Contacts of the strand formed by residues 107 - 111 (chain B) in PDB entry 2VUU
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 107 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B HIS 3.4 1.8 + - - -
76B LEU* 3.5 13.3 - - + +
77B ALA 3.1 22.9 + - - -
105B ILE* 3.6 2.8 - - - +
106B GLN* 1.3 82.9 - - + +
108B TYR* 1.3 63.1 + - - +
109B ILE* 3.9 4.3 - - + -
144B PRO 3.4 8.5 - - - -
145B SER 4.4 2.7 - - - -
146B THR* 2.9 30.8 + - - -
203B ILE* 3.4 27.5 + - + -
204B PHE* 3.5 28.2 + + + -
207B GLY* 3.4 28.9 - - - -
208B PRO* 3.7 23.8 - - + +
211B TRP* 4.2 0.9 - - + +
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Residues in contact with TYR 108 (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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71B PHE* 4.3 5.8 - + - -
77B ALA* 3.7 16.6 - - + -
79B ILE* 3.7 31.5 - - + +
92B GLY 4.2 2.8 + - - -
95B LEU* 3.8 6.8 - - - +
96B ALA* 3.4 30.4 + - + +
99B ALA* 3.5 33.7 - - + -
105B ILE* 3.8 12.1 - - + -
107B HIS* 1.3 73.6 - - - +
109B ILE* 1.3 63.3 + - - +
110B TYR* 3.8 14.6 + + + -
138B VAL* 4.0 28.7 - - + +
143B LEU* 4.1 16.2 - - + -
144B PRO 2.8 13.7 + - - +
145B SER* 3.1 27.5 - - - -
146B THR 3.3 1.3 + - - +
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Residues in contact with ILE 109 (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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77B ALA 2.9 12.9 + - - +
78B PHE* 3.4 13.0 - - + -
79B ILE* 2.8 28.1 + - - +
107B HIS* 4.6 4.0 - - + -
108B TYR* 1.3 73.4 - - - +
110B TYR* 1.3 59.4 + - - +
146B THR* 3.2 23.6 - - + +
148B VAL* 3.4 34.5 - - + -
200B LEU* 3.9 19.5 - - + +
203B ILE* 3.9 25.1 - - + -
204B PHE* 3.7 38.1 - - + -
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Residues in contact with TYR 110 (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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79B ILE* 3.3 38.6 - - + -
81B THR* 3.8 24.4 + - + +
88B GLU* 4.3 3.5 + - - +
92B GLY* 4.5 2.6 - - - -
108B TYR* 3.8 18.7 + + + -
109B ILE* 1.3 75.8 - - - +
111B SER* 1.3 81.3 + - - +
112B SER* 3.4 3.2 + - - -
131B LYS* 3.4 32.6 - - - +
134B VAL* 3.6 35.5 - - + +
135B GLU* 4.2 9.0 - - - -
138B VAL* 4.7 1.6 - - + -
146B THR 3.0 6.1 + - - -
147B PHE* 3.4 33.3 - + + -
148B VAL* 3.0 24.3 + - - -
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Residues in contact with SER 111 (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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17B GLN* 2.9 19.4 + - - -
78B PHE* 4.2 6.7 - - - -
79B ILE 2.7 8.5 + - - +
80B ASN* 2.8 42.5 + - - -
109B ILE 4.2 0.2 + - - -
110B TYR* 1.3 89.2 - - - +
112B SER* 1.3 59.0 + - - +
131B LYS* 3.9 12.8 + - - +
148B VAL* 3.4 15.9 + - - +
150B ALA* 5.1 4.5 + - - +
1353B NAP 5.7 1.6 - - - -
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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