Contacts of the strand formed by residues 107 - 110 (chain B) in PDB entry 3UXA
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 ILE 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B ARG* 3.3 23.8 - - - +
33B LEU* 6.0 0.2 - - - -
80B LEU* 3.3 35.9 - - + +
82B ILE* 3.7 25.6 - - + -
96B LEU* 4.3 19.3 - - + +
99B ILE* 4.1 6.7 - - + -
100B ALA* 4.9 7.9 - - + -
103B VAL* 3.9 11.7 - - + -
105B ILE 3.5 13.0 - - - +
106B PRO* 1.3 72.5 - - - +
108B LEU* 1.3 66.6 + - - +
126B GLY 4.8 1.6 - - - +
127B ALA* 3.6 5.3 - - + -
128B ASP* 2.6 42.2 + - - +
129B THR* 3.3 8.3 + - - -
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Residues in contact with LEU 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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33B LEU* 4.1 16.4 - - + +
49B ILE* 5.9 0.2 - - + -
80B LEU 2.6 14.2 + - - +
81B VAL* 3.3 15.5 - - + -
82B ILE 3.0 25.3 + - - -
106B PRO 4.2 0.8 - - - -
107B ILE* 1.3 76.0 - - - +
109B MET* 1.3 90.2 + - - +
110B TRP* 3.7 22.7 - - + +
129B THR* 3.6 24.9 - - + -
130B VAL 3.8 6.1 - - - +
131B GLY* 3.5 9.2 - - - +
157B ALA* 3.5 31.9 - - + -
178B ILE* 4.3 9.9 - - + -
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Residues in contact with MET 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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82B ILE* 3.8 3.6 - - - -
84B THR* 3.5 34.3 - - + +
93B TYR* 4.0 19.7 - - + +
96B LEU* 3.5 23.6 - - + -
107B ILE* 3.9 2.3 + - - -
108B LEU* 1.3 83.5 - - - +
110B TRP* 1.3 60.5 + - - +
111B ASP* 4.1 13.0 + - + +
113B ILE* 4.4 13.4 - - + +
118B GLN* 3.6 26.5 - - + +
122B ALA* 3.7 14.4 - - + -
127B ALA* 3.7 17.9 - - + +
129B THR 2.9 11.7 + - - +
130B VAL* 3.3 8.5 - - + +
131B GLY 3.2 13.3 + - - -
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Residues in contact with TRP 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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81B VAL* 3.5 33.9 - - + -
82B ILE 3.1 9.8 + - - +
83B LEU* 3.6 28.7 - - + +
84B THR* 3.0 25.8 + - - -
89B PHE* 4.5 9.4 - + - -
108B LEU* 3.6 13.2 + - + -
109B MET* 1.3 72.5 - - - +
111B ASP* 1.3 79.1 + - - +
112B PHE* 3.7 35.2 - + - -
131B GLY* 4.9 7.9 - - - +
133B ILE* 4.0 24.0 - - + -
159B VAL* 4.4 23.5 - - + +
178B ILE* 5.1 4.8 - - + +
184B LEU* 5.1 9.9 - - + -
231B GLU* 4.5 16.8 + - - -
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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