Contacts of the strand formed by residues 134 - 142 (chain O) in PDB entry 3SDI
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 VAL 134 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31O VAL* 3.5 7.6 - - - +
78O TYR* 3.8 17.5 - - + -
79O SER 3.5 4.9 - - - +
81O MET 3.2 34.3 - - - +
84O ASP* 4.2 4.5 - - + -
85O TYR* 4.0 7.2 - - + +
88O LEU* 3.5 32.3 - - + -
120O MET* 3.7 8.7 - - + +
132O PHE* 3.2 12.3 + - + -
133O GLY* 1.3 82.3 - - - +
135O SER* 1.3 62.3 + - - +
136O LEU* 4.4 8.7 - - + -
153O PRO* 3.1 24.4 - - - +
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Residues in contact with SER 135 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28O LEU* 4.8 2.1 - - - +
31O VAL* 3.5 24.3 - - - +
78O TYR* 3.2 5.0 - - - +
79O SER 2.9 31.1 + - - -
134O VAL* 1.3 75.1 + - - +
136O LEU* 1.3 63.7 + - - +
150O GLN* 4.7 1.1 + - - -
151O VAL 3.1 8.2 + - - -
152O ASP* 2.7 26.2 + - - -
153O PRO* 3.7 4.0 - - - +
165O ILE* 3.4 20.4 - - - +
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Residues in contact with LEU 136 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76O ALA* 5.3 3.1 - - + -
77O VAL 3.3 3.4 - - - +
78O TYR* 3.7 7.9 - - + -
85O TYR* 3.3 39.5 - - + -
88O LEU* 4.2 18.2 - - + -
89O VAL* 6.0 0.2 - - + -
116O VAL* 3.7 29.4 - - + -
120O MET* 4.3 7.2 - - - -
134O VAL* 4.4 11.9 - - + -
135O SER* 1.3 75.9 - - - +
137O LEU* 1.3 65.7 + - - +
138O ILE* 4.0 22.2 - - + -
149O TYR 3.6 0.5 - - - +
150O GLN* 3.2 7.1 - - - +
151O VAL* 2.9 39.8 + - + +
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Residues in contact with LEU 137 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O SER 3.9 8.5 - - - +
38O LEU* 3.4 41.5 - - - +
39O GLY* 3.5 4.9 - - - +
48O ILE* 4.4 9.2 - - + +
75O GLY 4.2 0.2 - - - +
76O ALA* 3.3 3.5 - - - -
77O VAL* 2.7 48.3 + - + +
135O SER 4.3 0.2 + - - -
136O LEU* 1.3 82.9 - - - +
138O ILE* 1.3 61.3 + - - +
139O ALA 4.2 0.5 + - - -
148O LEU* 4.5 5.8 - - + -
149O TYR 3.3 4.3 - - - +
150O GLN* 3.6 27.8 - - + +
163O THR* 3.9 20.4 - - + +
165O ILE* 3.8 20.9 - - + -
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Residues in contact with ILE 138 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70O LEU* 4.3 13.7 - - + -
74O ILE* 3.6 20.2 - - + -
75O GLY 3.4 9.9 - - - +
76O ALA* 3.8 13.2 - - + -
109O THR* 4.4 4.3 - - + +
112O LEU* 5.9 1.6 - - + -
113O VAL* 3.6 28.7 - - + +
116O VAL* 4.3 15.0 - - + -
136O LEU* 4.1 27.6 - - + -
137O LEU* 1.3 77.4 - - - +
139O ALA* 1.3 61.5 + - - +
140O GLY 4.2 0.2 + - - -
147O SER 4.2 0.2 - - - +
148O LEU* 3.5 3.5 - - - -
149O TYR* 2.8 42.3 + - + +
151O VAL* 4.2 14.6 - - + -
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Residues in contact with ALA 139 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46O VAL* 3.7 27.6 - - + -
48O ILE* 3.9 25.1 - - + -
74O ILE* 3.4 4.2 - - - +
75O GLY 2.8 36.9 + - - +
109O THR* 4.6 0.7 - - - -
137O LEU 4.1 1.2 + - - -
138O ILE* 1.3 74.5 - - - +
140O GLY* 1.3 59.6 + - - +
147O SER 3.5 4.5 - - - -
148O LEU* 4.0 2.5 - - + -
215O ILE* 3.5 15.6 - - + +
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Residues in contact with GLY 140 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46O VAL* 4.4 1.1 - - - +
73O ASP 3.2 12.3 - - - -
74O ILE* 4.2 2.0 - - - -
109O THR* 3.2 21.0 - - - +
139O ALA* 1.3 74.3 - - - +
141O HIS* 1.3 61.2 + - - -
147O SER* 2.8 43.8 + - - +
215O ILE* 3.9 9.7 - - - +
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Residues in contact with HIS 141 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73O ASP* 3.1 28.3 + - + +
74O ILE* 4.8 3.1 - - - +
107O PRO 5.4 1.0 - - - +
109O THR* 3.4 4.9 + - - -
140O GLY* 1.3 74.3 - - - +
142O ASP* 1.3 90.7 + - - +
143O GLU* 4.1 9.3 + - + -
146O GLY* 3.3 32.8 - - - -
147O PHE* 3.9 31.6 - + + -
215O ILE* 3.9 5.2 - - + -
220O ARG* 3.1 51.4 + - - -
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Residues in contact with ASP 142 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73O ASP* 5.5 1.6 - - - -
107O PRO 5.0 1.3 - - - +
108O PRO* 3.4 29.2 - - + +
109O THR* 3.3 23.7 + - - -
110O LYS* 4.9 1.2 + - - +
141O HIS* 1.3 85.3 - - - +
143O GLU* 1.3 67.0 + - - +
144O PHE* 3.3 4.2 + - - +
145O ASN* 2.8 49.6 + - - +
146O GLY* 2.9 27.5 + - - +
147O SER* 4.8 0.7 - - - +
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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