Contacts of the strand formed by residues 129 - 135 (chain A) in PDB entry 3BYQ
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 MSE 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ALA* 3.7 27.8 - - + -
83A ALA 3.6 10.8 - - - +
84A ILE* 3.6 29.6 - - + -
119A VAL* 3.8 19.3 - - + +
120A LYS* 4.0 23.6 - - - +
121A ALA* 4.1 13.2 - - - -
127A TYR* 4.1 13.0 - - + +
128A ARG* 1.3 76.0 - - - +
130A MSE 1.3 73.2 + - - +
131A VAL* 3.6 5.3 + - + +
149A GLU* 3.3 5.5 - - - +
150A ILE* 2.9 40.5 + - + +
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Residues in contact with MSE 130 (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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119A VAL* 3.5 18.5 - - - +
129A MSE 1.3 74.8 - - - +
131A VAL* 1.3 60.5 + - - +
132A PRO* 3.8 3.5 - - - +
147A SER* 3.5 34.1 - - - +
148A ILE* 3.7 1.8 - - - -
149A GLU* 3.7 33.0 - - + +
153B GLN* 3.8 32.1 - - - +
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Residues in contact with VAL 131 (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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80A SER* 3.1 31.6 - - - +
81A LYS 4.2 2.5 - - - +
82A ALA* 3.8 25.6 - - + -
119A VAL* 4.0 5.6 - - + -
129A MSE 3.7 13.7 - - + +
130A MSE 1.3 77.8 - - - +
132A PRO* 1.3 64.6 - - + +
133A VAL* 3.8 1.6 + - - +
147A SER* 3.2 5.3 - - - -
148A ILE* 2.8 40.5 + - - +
150A ILE* 3.7 23.1 - - + -
166A VAL* 4.0 18.6 - - + -
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Residues in contact with PRO 132 (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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80A SER* 2.6 28.8 + - - +
117A PRO* 3.3 14.7 - - + +
118A ALA 4.3 14.8 - - - +
119A VAL* 3.9 14.8 - - + -
130A MSE 3.8 7.2 - - - +
131A VAL* 1.3 88.4 - - + +
133A VAL* 1.3 59.5 + - - +
146A ASN 3.3 9.0 - - - +
147A SER* 4.2 5.8 - - - +
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Residues in contact with VAL 133 (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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30A LEU* 4.6 6.7 - - + -
78A VAL* 3.8 27.1 - - + -
79A TYR* 3.4 13.7 - - - +
80A SER* 3.7 9.4 - - - -
117A PRO* 4.0 1.3 - - - -
131A VAL 4.2 7.0 - - - +
132A PRO* 1.3 79.7 - - - +
134A HIS* 1.3 64.1 + - - +
144A HIS 4.0 1.6 - - - +
145A PHE* 3.5 6.2 - - - +
146A ASN* 2.8 56.2 + - + +
147A SER* 4.3 1.3 - - - +
148A ILE* 5.0 2.9 - - + -
166A VAL* 3.6 31.6 - - + -
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Residues in contact with HIS 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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78A VAL* 3.1 24.1 - - - -
79A TYR* 3.2 13.6 + + - +
114A ALA* 4.1 2.3 - - + +
115A MSE 2.7 35.5 + - + -
117A PRO* 3.6 29.8 - - + +
133A VAL* 1.3 76.0 - - - +
135A TYR* 1.3 78.8 + - - +
136A ILE 3.5 0.2 + - - -
139A SER* 3.6 30.9 + - - +
144A HIS 4.3 6.3 - - - -
145A PHE* 3.7 26.4 - - + -
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Residues in contact with TYR 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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77A GLU* 3.1 35.0 - - + -
78A VAL* 4.1 2.2 - - - -
114A ALA* 3.3 15.1 - - - +
134A HIS* 1.3 80.4 - - - +
136A ILE* 1.3 63.8 + - - +
137A HIS* 3.3 41.6 + + + +
138A ALA 3.4 36.2 + - - +
139A SER 4.9 0.6 + - - -
141A VAL* 3.5 30.9 + - + +
144A HIS* 3.5 25.4 - + + +
182A LYS* 3.6 38.7 + - + +
185A VAL* 4.3 9.6 - - + -
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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