Contacts of the strand formed by residues 130 - 134 (chain A) in PDB entry 1X3B
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A VAL* 4.0 0.7 - - - +
43A TYR 3.1 16.3 + - - +
44A THR* 3.3 22.2 - - + +
45A VAL 3.6 4.2 + - - -
83A ILE* 3.3 23.5 - - + +
84A LEU 4.1 0.9 - - - +
85A VAL* 3.4 23.6 - - + -
123A ASP 4.7 0.2 - - - -
124A ILE 3.2 32.1 - - - +
125A MET* 4.2 10.1 - - + +
126A ALA* 4.4 0.4 - - - -
129A GLY* 1.3 75.0 - - - +
131A VAL* 1.3 74.5 + - - +
132A HIS* 3.2 25.8 - - + +
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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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11A VAL* 3.2 41.7 - - + +
14A VAL* 5.1 3.4 - - + -
15A LEU* 4.1 22.4 - - + -
45A VAL* 3.4 16.8 - - + +
47A ALA 4.8 1.8 - - - +
124A ILE* 2.9 62.5 + - + +
126A ALA* 5.2 0.4 - - + -
130A VAL* 1.3 86.1 - - - +
132A HIS* 1.3 77.5 + - - +
133A VAL* 4.4 3.4 - - + +
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Residues in contact with HIS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 3.5 25.1 - - + +
45A VAL 3.1 5.3 + - - -
46A PHE* 3.1 48.3 - + + -
84A LEU 2.7 29.9 + - - -
85A VAL* 3.4 22.9 - - + -
86A SER 5.3 0.7 - - - -
105A VAL* 6.4 0.9 - - + -
112A VAL* 5.4 4.4 - - + +
119A VAL* 4.3 4.0 - - + -
122A PRO* 3.2 18.4 - - + +
123A ASP 3.1 25.8 + - - -
124A ILE* 3.6 1.3 - - - -
130A VAL* 3.2 13.1 - - + +
131A VAL* 1.3 81.9 + - - +
133A VAL* 1.3 66.3 + - - +
134A ILE 3.3 1.6 + - - -
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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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21A PHE* 3.6 39.7 - - + -
47A ALA* 3.1 19.3 - - + +
48A PRO 4.6 0.4 - - - -
49A THR* 4.9 3.1 - - + -
119A VAL* 2.8 13.2 - - - +
120A ALA* 2.4 49.8 + - + +
121A GLU* 3.2 14.9 + - + +
124A ILE* 3.3 24.1 - - + +
131A VAL* 4.7 4.5 - - + -
132A HIS* 1.3 69.9 - - - +
134A ILE* 1.3 58.4 + - - +
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Residues in contact with ILE 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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46A PHE* 3.6 31.2 - - + +
47A ALA 3.0 4.5 + - - -
48A PRO* 3.1 41.1 - - + +
49A THR* 3.2 11.8 + - - +
78A HIS* 3.6 25.8 - - - +
114A VAL* 3.5 31.6 - - + -
117A GLU* 5.4 1.1 - - + -
118A PRO 4.2 5.4 - - - +
119A VAL* 4.2 7.0 - - + -
120A ALA* 3.6 5.1 - - - +
133A VAL* 1.3 77.9 - - - +
135A THR* 1.3 64.3 + - - +
136A ASN 3.1 24.2 - - - +
138A LEU* 3.8 6.7 - - + -
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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