Contacts of the strand formed by residues 128 - 134 (chain C) in PDB entry 2X2D
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 128 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25C PHE* 4.9 1.6 - - + -
29C VAL* 3.9 9.4 - - - +
87C ASN 5.4 0.4 + - - -
88C PHE* 5.9 0.8 - - - +
90C LEU* 3.6 55.8 + - + +
91C LYS 3.8 7.0 - - - +
92C HIS* 3.4 44.0 - - + +
97C ILE* 3.6 33.9 - - + -
98C LEU 3.6 6.1 - - - +
99C SER* 4.0 0.9 - - - +
126C HIS 3.4 0.8 + - - +
127C VAL* 1.3 74.8 - - - +
129C PHE* 1.3 62.4 + - - +
130C GLY 4.2 4.9 - - - +
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Residues in contact with PHE 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LEU* 3.4 9.0 - - + +
25C PHE* 2.8 29.1 + - - -
29C VAL* 3.6 22.6 - - + +
32C THR* 3.7 26.5 - - + -
33C ALA* 4.5 5.2 - - - +
36C PHE* 3.4 46.2 - + + -
98C LEU* 3.0 37.5 + - + -
99C SER* 3.4 28.3 - - - -
100C MET* 3.6 17.9 - - - -
112C PHE* 4.2 2.9 - - + -
127C VAL 3.5 13.0 - - - -
128C VAL* 1.3 73.2 - - - +
130C GLY* 1.3 59.2 + - - +
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Residues in contact with GLY 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C GLU 3.1 13.5 - - - -
24C LEU* 4.2 0.4 - - - -
25C PHE* 3.3 20.1 - - - -
97C ILE* 3.8 6.9 - - - +
98C LEU* 3.1 33.3 + - - +
128C VAL* 4.2 0.5 - - - +
129C PHE* 1.3 80.6 - - - +
131C LYS* 1.3 63.6 + - - +
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Residues in contact with LYS 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C PHE* 3.2 8.2 - - - -
23C GLU* 2.8 37.5 + - + +
25C PHE* 3.6 18.6 - - + -
93C THR* 4.8 5.7 + - - -
94C GLY* 5.0 2.2 + - - -
95C PRO 3.4 20.9 + - - -
96C GLY* 3.3 15.3 - - - +
97C ILE* 4.2 19.1 - - + +
98C LEU* 4.2 2.9 - - - +
130C GLY* 1.3 76.5 - - - +
132C VAL* 1.3 74.5 + - - +
133C LYS 3.4 0.2 + - - -
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Residues in contact with VAL 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C VAL* 4.1 7.9 - - + -
21C SER 3.4 4.7 - - - -
22C PHE* 3.7 24.9 - - + -
96C GLY* 2.8 32.3 + - - +
114C ILE* 4.1 11.7 - - + -
131C LYS* 1.3 85.4 - - - +
133C LYS* 1.3 61.1 + - - +
134C GLU 3.8 11.7 - - - +
135C GLY 4.3 0.9 - - - -
136C MET* 3.7 42.2 - - + +
139C VAL* 4.6 2.5 - - + -
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Residues in contact with LYS 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C THR* 4.6 15.7 - - + +
21C SER* 2.6 25.0 + - - +
23C GLU* 4.3 22.2 - - + +
131C LYS 3.4 1.4 + - - -
132C VAL* 1.3 74.8 - - - +
134C GLU* 1.3 82.5 + - + +
164C LEU* 6.4 0.2 - - + -
165C GLU* 4.1 18.7 + - - +
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Residues in contact with GLU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ARG 4.8 0.7 - - - -
20C VAL* 3.6 3.2 - - - +
21C SER* 2.9 45.2 + - - +
132C VAL* 3.8 1.8 - - - +
133C LYS* 1.3 105.2 + - + +
135C GLY* 1.3 62.6 + - - +
136C MET 3.5 2.0 - - - -
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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