Contacts of the strand formed by residues 116 - 121 (chain Z) in PDB entry 2XB2
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 TYR 116 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59Y GLU* 3.9 32.3 - - + +
63Y ILE* 4.0 13.7 - - + -
128Y ASP 4.3 2.6 + - - -
131Y CYS* 3.9 2.6 - - - -
132Y LEU* 3.1 47.1 + - + +
76Z PHE* 4.0 11.9 - + + -
77Z VAL 3.3 15.9 - - - +
80Z VAL* 4.1 2.5 - - - -
104Z LEU* 3.4 14.0 - - - +
105Z ASN* 3.1 45.9 + - + +
114Z LYS* 3.9 27.5 - - + +
115Z GLY* 1.3 79.1 - - - +
117Z THR* 1.3 67.2 + - - +
118Z LEU* 3.9 15.7 - - + -
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Residues in contact with THR 117 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Z PHE* 4.8 0.4 - - - -
77Z VAL* 2.9 53.0 + - + +
80Z VAL* 3.7 16.2 - - + -
89Z ILE* 4.2 23.2 - - + +
102Z ILE* 3.9 14.7 - - - +
103Z HIS 3.0 20.9 + - - -
104Z LEU* 3.6 13.5 - - - +
116Z TYR* 1.3 79.3 - - - +
118Z LEU* 1.3 65.3 + - - +
119Z VAL* 4.9 0.2 - - + -
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Residues in contact with LEU 118 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132Y LEU* 5.3 0.9 - - + -
135Y SER* 4.4 14.1 - - - +
136Y LEU* 4.0 27.8 - - + -
139Y LEU* 3.8 30.8 - - + +
74Z ILE* 4.1 6.5 - - + -
75Z LEU 3.4 7.9 - - - +
76Z PHE* 4.0 14.4 - - + -
101Z ASN 4.4 0.3 - - - -
102Z ILE* 3.2 6.2 - - - +
103Z HIS* 2.9 46.1 + - + +
116Z TYR* 3.9 27.4 - - + -
117Z THR* 1.3 76.4 - - - +
119Z VAL* 1.3 61.7 + - - +
149Z CYS* 4.1 11.2 - - - -
150Z PHE* 5.3 0.4 - - + -
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Residues in contact with VAL 119 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73Z TRP 4.1 0.3 - - - +
74Z ILE* 3.5 2.1 - - - +
75Z LEU* 2.8 38.9 + - + +
77Z VAL* 4.5 6.1 - - + -
89Z ILE* 4.0 27.1 - - + -
93Z PHE* 4.1 25.8 - - + -
99Z ILE* 4.0 18.8 - - + -
101Z ASN 3.6 2.7 - - - -
102Z ILE* 4.3 6.5 - - + -
117Z THR* 4.1 4.0 + - - +
118Z LEU* 1.3 78.3 - - - +
120Z GLU* 1.3 64.9 + - - +
121Z TYR* 4.0 32.1 - - + +
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Residues in contact with GLU 120 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139Y LEU* 3.8 20.7 - - + +
69Z SER* 4.3 1.0 - - - -
71Z GLU* 3.7 10.6 + - - +
72Z GLY* 3.5 26.9 + - - +
73Z TRP 3.2 11.4 - - - +
74Z ILE* 3.7 24.3 - - + +
99Z ILE* 3.7 5.9 - - - +
100Z LYS* 2.9 34.4 + - + +
101Z ASN* 3.0 37.6 + - + +
119Z VAL* 1.3 77.0 - - - +
121Z TYR* 1.3 72.9 + - - +
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Residues in contact with TYR 121 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72Z GLY* 3.3 3.5 - - - -
73Z TRP 2.7 34.0 + - - -
75Z LEU* 4.0 13.5 - - + -
93Z PHE* 2.6 42.9 + - - +
96Z TYR* 4.4 2.5 - - + -
97Z GLY 3.8 19.3 - - - -
98Z GLU 3.5 17.9 - - - -
99Z ILE* 3.7 20.4 - - + -
100Z LYS* 4.3 2.5 - - - -
119Z VAL* 4.0 13.2 - - + -
120Z GLU* 1.3 79.7 - - - +
122Z GLU* 1.3 58.4 + - - +
123Z THR 3.5 2.9 - - - +
126Z GLU* 3.7 22.2 - - + -
127Z ALA* 3.5 27.8 - - + +
130Z ALA* 3.3 26.4 - - + +
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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