Contacts of the strand formed by residues 146 - 151 (chain C) in PDB entry 3S52
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 146 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C GLN 3.9 3.6 - - - +
145C ALA* 1.3 72.7 - - - +
147C LEU* 1.3 61.5 + - - +
159C GLY 3.5 5.5 - - - +
160C ASN* 3.0 26.0 + - - +
162C ARG* 5.0 2.1 + - - -
207C MSE 3.7 1.6 - - + +
208C LEU* 3.6 8.5 - - - +
209C ASN* 2.9 47.5 + - - +
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Residues in contact with LEU 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C TYR* 4.4 16.8 - - - +
71C ILE* 4.2 18.6 - - + +
72C GLU* 4.1 9.2 - - - +
73C LEU* 3.8 30.1 - - + +
98C VAL* 4.0 21.1 - - + -
145C ALA* 4.7 4.9 - - + +
146C ASP* 1.3 75.7 - - - +
148C SER* 1.3 60.1 + - - +
157C GLN 4.7 0.2 - - - -
158C GLN* 3.3 4.9 - - - +
159C GLY 2.8 38.1 + - - +
161C THR* 4.5 7.6 - - + -
192C PRO* 4.6 11.0 - - + -
207C MSE 3.5 2.2 - - - +
208C LEU* 3.6 28.5 - - + -
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Residues in contact with SER 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C ILE* 3.4 8.6 - - - +
147C LEU* 1.3 75.8 - - - +
149C LEU* 1.3 61.2 + - - +
150C THR* 4.2 3.3 + - - -
155C ILE* 3.6 25.8 - - - +
157C GLN 3.4 7.0 + - - -
158C GLN* 4.1 8.4 + - - +
205C LYS* 4.4 1.5 + - - -
206C ILE* 3.3 4.7 - - - -
207C MSE 2.8 57.9 + - - +
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Residues in contact with LEU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C HIS* 3.3 51.6 - - + +
71C ILE* 4.1 11.9 - - + +
100C LEU* 4.2 10.5 - - + -
148C SER* 1.3 74.3 + - - +
150C THR* 1.3 73.0 + - - +
151C ILE* 4.2 9.2 - - + -
155C ILE* 3.9 1.4 - - - +
156C ARG* 2.9 25.3 + - + -
157C GLN* 2.9 25.6 + - + +
204C LEU* 4.0 18.8 - - + -
205C LYS 3.6 1.1 - - - -
206C ILE* 3.6 24.7 - - + -
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Residues in contact with THR 150 (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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148C SER* 4.3 1.9 + - - -
149C LEU* 1.3 73.2 - - - +
151C ILE* 1.3 65.1 + - - +
153C GLY* 3.4 17.3 - - - +
154C GLU 3.4 30.3 - - - +
155C ILE* 3.2 25.5 - - + +
203C MSE 3.5 0.9 - - - +
204C LEU* 3.3 5.7 - - - -
205C LYS* 2.7 71.1 + - + -
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Residues in contact with ILE 151 (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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69C HIS* 3.6 21.3 - - + +
149C LEU* 4.2 10.3 - - + -
150C THR* 1.3 77.6 - - - +
152C ASN* 1.3 80.3 + - - +
153C GLY 3.2 0.7 - - - -
154C GLU* 3.0 18.8 + - - +
156C ARG* 3.6 38.6 + - + +
197C PRO 4.6 0.4 - - - +
198C MSE 3.5 35.7 - - + -
202C ASP* 3.7 32.1 - - + +
203C MSE 3.2 4.0 - - - +
204C LEU* 4.1 10.1 - - + -
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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