Contacts of the strand formed by residues 121 - 125 (chain A) in PDB entry 1XB2
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 HIS 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A PRO* 2.9 23.5 + - + +
57A HIS* 3.6 25.1 - + + +
58A VAL 3.0 25.5 + - - +
116A SER* 3.3 21.2 + - - +
120A ARG* 1.3 78.5 - - - +
122A TYR* 1.3 62.7 + - - +
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Residues in contact with TYR 122 (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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57A HIS* 4.5 3.7 + - - -
58A VAL* 3.6 34.8 - - + -
60A VAL* 4.3 14.4 - - + -
114A GLU* 3.4 10.9 - - - +
115A TYR* 2.8 68.9 + + + +
117A THR* 3.2 22.4 - - + -
120A ARG* 2.7 41.3 + - - -
121A HIS* 1.3 73.0 - - - +
123A ALA* 1.3 59.8 + - - +
124A HIS 3.8 0.7 - - - -
243A VAL* 3.4 23.5 - - + +
244A ASP* 2.5 34.7 + - - -
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Residues in contact with ALA 123 (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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57A HIS* 3.8 16.6 - - - +
58A VAL 2.9 12.7 + - - +
59A ASN* 3.3 24.5 - - - +
60A VAL* 3.1 26.5 + - - +
112A HIS* 4.5 14.8 - - + -
113A VAL 3.8 4.9 - - - -
114A GLU* 4.3 5.8 - - + +
122A TYR* 1.3 71.6 - - - +
124A HIS* 1.3 61.1 + - - +
125A THR* 3.7 4.2 + - - +
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Residues in contact with HIS 124 (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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60A VAL* 3.5 10.4 - - + +
62A THR* 2.6 30.7 + - - -
73A LEU* 6.4 0.9 - - + -
74A THR* 3.2 32.1 + - + -
77A ILE* 4.8 9.6 - - + -
112A HIS* 3.4 6.6 + - - -
113A VAL* 2.9 46.6 + - + +
115A TYR* 2.8 43.6 + + + -
122A TYR 3.8 1.2 - - - -
123A ALA* 1.3 72.2 - - - +
125A THR* 1.3 69.6 + - - +
126A ASP* 5.0 3.1 - - + -
148A ILE* 3.9 19.3 - - + -
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Residues in contact with THR 125 (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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59A ASN* 4.9 1.4 + - - -
60A VAL 2.8 12.2 + - - -
61A GLY* 3.0 4.7 - - - -
62A THR* 2.9 27.9 + - - -
112A HIS* 3.9 22.2 + - + +
123A ALA 4.1 4.9 + - - -
124A HIS* 1.3 78.9 + - - +
126A ASP* 1.3 66.0 + - - +
127A CYS* 3.7 26.2 - - - +
133A TYR* 4.2 6.5 - - + -
136A ASN* 4.6 6.5 - - - +
142A ALA* 4.1 16.6 - - + +
144A LEU* 4.3 12.6 - - + +
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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