Contacts of the strand formed by residues 153 - 158 (chain A) in PDB entry 3SAJ
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 GLN 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A GLN 2.9 8.9 + - - -
126A THR* 2.9 25.8 - - + +
127A PHE 3.0 23.0 + - - +
151A ASN* 4.5 16.7 + - - +
152A TRP* 1.3 76.5 + - - +
154A VAL* 1.3 62.6 + - - +
155A THR* 4.0 2.1 + - - -
153C GLN* 2.6 42.8 + - + +
155C THR* 5.5 9.6 - - - +
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Residues in contact with VAL 154 (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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127A PHE* 3.4 37.7 - - + +
129A TYR* 3.9 26.2 - - + -
140A LEU* 6.1 0.2 - - + -
143A VAL* 4.4 7.9 - - + -
144A LEU* 4.2 25.3 - - + +
147A ALA* 3.7 26.2 - - + -
152A TRP* 3.5 5.2 + - + -
153A GLN* 1.3 75.4 + - - +
155A THR* 1.3 65.8 + - - +
156A ALA* 4.2 2.8 + - + +
153C GLN* 4.1 8.9 + - - -
154C VAL 4.8 9.2 + - - +
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Residues in contact with THR 155 (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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127A PHE 3.0 10.3 + - - -
128A VAL* 3.4 14.0 - - - +
129A TYR* 2.6 33.8 + - - +
153A GLN 4.0 2.3 + - - -
154A VAL* 1.3 75.9 - - - +
156A ALA* 1.3 59.9 + - - +
157A VAL* 4.8 1.8 - - + -
170A LEU* 3.7 28.9 - - + -
147C ALA* 5.4 0.9 - - + -
148C ALA* 4.1 20.6 - - + +
152C TRP 6.0 1.1 - - - +
153C GLN* 3.8 16.3 + - - +
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Residues in contact with ALA 156 (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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129A TYR* 3.3 8.7 - - + +
131A TYR* 4.0 14.4 - - + -
140A LEU* 4.2 11.4 - - + -
144A LEU* 5.3 2.7 - - + -
154A VAL* 4.1 4.6 + - + +
155A THR* 1.3 74.0 - - - +
157A VAL* 1.3 64.4 + - - +
144C LEU* 3.6 50.7 + - + +
145C ASP* 3.7 6.4 - - - +
148C ALA* 3.8 5.9 - - - +
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Residues in contact with VAL 157 (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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128A VAL* 4.0 23.1 - - + -
129A TYR 2.8 10.9 + - - +
130A ILE* 3.1 12.5 - - + +
131A TYR* 2.7 33.3 + - - -
155A THR* 4.7 1.1 - - + +
156A ALA* 1.3 80.3 - - - +
158A ASN* 1.3 55.6 + - - +
159A ILE* 3.5 1.3 + - + -
162A THR* 3.2 42.0 - - + +
166A GLY 5.8 2.0 - - - +
167A TYR* 4.2 16.4 - - + +
170A LEU* 4.2 22.4 - - + -
145C ASP* 4.1 2.2 - - - +
148C ALA* 4.5 7.9 - - + -
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Residues in contact with ASN 158 (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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131A TYR* 2.6 66.1 + - + +
132A ASP* 3.4 11.5 - - - -
133A ALA* 3.7 9.4 + - - +
157A VAL* 1.3 70.1 - - - +
159A ILE* 1.3 66.0 + - - +
160A LEU* 3.7 16.6 + - - +
161A THR* 3.2 24.3 + - + +
162A THR* 3.4 8.7 + - - +
141C GLN* 3.1 20.4 - - - +
145C ASP* 3.5 15.9 + - - +
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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