Contacts of the strand formed by residues 36 - 41 (chain H) 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 MET 36 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4H LEU* 4.9 1.1 - - + -
29H PHE* 3.3 69.5 - - + +
34H TYR* 3.3 5.4 + - - -
35H ILE* 1.3 75.8 - - - +
37H SER* 1.3 59.8 + - - +
52H SER* 3.1 2.8 - - - -
53H ILE* 2.9 42.7 + - + +
71H ILE* 3.8 2.3 - - - +
73H ARG* 3.9 4.7 - - - +
80H LEU* 4.0 18.8 - - + -
97H CYS* 4.5 11.2 - - - -
98H ALA 3.6 23.3 - - - +
99H ARG* 4.0 28.0 - - + +
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Residues in contact with SER 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H ILE* 4.1 8.1 + - - +
36H MET* 1.3 77.1 - - - +
38H TRP* 1.3 71.5 + - - +
39H VAL* 4.8 6.1 - - - -
49H TRP* 4.7 5.8 - - - -
51H ALA 3.1 11.4 - - - -
52H SER* 2.5 21.1 + - - -
71H ILE* 4.4 0.9 - - - -
80H LEU* 4.0 4.4 - - - +
97H CYS* 3.7 3.5 - - - -
98H ALA* 2.9 41.4 + - - -
100H GLY* 5.6 2.1 + - - -
99L LEU* 5.1 1.2 - - - +
101L PRO* 5.1 4.8 - - - +
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Residues in contact with TRP 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H GLU* 3.9 22.4 - - + -
20H LEU* 3.7 31.9 - - + -
21H SER 3.6 21.8 - - - -
22H CYS* 3.9 7.6 - - + -
37H SER* 1.3 74.3 - - - +
39H VAL* 1.3 66.7 + - - +
49H TRP* 3.9 1.2 - - - -
50H VAL* 2.9 33.3 + - + -
51H ALA 2.8 13.2 + - - +
71H ILE* 3.4 29.6 - - + -
80H LEU* 3.2 41.0 - - + +
81H TYR 3.1 17.1 + - - -
82H LEU* 3.3 34.3 - - + +
95H TYR* 4.5 6.1 - - + -
96H TYR 3.2 29.4 - - - -
97H CYS 3.9 1.8 - - - -
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Residues in contact with VAL 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H SER* 4.8 6.5 - - - -
38H TRP* 1.3 82.4 - - - +
40H ARG* 1.3 64.4 + - - +
47H LEU* 4.4 18.4 - - + -
48H GLU 3.3 11.4 - - - +
49H TRP* 4.2 16.2 - - + -
50H VAL* 3.8 3.5 - - - +
95H TYR* 3.4 3.5 - - - +
96H TYR* 2.7 58.0 + - + +
98H ALA* 4.9 13.0 - - + -
106H TRP* 6.1 0.2 - - + -
101L PRO* 5.2 1.8 - - + -
103L PHE* 4.3 19.1 - - + -
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Residues in contact with ARG 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H VAL* 1.3 77.7 - - - +
41H GLN* 1.3 61.3 + - - +
42H ILE* 4.6 3.6 - - + +
46H ARG 4.2 0.2 - - - +
47H LEU* 3.5 5.1 - - - -
48H GLU* 2.7 77.0 + - + +
50H VAL* 3.5 17.0 - - + +
64H SER* 4.0 16.0 + - - -
65H VAL* 4.3 5.3 - - - +
69H PHE* 4.1 9.1 - - - -
90H GLU* 4.1 14.8 + - - +
91H ASP* 2.9 29.0 + - - +
93H ALA* 4.1 13.7 - - + -
94H LEU 3.1 12.1 - - - +
95H TYR* 2.7 48.7 + - + -
96H TYR* 4.8 0.9 - - - -
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Residues in contact with GLN 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H ARG* 1.3 77.6 - - - +
42H ILE* 1.3 66.0 + - - +
43H PRO* 3.8 2.1 - - + +
45H LYS* 4.0 25.1 + - - +
46H ARG 4.4 13.3 - - - +
47H LEU* 3.6 17.3 - - + +
93H ALA* 3.3 4.1 - - - +
94H LEU* 3.0 38.1 + - + +
96H TYR* 2.7 40.5 + - + -
41L TYR* 6.4 0.4 - - - -
43L GLN* 3.4 22.7 + - - +
47L GLN 5.4 0.3 - - - +
49L PRO* 3.9 9.4 - - - +
92L TYR* 6.4 0.4 - - - -
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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