Contacts of the strand formed by residues 39 - 45 (chain W) in PDB entry 1UW9
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 39 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73R GLY 3.4 25.4 - - - +
74R LEU* 4.9 1.6 - - + -
37W GLY 4.9 1.3 - - - +
38W TRP* 1.3 72.5 - - - +
40W PRO* 1.3 65.3 - - - +
41W CYS 3.8 0.3 + - - -
79W PRO* 3.6 29.2 - - + -
80W MET 3.7 14.8 - - - +
81W PHE* 3.7 19.3 - - + -
109W ALA* 3.1 4.7 - - - -
110W PHE* 2.8 61.5 + - + +
112W ASN* 4.2 17.3 - - + +
1142W EDO 3.5 21.3 - - - +
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Residues in contact with PRO 40 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33W ILE* 4.0 16.1 - - + -
34W VAL* 5.6 2.2 - - + -
38W TRP 3.3 10.5 - - - +
39W ILE* 1.3 85.3 - - - +
41W CYS* 1.3 57.9 + - - +
79W PRO* 3.6 0.7 - - - +
80W MET* 2.7 58.2 + - + +
83W CYS* 4.4 10.3 - - + +
89W VAL* 3.7 41.5 - - + -
107W LEU* 4.6 2.9 - - + -
108W VAL 3.5 9.0 - - - +
109W ALA* 4.3 4.0 - - + -
1142W EDO 4.9 0.7 - - - -
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Residues in contact with CYS 41 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40W PRO* 1.3 76.7 - - - +
42W LEU* 1.3 76.6 + - - +
43W GLU* 4.9 4.5 - - - -
75W MET* 4.0 17.7 - - - -
76W TRP 4.7 0.9 - - - -
78W LEU 4.3 3.6 - - - -
79W PRO* 3.8 31.4 - - + -
80W MET* 4.9 4.3 - - - +
107W LEU* 3.6 5.1 - - - +
108W VAL* 2.9 39.6 + - + +
110W PHE* 3.6 28.3 - - + -
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Residues in contact with LEU 42 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41W CYS* 1.3 83.0 - - - +
43W GLU* 1.3 65.9 + - - +
75W MET 3.8 0.2 - - - -
76W TRP* 2.9 48.2 + - + +
80W MET* 5.8 3.8 - - - -
89W VAL* 4.8 1.8 - - + +
92W GLU* 3.5 46.0 - - + +
93W ILE* 3.6 26.0 - - + +
96W CYS* 4.1 7.4 - - + -
105W VAL* 4.0 15.9 - - + -
106W ARG 3.5 14.8 - - - +
107W LEU* 3.9 18.8 - - + -
123W VAL* 4.4 1.8 - - + -
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Residues in contact with GLU 43 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187H ARG* 2.9 34.8 + - - -
41W CYS* 4.9 5.1 - - - -
42W LEU* 1.3 79.2 - - - +
44W PHE* 1.3 63.7 + - - +
73W TRP* 3.8 19.4 + - + +
74W THR 3.2 12.1 - - - +
75W MET* 4.6 8.4 + - + +
76W TRP 4.4 0.4 - - - +
105W VAL* 3.4 5.5 - - - +
106W ARG* 2.8 70.2 + - + +
108W VAL* 3.8 23.4 - - + +
110W PHE* 4.7 1.8 - - - -
117W GLN* 4.7 2.4 - - - +
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Residues in contact with PHE 44 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J VAL* 4.0 7.0 - - + -
6J PRO* 3.6 22.4 - - + -
7J VAL* 5.9 1.1 - - + -
43W GLU* 1.3 77.3 - - - +
45W ALA* 1.3 65.8 + - - +
46W GLU 5.5 0.2 - - - -
73W TRP* 3.4 5.1 - - - +
74W THR* 2.9 61.5 + - + -
75W MET 3.7 14.8 - - - -
76W TRP* 3.9 25.8 - + + -
96W CYS* 4.3 7.0 - - - -
100W PHE* 3.5 50.7 - + + -
103W ALA* 4.4 6.1 - - + -
104W TYR 3.1 15.7 - - - +
105W VAL* 3.9 13.7 - - + -
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Residues in contact with ALA 45 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227H LYS* 5.7 1.6 - - - +
6J PRO* 6.1 1.8 - - - -
44W PHE* 1.3 78.8 - - - +
46W GLU* 1.3 65.3 + - - +
49W LYS* 3.8 25.1 - - + +
50W ALA* 4.4 0.9 - - - -
73W TRP* 3.6 31.4 - - + -
74W THR* 5.5 1.8 - - - -
103W ALA* 3.4 5.4 - - - +
104W TYR* 2.8 33.6 + - - +
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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