Contacts of the strand formed by residues 162 - 167 (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 LYS 162 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112C ARG* 4.9 12.2 - - - +
114C LEU* 3.8 24.7 - - + -
115C ILE 3.3 4.0 - - - -
116C THR* 3.8 22.9 - - + +
117C LEU* 5.9 0.4 - - - -
153C VAL 3.8 1.1 - - - +
154C VAL* 3.2 4.9 - - - +
155C ASN* 2.8 62.8 + - + +
157C ARG* 4.6 1.3 - - - -
160C GLY 4.0 10.3 - - - +
161C ASP* 1.3 80.0 - - - +
163C ILE* 1.3 65.5 + - - +
301C MGP 2.7 53.0 + - - -
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Residues in contact with ILE 163 (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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113C TRP 3.8 0.5 - - - +
114C LEU* 3.5 1.6 - - - +
115C ILE* 2.9 47.7 + - + +
117C LEU* 5.2 2.2 - - + +
126C LEU* 3.8 20.9 - - + +
129C PHE* 3.5 31.6 - - + -
130C TRP* 3.6 30.5 - - + +
133C THR* 3.6 12.6 - - + +
153C VAL 3.3 3.8 - - - -
154C VAL* 3.9 14.6 - - + -
162C LYS* 1.3 79.1 - - - +
164C ALA* 1.3 65.2 + - - +
183C TYR* 3.3 22.4 + - - +
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Residues in contact with ALA 164 (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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112C ARG* 3.8 34.5 - - + +
113C TRP 3.0 14.6 - - - +
114C LEU* 4.0 7.2 - - + -
152C ALA* 3.0 6.7 - - - +
153C VAL* 2.9 35.5 + - + +
155C ASN* 6.1 0.7 - - - +
163C ILE* 1.3 78.3 - - - +
165C ILE* 1.3 62.6 + - - +
166C TRP* 4.0 7.4 + - + +
183C TYR* 4.4 2.7 - - - -
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Residues in contact with ILE 165 (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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112C ARG* 3.1 2.1 - - - -
113C TRP* 2.8 34.3 + - + +
133C THR* 3.7 14.8 - - + -
136C CYS* 4.7 2.0 - - + -
137C LEU* 3.8 15.9 - - + -
142C PHE* 3.8 19.3 - - + -
149C VAL* 4.2 14.4 - - + -
151C GLY 3.5 9.2 - - - +
152C ALA* 4.2 0.7 - - + -
164C ALA* 1.3 71.9 - - - +
166C TRP* 1.3 72.8 + - - +
167C THR* 4.0 12.1 + - + +
179C ILE* 4.4 10.5 - - + -
183C TYR* 3.5 50.6 - - + -
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Residues in contact with TRP 166 (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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94C PHE* 3.5 23.6 - + + -
100C PRO 4.0 15.0 - - - -
101C MET 3.8 24.0 - - - -
102C TRP* 3.6 28.5 - + - -
107C ASN* 3.7 17.7 - - + +
111C GLY 3.3 5.8 - - - +
112C ARG* 3.7 32.6 - - + +
149C VAL* 3.7 2.4 - - - -
150C CYS* 2.8 31.4 + - + -
151C GLY 2.8 16.1 + - - +
153C VAL* 3.5 33.0 - - + +
164C ALA* 4.2 8.8 - - + +
165C ILE* 1.3 75.8 - - - +
167C THR* 1.3 57.9 + - - +
200C HIS* 3.4 27.6 - + - +
301C MGP 4.2 12.6 - - - -
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Residues in contact with THR 167 (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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106C LYS 4.5 0.5 - - - +
107C ASN* 4.9 1.2 - - - +
110C GLY* 3.2 20.6 - - - -
111C GLY 2.8 9.8 + - - +
113C TRP* 4.5 2.9 - - + +
148C ASP* 3.1 17.0 + - - +
149C VAL* 4.8 0.9 - - - -
150C CYS* 3.8 5.9 - - - +
165C ILE* 4.3 14.6 - - + +
166C TRP* 1.3 79.8 - - - +
168C THR* 1.3 60.9 + - - +
169C GLU 4.1 3.3 + - - -
176C VAL* 4.0 10.6 - - + +
179C ILE* 3.9 29.8 - - + -
197C TYR* 2.8 35.7 + - + -
200C HIS* 4.6 2.4 + - - -
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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