Contacts of the strand formed by residues 100 - 103 (chain A) in PDB entry 1UEX
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 CYS 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A TRP* 3.2 47.6 - - + -
67A TRP* 3.2 18.2 - - + -
70A LEU 3.9 3.6 - - - -
71A ARG* 3.7 5.6 - - - -
98A THR 3.6 0.6 - - - -
99A LYS* 1.3 82.3 - - - +
101A PHE* 1.3 57.8 + - - +
115A LEU 2.5 33.0 + - - +
117A CYS* 2.0 45.5 - - - -
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Residues in contact with PHE 101 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A TRP* 4.2 0.3 + - - -
67A TRP* 3.2 16.6 - - - -
68A ILE* 3.2 26.4 + - + +
70A LEU* 2.9 44.1 + - + +
71A ARG* 4.1 7.6 - - - -
72A ASP* 4.4 1.6 - - + -
99A LYS* 4.4 6.7 - - - -
100A CYS* 1.3 75.5 - - - +
102A GLY* 1.3 59.7 + - - +
112A TRP* 5.0 0.9 - - + -
113A THR 3.3 6.1 - - - +
114A ASP* 3.4 31.2 - - + -
74B TRP* 3.6 37.9 - + - -
79B LEU* 3.7 22.0 - - + -
92B LEU* 3.3 41.3 - - + -
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Residues in contact with GLY 102 (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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66A ALA 3.2 17.0 - - - -
67A TRP* 4.2 0.9 - - - -
68A ILE* 3.6 11.2 - - - -
101A PHE* 1.3 78.1 - - - +
103A LEU* 1.3 64.5 + - - -
112A TRP* 4.4 0.2 - - - -
113A THR* 2.8 38.1 + - - +
115A LEU* 4.1 10.0 - - - +
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Residues in contact with LEU 103 (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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42A ILE* 4.3 9.0 - - + -
48A ALA 6.0 0.4 - - - +
51A VAL* 3.9 15.3 - - + +
52A THR* 5.6 1.1 - - - +
55A ALA* 3.9 16.8 - - + -
65A ASP* 3.6 4.0 - - - -
66A ALA* 2.8 31.0 + - + +
68A ILE* 3.8 18.8 - - + +
102A GLY* 1.3 68.6 - - - -
104A ASP* 1.3 63.2 + - - +
105A VAL 3.2 3.8 + - - -
109A TYR* 3.5 37.5 - - + +
110A ARG 5.4 0.2 - - - -
111A THR 3.4 2.9 - - - -
112A TRP* 3.7 28.9 - - + +
113A THR* 4.2 0.2 - - - -
124A ILE* 3.6 25.8 - - + -
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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