Contacts of the strand formed by residues 38 - 43 (chain B) in PDB entry 1UB6
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 LEU 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B LEU* 4.0 19.7 - - + -
29B LEU* 3.9 16.4 - - + -
36B THR* 2.9 7.6 + - + +
37B TYR* 1.3 74.2 - - - +
39B TYR* 1.3 66.9 + - - +
40B TRP* 3.8 21.0 - - + +
53B ILE* 5.2 0.2 - - - +
54B TYR* 3.5 0.3 - - - -
55B GLN* 3.0 7.8 + - - +
56B MET* 2.8 48.2 + - + -
69B SER* 4.1 0.7 - - - +
76B PHE* 3.4 44.4 - - + -
93B CYS* 4.1 9.4 - - + -
94B ALA 3.5 16.6 - - - +
96B ASN* 4.0 0.4 - - - +
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Residues in contact with TYR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 5.5 0.2 - - - +
100A GLY* 6.1 1.0 - - - -
104A PRO* 3.9 26.1 - - + +
106A TRP* 4.4 7.8 - + - -
38B LEU* 1.3 76.0 - - - +
40B TRP* 1.3 64.6 + - - +
41B TYR* 3.9 23.7 - + - -
51B LEU* 3.9 13.2 - - + -
53B ILE 3.1 13.7 - - - +
54B TYR* 3.7 13.7 - - + -
55B GLN 4.6 0.7 - - - +
93B CYS* 3.4 4.2 - - - +
94B ALA* 2.9 57.8 + - + -
95B GLN 3.9 12.8 + - - -
96B ASN* 4.0 25.8 - - + +
101B PRO* 5.6 1.6 - - - +
103B PHE* 3.3 28.1 - - - -
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Residues in contact with TRP 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLN* 4.2 4.7 - - - -
21B ILE* 3.4 36.1 - - + -
22B SER 4.4 0.2 - - - -
23B CYS* 3.6 24.5 - - + -
38B LEU* 3.8 11.8 - - + +
39B TYR* 1.3 79.5 - - - +
41B TYR* 1.3 56.5 + - - +
51B LEU* 3.4 5.2 - - - +
52B LEU* 2.7 47.2 + - + -
53B ILE* 2.7 33.3 + - + +
56B MET 5.1 0.2 - - - -
69B SER* 3.1 24.7 + - - -
76B PHE* 4.4 10.8 - - + -
77B THR 4.0 4.5 - - - -
78B LEU* 3.5 42.6 - - + -
91B TYR* 4.9 1.3 - - + -
92B TYR 3.2 22.9 - - - -
93B CYS* 3.7 18.8 - - + -
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Residues in contact with TYR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLN* 6.2 1.6 - - - -
47A LEU* 3.2 40.9 + - + +
106A TRP* 3.6 22.2 - + + -
39B TYR* 3.9 26.9 - + - -
40B TRP* 1.3 75.1 - - - +
42B LEU* 1.3 62.7 + - - +
43B GLN* 5.4 1.3 - - + -
49B PRO* 4.0 24.9 - - + -
50B GLN 3.1 13.7 - - - +
51B LEU* 4.8 0.7 - - + -
52B LEU* 4.0 4.9 - - - +
91B TYR* 3.6 4.2 - - - +
92B TYR* 2.9 81.1 + + + +
94B ALA* 4.3 13.0 - - + -
103B PHE* 4.1 7.9 - + - +
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Residues in contact with LEU 42 (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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41B TYR* 1.3 77.4 - - - +
43B GLN* 1.3 68.2 + - - +
44B LYS* 3.6 38.3 + - + +
48B SER 4.2 1.2 - - - +
49B PRO* 3.5 3.5 - - - +
50B GLN* 2.7 55.4 + - + +
52B LEU* 4.1 19.5 - - + -
67B PHE* 5.2 4.0 - - + -
87B ASP* 4.6 0.7 - - - +
89B GLY* 4.2 7.9 - - - -
90B VAL 3.6 14.8 - - - +
91B TYR* 3.4 45.5 - - + +
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Residues in contact with GLN 43 (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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41A GLN* 3.5 23.2 + - - +
45A LYS* 4.5 19.6 - - + +
41B TYR* 5.3 1.0 - - + -
42B LEU* 1.3 74.0 - - - +
44B LYS* 1.3 69.9 + - - +
45B PRO* 4.5 0.2 - - - +
46B GLY 5.3 0.6 - - - +
47B GLN 2.6 32.3 + - - +
48B SER 5.1 0.7 - - - -
49B PRO* 3.4 27.9 - - + +
89B GLY* 3.6 1.2 - - - -
90B VAL* 2.9 38.1 + - + +
92B TYR* 3.7 30.9 - - + +
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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