Contacts of the strand formed by residues 133 - 137 (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 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A THR* 4.6 9.4 - - + +
131A ASP 3.7 3.0 + - - -
132A ALA* 1.3 78.0 - - - +
134A LEU* 1.3 75.0 + - - +
160A ARG* 4.2 8.5 - - - +
162A PHE* 5.8 0.9 - - + -
177A PHE* 3.9 18.6 - - + -
178A ALA 3.6 10.5 - - - +
179A GLU* 3.8 22.7 - - + +
207A TRP* 3.6 8.4 - - - -
208A THR* 2.9 48.1 + - - +
210A ALA* 3.6 32.5 - - + +
213A LEU* 3.8 20.6 - - + -
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Residues in contact with LEU 134 (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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133A LEU* 1.3 74.5 - - - +
135A CYS* 1.3 62.0 + - - +
136A VAL* 4.0 8.7 + - + -
152A VAL* 6.6 0.4 - - + -
177A PHE* 3.3 11.7 - - - +
178A ALA* 3.0 38.2 + - + +
180A TYR* 4.1 9.4 - - + -
186A ALA* 3.4 26.7 - - + +
189A ALA* 3.8 13.2 - - + -
190A LYS* 3.8 28.9 - - + +
193A LEU* 5.7 1.3 - - + -
205A VAL* 4.0 17.9 - - + -
206A HIS 3.5 5.8 - - - +
207A TRP* 3.7 39.0 - - + -
208A THR* 4.3 1.1 - - - -
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Residues in contact with CYS 135 (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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134A LEU* 1.3 72.6 - - - +
136A VAL* 1.3 62.8 - - - +
137A ALA* 3.9 0.7 + - - +
175A TYR* 4.1 14.1 - - - -
176A GLY 3.4 10.3 - - - -
177A PHE* 3.5 15.0 - - + -
204A TYR 3.9 0.3 - - - +
205A VAL* 3.3 7.3 - - - +
206A HIS* 2.9 41.3 + - + -
208A THR* 3.5 18.5 + - - +
298A ALA* 3.5 26.7 - - + +
299A PRO* 3.9 16.6 - - - -
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Residues in contact with VAL 136 (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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134A LEU* 4.8 9.4 - - + -
135A CYS* 1.3 73.7 - - - +
137A ALA* 1.3 62.8 + - - +
139A LEU* 4.0 25.4 - - + +
148A PHE* 3.7 26.2 - - + -
151A LEU* 4.6 3.8 - - + -
152A VAL* 4.3 4.9 - - + -
175A TYR* 3.2 3.9 - - - +
176A GLY 2.9 32.2 + - - +
178A ALA* 5.0 3.6 - - + -
193A LEU* 4.3 19.5 - - + -
203A LEU* 4.1 18.2 - - + -
204A TYR 3.6 7.4 - - - +
205A VAL* 4.3 16.4 - - + -
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Residues in contact with ALA 137 (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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135A CYS 3.9 0.2 - - - -
136A VAL* 1.3 75.7 - - - +
138A ASN* 1.3 67.7 + - + +
139A LEU* 3.3 2.4 + - - -
174A GLY 3.8 0.2 - - - -
175A TYR* 3.7 17.9 - - + -
203A LEU* 3.6 7.4 - - - +
204A TYR* 2.7 45.2 + - + +
296A PHE 4.8 2.2 - - - +
297A CYS* 4.7 2.0 - - - -
298A ALA* 3.9 31.6 - - + +
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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