Contacts of the strand formed by residues 148 - 156 (chain C) in PDB entry 3JRS
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 148 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C TYR* 4.9 1.7 + - - -
122C ARG* 5.1 4.0 - - - +
124C ASP* 3.2 37.0 + - - +
125C LEU* 6.4 0.7 - - - -
135C PHE 3.4 4.5 - - - -
136C SER* 3.8 7.4 + - - +
146C ASN 4.0 7.0 - - - +
147C TYR* 1.3 79.5 - - - +
149C SER* 1.3 66.9 + - - +
150C VAL* 5.5 7.0 - - + -
173C TYR* 3.1 2.3 - - - -
174C VAL* 2.9 46.5 + - + +
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Residues in contact with SER 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C TYR* 5.2 0.4 - - - -
124C ASP* 4.9 0.2 - - - +
134C GLY* 3.1 4.3 - - - -
135C PHE* 2.8 63.3 + - - +
147C TYR* 3.7 22.6 - - - -
148C LYS* 1.3 77.1 - - - +
150C VAL* 1.3 69.4 + - - +
151C THR* 5.1 0.9 + - - -
171C GLU* 4.0 12.9 + - - -
172C SER 3.2 13.7 - - - -
173C TYR* 3.8 0.7 - - - +
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Residues in contact with VAL 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PHE* 4.0 39.0 - - + +
48C HIS* 3.2 10.7 - - + +
50C TYR* 4.6 7.0 - - + +
125C LEU* 4.1 24.0 - - + -
132C VAL* 4.2 0.9 - - + -
133C THR 3.5 11.9 - - - +
134C GLY* 4.8 0.7 - - - -
148C LYS* 5.5 8.7 - - + -
149C SER* 1.3 80.3 - - - +
151C THR* 1.3 64.0 + - - +
152C THR* 4.1 8.1 - - + -
171C GLU* 3.2 5.0 - - - -
172C SER* 3.0 30.4 + - - +
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Residues in contact with THR 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C TRP* 4.9 1.2 - - - -
76C VAL* 3.6 27.4 - - + -
85C TYR* 5.4 4.7 + - - +
131C ARG 4.2 0.5 - - - +
132C VAL* 3.7 0.9 - - - -
133C THR* 2.8 49.0 + - - +
134C GLY* 4.5 0.6 - - - -
135C PHE* 5.9 1.9 - - - -
149C SER* 5.1 1.7 + - - -
150C VAL* 1.3 70.9 + - - +
152C THR* 1.4 67.0 + - - +
169C VAL* 3.7 25.8 - - + -
170C LEU 3.3 4.3 - - - +
171C GLU* 3.1 29.4 + - - +
198C LEU* 5.4 0.7 - - + -
201C LEU* 5.9 0.2 - - + -
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Residues in contact with THR 152 (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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47C PHE* 4.0 16.2 - - + -
48C HIS* 3.0 28.0 + - - +
131C ARG 3.6 6.5 - - - -
132C VAL* 3.8 29.6 - - + -
150C VAL* 4.1 2.2 - - + -
151C THR* 1.4 78.0 - - - +
153C VAL* 1.3 62.4 + - - +
154C HIS* 2.5 34.4 + - - -
169C VAL* 3.3 6.1 - - - +
170C LEU* 2.9 34.4 + - - +
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Residues in contact with VAL 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C PRO* 3.6 30.7 - - + +
72C VAL* 4.1 17.5 - - + -
73C TRP* 3.9 25.8 - - + +
76C VAL* 4.3 15.9 - - + -
130C ARG 4.3 4.7 - - - +
131C ARG* 3.1 33.7 + - + +
151C THR* 4.8 1.6 - - + -
152C THR* 1.3 78.2 - - - +
154C HIS* 1.3 69.1 + - - +
155C ARG 4.4 0.2 + - - -
167C THR* 3.7 19.5 - - + -
168C VAL 3.7 2.7 - - - -
169C VAL* 4.4 4.0 - - + -
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Residues in contact with HIS 154 (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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40C LEU* 4.0 25.1 - - + +
43C SER* 3.3 35.5 + - - -
47C PHE* 5.8 0.9 - + - -
69C PRO* 4.5 4.0 - - - -
130C ARG 6.1 0.4 - - - -
132C VAL* 6.3 0.2 - - + -
152C THR* 2.5 40.7 + - - -
153C VAL* 1.3 81.2 + - - +
155C ARG* 1.3 62.5 + - - +
156C PHE* 3.6 6.9 + - + -
167C THR* 3.2 9.5 - - - +
168C VAL* 2.8 47.7 + - + +
170C LEU* 3.8 20.7 - - + +
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Residues in contact with ARG 155 (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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39C GLN* 4.8 8.5 + - - -
69C PRO* 3.9 15.5 - - + +
131C ARG* 4.0 16.9 - - - +
153C VAL 4.4 0.4 + - - -
154C HIS* 1.3 73.9 - - - +
156C PHE* 1.3 74.1 + - - +
157C GLU* 3.7 28.2 + - + +
165C ILE* 3.7 32.3 - - + -
166C TRP 3.9 3.4 - - - -
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Residues in contact with PHE 156 (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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39C GLN* 3.3 40.8 - - + -
40C LEU* 3.4 37.0 - - + -
154C HIS* 3.8 10.1 - - + -
155C ARG* 1.3 78.8 - - - +
157C GLU* 1.3 63.1 - - - +
165C ILE* 3.1 4.7 - - - +
166C TRP* 2.6 77.0 + + + +
168C VAL* 3.5 37.7 - - + -
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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