Contacts of the strand formed by residues 130 - 136 (chain C) in PDB entry 4SBV
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 ALA 130 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C VAL* 4.2 5.4 - - - +
129C GLY* 1.3 78.0 - - - -
131C ILE* 1.3 63.3 + - - +
132C HIS* 4.3 9.2 - - + +
158C THR* 4.2 8.7 - - - +
159C GLY 3.0 24.2 - - - +
160C PRO* 3.6 6.1 - - + -
161C VAL* 3.8 3.8 - - - +
228C MET* 3.8 5.7 - - - +
229C GLU* 3.7 31.3 + - + +
230C GLY* 4.2 1.0 - - - -
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Residues in contact with ILE 131 (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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78C LEU* 4.2 6.7 - - + -
119C TYR* 3.7 32.8 - - + -
130C ALA* 1.3 75.2 - - - +
132C HIS* 1.3 80.0 - - - +
133C MET* 4.2 22.2 - - + -
158C THR* 2.6 37.0 + - - -
159C GLY 2.6 21.8 + - - +
160C PRO 4.9 1.6 - - - +
161C VAL* 5.1 4.3 - - + -
183C ILE* 3.8 26.5 - - + -
226C THR* 4.7 1.1 - - + -
227C ALA 3.5 3.6 - - - +
228C MET* 3.0 37.7 - - + -
242C LEU* 5.1 0.2 - - + -
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Residues in contact with HIS 132 (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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130C ALA* 4.3 3.1 - - + +
131C ILE* 1.3 90.9 + - - +
133C MET* 1.3 68.6 - - - +
147C VAL* 3.4 25.5 - - + +
150C LEU* 4.0 7.8 - - + +
156C TYR* 2.6 37.5 + + + -
157C VAL 3.3 5.2 - - - -
158C THR* 3.1 20.2 + - + -
183C ILE* 6.5 0.2 - - - -
226C THR* 3.5 1.0 - - - -
227C ALA* 2.8 52.4 + - + +
229C GLU* 2.9 32.0 + - + +
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Residues in contact with MET 133 (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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117C TYR 4.6 2.9 - - - +
119C TYR* 4.4 2.5 - - + -
131C ILE* 4.2 13.9 - - + -
132C HIS* 1.3 78.3 - - - +
134C GLY* 1.3 59.4 + - - +
150C LEU* 4.1 5.6 - - - -
155C GLY 3.4 1.6 - - - +
156C TYR* 3.3 7.1 - - - -
157C VAL* 2.9 40.9 + - + +
183C ILE* 3.9 38.8 - - + +
185C ILE* 3.5 30.1 - - + -
224C LEU* 3.9 14.6 - - + -
225C VAL 2.9 12.6 - - - +
226C THR* 4.5 6.1 - - - +
242C LEU* 3.4 34.1 - - + -
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Residues in contact with GLY 134 (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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133C MET* 1.3 78.0 - - - +
135C PHE* 1.3 59.4 - - - -
150C LEU* 4.3 2.2 - - - +
153C LEU* 3.9 19.9 - - - +
155C GLY 4.0 8.7 - - - -
156C TYR* 4.4 0.7 - - - -
185C ILE* 3.5 15.1 - - - +
224C LEU* 3.6 1.9 - - - +
225C VAL* 2.7 35.0 + - - +
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Residues in contact with PHE 135 (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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253A PRO 5.4 0.5 - - - +
91C VAL* 4.2 14.4 - - + -
115C ILE 5.3 0.2 - - - -
117C TYR* 4.5 14.4 - + - -
134C GLY* 1.3 74.8 - - - -
136C GLN* 1.3 60.4 - - - +
137C TYR* 3.3 31.9 - + + +
153C LEU* 3.0 24.3 - - - +
154C LYS* 3.9 8.4 + - + -
155C GLY* 3.7 14.2 - - - +
185C ILE* 3.4 31.6 - - + -
186C ALA* 3.2 36.6 - - - -
187C LEU* 3.8 20.6 - - + -
188C ASP* 4.9 0.9 - - - -
222C ALA* 4.9 4.0 - - + -
223C ARG 3.7 14.4 - - - -
224C LEU* 3.9 23.6 - - + -
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Residues in contact with GLN 136 (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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108A SER* 5.0 2.2 - - - -
254A ILE* 3.4 26.5 - - + +
258A LEU* 4.3 1.8 - - - +
135C PHE* 1.3 78.3 - - - +
137C TYR* 1.4 73.5 + - - +
138C ASP 5.3 0.7 - - - +
141C ASP* 4.2 4.6 - - - +
142C THR 3.2 21.6 + - - -
143C LEU* 2.8 32.4 - - - +
144C PRO* 4.0 13.2 - - - +
153C LEU* 4.2 11.6 - - + +
222C ALA* 3.4 2.8 - - - +
223C ARG* 2.9 63.7 + - + +
225C VAL* 4.0 9.9 - - + -
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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