Contacts of the strand formed by residues 158 - 165 (chain A) in PDB entry 3SMZ
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 LEU 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A GLU* 4.7 3.8 - - + +
152A VAL* 4.0 9.2 - - + -
153A ARG* 3.8 42.8 - - + +
156A GLY 4.0 3.8 - - - +
157A SER* 1.3 79.3 - - - +
159A GLU* 1.3 66.9 + - - +
160A ARG 3.9 16.8 - - - +
161A CYS* 4.3 12.8 - - + -
178A ALA* 4.0 15.3 - - + -
179A GLU 3.5 11.2 - - - +
180A TYR* 3.6 30.5 - - + -
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Residues in contact with GLU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SO4 4.4 4.9 + - - -
54A GLN* 4.5 2.3 - - - +
57A ASN* 3.5 21.4 + - - +
59A ARG* 3.2 26.7 + - - -
60A LYS* 3.5 13.5 + - - -
157A SER* 5.5 0.3 - - - -
158A LEU* 1.3 77.1 - - - +
160A ARG* 1.4 66.7 + - + +
179A GLU* 2.7 36.9 + - - +
180A TYR 4.0 1.3 - - - +
181A MET* 3.4 48.3 - - - +
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Residues in contact with ARG 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLN* 3.1 33.7 - - - +
55A PHE* 3.0 45.7 + - - +
57A ASN* 3.4 18.4 - - + +
58A ARG* 3.5 22.3 - - - +
133A LEU* 4.2 13.9 - - - +
158A LEU* 3.9 4.6 - - - +
159A GLU* 1.4 84.9 - - + +
161A CYS* 1.3 64.0 + - - +
162A PHE* 4.2 16.5 - - + -
177A PHE 4.4 1.8 - - - -
178A ALA* 3.7 0.5 - - - -
179A GLU* 2.8 63.5 + - + +
210A ALA* 3.8 21.8 + - - +
213A LEU* 5.2 3.0 - - - +
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Residues in contact with CYS 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A HIS* 4.5 0.2 - - - -
54A GLN* 2.9 22.7 + - - +
145A GLN* 3.0 14.4 + - - -
148A PHE* 3.7 20.6 - - - -
149A GLU* 3.6 29.2 - - + +
152A VAL* 3.7 26.7 - - - -
158A LEU* 4.3 16.8 - - + -
160A ARG* 1.3 77.2 - - - +
162A PHE* 1.3 65.4 + - - +
177A PHE 3.3 5.2 - - - -
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Residues in contact with PHE 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A THR* 3.8 21.8 - - + +
54A GLN* 3.7 25.1 - - + -
55A PHE* 3.8 31.9 - + + -
133A LEU* 5.8 0.4 - - + -
145A GLN* 3.4 8.5 - - - +
148A PHE* 4.1 4.5 - - - -
160A ARG* 4.2 21.1 - - + -
161A CYS* 1.3 85.1 - - - +
163A LEU* 1.3 70.6 + - - +
164A VAL* 4.2 3.8 - - + -
176A GLY* 3.0 2.8 - - - -
177A PHE* 2.8 78.7 + + + -
213A LEU* 5.3 2.0 - - + -
218A LEU* 3.8 21.5 - - + -
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A THR* 2.6 30.5 + - - +
139A LEU* 3.6 31.2 - - + -
143A LEU* 3.4 26.0 - - + +
144A THR* 3.6 2.5 - - - +
145A GLN* 2.9 36.4 + - - +
148A PHE* 3.7 23.6 - - + -
162A PHE* 1.3 75.1 - - - +
164A VAL* 1.3 59.9 + - - +
165A TYR* 3.8 24.0 - - + +
172A SER* 3.9 17.0 - - - +
175A TYR 3.6 9.6 - - - +
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Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A THR* 4.7 4.0 - - + -
162A PHE* 4.2 8.3 - - + -
163A LEU* 1.3 75.1 - - - +
165A TYR* 1.3 63.9 + - - +
172A SER* 3.8 3.8 + - - -
173A LYS* 3.0 28.3 + - + +
175A TYR* 3.1 40.1 + - + +
177A PHE* 4.1 18.6 - - + -
218A LEU* 3.7 35.0 - - + +
219A HIS* 3.7 28.9 - - + +
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Residues in contact with TYR 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG* 3.7 58.0 + - + +
48A LEU* 4.0 19.8 - - + +
50A HIS* 5.9 1.6 - - + -
51A THR* 3.3 28.9 + - - +
144A THR* 5.5 0.4 - - - -
145A GLN* 3.4 32.3 + - + +
163A LEU* 3.8 28.4 - - + +
164A VAL* 1.3 74.9 - - - +
166A SER* 1.3 65.2 - - - +
167A GLU 3.3 0.7 + - - -
170A GLY* 3.3 21.8 - - - +
171A GLN 3.4 3.8 - - - +
172A SER* 3.7 17.9 - - - -
173A LYS* 4.2 4.7 - - - -
219A HIS* 3.3 20.8 - - - -
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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