Contacts of the strand formed by residues 126 - 131 (chain B) in PDB entry 2YXD
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 126 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B LYS 3.0 26.5 - - - -
31B LEU* 3.7 14.2 + - - -
32B ASN* 3.3 21.4 + - + -
102B ASN 4.6 1.1 - - - +
103B LYS* 3.6 36.3 - - - +
104B ALA 3.2 22.0 + - - +
124B ILE* 3.2 5.5 + - - +
125B ASN* 1.3 91.8 + - - +
127B ILE* 1.3 63.9 + - - +
128B VAL* 4.1 4.5 - - + +
180B LYS* 3.8 14.1 - - + -
181B ALA 3.4 3.1 + - - -
182B VAL* 3.6 19.5 - - + +
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ALA* 3.2 11.4 - - + +
106B ILE* 4.2 9.6 - - + -
119B LEU* 3.7 33.0 - - + -
124B ILE* 4.0 13.7 - - + +
126B HIS* 1.3 80.5 + - - +
128B VAL* 1.3 75.1 + - - +
129B ALA* 4.2 2.0 - - + +
144B PHE* 3.2 49.8 - - + -
149B TYR* 4.0 17.0 - - + +
179B ILE 3.7 0.5 - - - +
180B LYS* 3.4 2.9 - - - +
181B ALA* 2.8 39.1 + - + +
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B SER* 4.3 11.4 - - - +
30B LYS* 3.4 34.8 - - + +
31B LEU* 3.4 24.9 - - + -
104B ALA 3.0 5.9 + - - +
105B PHE* 3.2 25.1 - - + -
106B ILE* 2.7 31.7 + - - +
126B HIS* 4.1 4.5 - - + -
127B ILE* 1.3 79.5 - - - +
129B ALA* 1.3 57.7 + - - +
130B ASN* 4.2 0.4 - - - +
178B ILE* 4.1 21.1 - - + -
179B ILE 3.0 8.5 - - - +
180B LYS* 4.3 4.5 - - + -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ILE* 3.2 22.0 - - + +
112B ILE* 5.8 0.2 - - + -
127B ILE* 4.9 5.2 - - + -
128B VAL* 1.3 76.9 - - - +
130B ASN* 1.3 66.5 + - - +
140B ILE* 3.9 35.9 - - + -
144B PHE* 5.5 1.1 - - + -
177B THR 3.6 1.6 - - - +
178B ILE* 3.6 0.7 - - - -
179B ILE* 2.8 37.2 + - + +
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Residues in contact with ASN 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B THR* 4.7 1.6 + - - +
23B ILE* 3.6 21.4 - - - +
27B SER* 3.1 28.2 + - - -
49B MSE 4.0 5.1 - - - +
105B PHE* 3.6 25.2 - - + -
106B ILE 2.8 14.7 + - - +
107B GLY* 4.0 17.2 - - - +
108B GLY* 5.2 0.7 - - - -
128B VAL* 4.2 0.3 - - - +
129B ALA* 1.3 75.6 - - - +
131B THR* 1.3 63.6 + - - +
140B ILE* 5.5 0.5 - - - +
176B ILE* 3.8 15.9 - - + +
177B THR 3.3 3.4 - - - +
178B ILE* 3.4 24.4 - - - +
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Residues in contact with THR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ASN* 1.3 77.1 - - - +
132B ILE* 1.3 66.3 + - - +
133B VAL* 3.1 20.3 + - - +
136B ASN* 3.6 16.1 + - - +
137B ALA* 3.7 37.9 - - + +
140B ILE* 4.4 7.4 - - + -
176B ILE* 3.7 1.7 - - - +
177B THR* 2.9 43.7 + - - +
179B ILE* 4.2 9.6 - - + -
2001B MES 3.6 3.3 - - - +
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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