Contacts of the strand formed by residues 109 - 113 (chain A) in PDB entry 1UXU
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 ASN 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A ARG* 3.8 34.0 - - + +
82A ILE* 3.3 8.6 - - - +
83A PRO* 3.4 25.5 - - - +
84A SER* 3.8 1.8 - - - +
108A THR* 1.3 78.2 - - - +
110A VAL* 1.3 64.6 + - - +
119A THR 4.4 0.2 - - - +
120A TRP* 3.4 16.6 - - - -
121A ASP* 4.2 9.2 + - - +
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A TRP* 4.7 1.6 - - + -
80A ILE 3.9 0.3 - - - +
81A ARG* 3.4 5.6 - - - +
82A ILE* 2.8 55.3 + - + +
84A SER* 3.6 24.7 - - - -
87A VAL* 4.2 26.5 - - + -
89A ARG* 5.2 0.2 - - + -
109A ASN* 1.3 75.2 - - - +
111A VAL* 1.3 66.6 + - - +
112A LEU* 5.0 3.1 - - + +
118A ILE* 3.8 18.2 - - + -
119A THR 3.3 6.5 - - - +
120A TRP* 3.7 24.9 - - + -
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A SER* 3.2 26.5 - - - +
80A ILE 3.5 4.9 - - - +
81A ARG* 3.7 42.8 - - + +
110A VAL* 1.3 76.3 - - - +
112A LEU* 1.3 62.1 + - - +
113A ARG* 4.9 2.9 - - + +
117A LEU 3.6 2.3 - - - +
118A ILE* 3.4 5.1 - - - -
119A THR* 2.9 43.7 + - + +
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.8 27.8 - - + -
14A PHE* 4.7 8.1 - - + -
67A LEU* 3.3 49.6 - - + +
69A TRP* 3.4 13.4 - - + -
79A SER* 3.2 5.9 - - - -
80A ILE* 2.8 47.5 + - + +
82A ILE* 4.7 5.8 - - + -
87A VAL* 5.3 0.9 - - + -
110A VAL* 4.0 7.4 - - + -
111A VAL* 1.3 72.3 - - - +
113A ARG* 1.3 64.5 + - - +
116A GLY* 4.4 3.1 - - - -
117A LEU 3.7 2.2 - - - +
118A ILE* 3.8 22.0 - - + -
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Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A HIS* 5.0 1.6 + - - -
69A TRP* 3.5 7.7 - - - -
78A ASP* 3.6 13.0 - - + +
79A SER* 4.4 6.3 - - - +
111A VAL* 3.9 3.3 + - + -
112A LEU* 1.3 75.7 - - - +
114A TYR* 1.3 77.1 + - + +
115A ASP* 2.7 41.0 + - - +
116A GLY* 2.9 23.6 + - - -
117A LEU* 2.8 50.0 + - + +
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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