +
48C PHE* 6.0 0.9 - - - +
60C LEU* 5.5 1.7 - - - +
90C ASP* 4.7 4.5 - - - +
91C TYR* 1.3 79.1 + - - +
93C LEU* 1.3 60.6 + - - +
94C PHE* 3.9 5.2 - - - -
100C PRO* 3.7 29.9 - - - +
130C TRP* 4.4 1.6 - - - -
152C ALA 3.2 11.7 - - - -
153C VAL* 3.7 14.7 - - - +
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Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C TRP* 3.8 24.0 - - + -
44C ALA 3.3 16.8 - - - +
45C LEU* 3.9 15.0 - - + +
66C PHE* 3.7 30.1 - - + -
72C PHE* 5.3 1.6 - - + -
92C SER* 1.3 72.1 - - - +
94C PHE* 1.3 61.6 + - - +
130C TRP* 4.2 2.1 - - + -
134C LEU* 3.7 32.8 - - + -
137C LEU* 3.6 15.2 - - + +
138C ILE* 3.8 23.3 - - + -
151C GLY* 2.9 3.8 - - - -
152C ALA 2.8 34.8 + - - +
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Residues in contact with PHE 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C TRP* 3.5 6.0 - - - -
44C ALA* 2.8 31.5 + - - +
46C TRP* 4.2 7.9 - + - +
92C SER* 3.9 4.7 - - - -
93C LEU* 1.3 81.3 - - - +
95C LYS* 1.3 66.9 + - - +
98C ILE* 3.3 34.3 - - + +
100C PRO* 3.6 30.1 - - + -
107C ASN* 3.9 7.0 - - - -
150C CYS* 3.4 32.3 - - + -
151C GLY* 3.9 3.4 - - - -
152C ALA 3.5 20.9 - - - -
153C VAL* 3.7 7.2 - - + -
166C TRP* 3.5 44.9 - + + -
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Residues in contact with LYS 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ASN* 3.7 31.5 - - + +
42C ARG 3.6 6.5 - - - +
43C TRP* 3.5 33.9 - - + -
44C ALA* 5.4 0.7 - - - +
94C PHE* 1.3 75.1 - - - +
96C ASP* 1.3 70.7 + - - +
97C GLY 3.2 0.2 + - - -
98C ILE* 3.0 35.5 + - + +
140C GLU* 4.8 1.8 + - - -
146C SER 3.0 22.5 + - - -
147C ASP* 3.6 17.6 + - - +
149C VAL* 2.9 27.6 + - - +
150C CYS 3.0 14.3 + - - +
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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