Contacts of the strand formed by residues 39 - 45 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37J GLY 4.9 0.9 - - - +
38J TRP* 1.3 71.4 - - - +
40J PRO* 1.3 65.0 - - - +
79J PRO* 3.6 30.1 - - + -
80J MET 3.7 10.1 - - - +
81J PHE* 3.7 23.6 - - + +
109J ALA* 3.0 5.0 - - - -
110J PHE* 2.8 57.7 + - + +
112J ASN* 4.2 17.7 - - + +
1142J EDO 3.4 21.5 - - - +
73K GLY 3.5 25.4 - - - +
74K LEU* 5.0 1.3 - - - -
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Residues in contact with PRO 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J ILE* 4.0 16.8 - - + -
34J VAL* 5.6 2.7 - - + -
38J TRP 3.3 9.2 - - - +
39J ILE* 1.3 84.5 - - - +
41J CYS* 1.3 61.5 + - - +
79J PRO* 3.6 0.5 - - - +
80J MET* 2.8 57.7 + - + +
83J CYS* 4.4 11.0 - - + +
89J VAL* 3.7 38.1 - - + -
107J LEU* 4.6 2.9 - - + -
108J VAL 3.5 8.3 - - - +
109J ALA* 4.3 3.6 - - + -
1142J EDO 4.9 1.1 - - - -
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Residues in contact with CYS 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40J PRO* 1.3 77.3 - - - +
42J LEU* 1.3 78.0 + - - +
43J GLU* 4.9 4.0 - - - -
75J MET* 4.0 17.9 - - - -
76J TRP 4.8 0.9 - - - -
78J LEU 4.3 3.6 - - - -
79J PRO* 3.7 31.4 - - + -
80J MET* 5.2 4.0 - - - -
107J LEU* 3.6 5.3 - - - +
108J VAL* 2.9 39.7 + - + +
110J PHE* 3.7 26.9 - - + -
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Residues in contact with LEU 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41J CYS* 1.3 83.1 - - - +
43J GLU* 1.3 64.9 + - - +
76J TRP* 2.9 48.2 + - + +
80J MET* 5.9 3.6 - - - -
89J VAL* 4.8 1.6 - - + +
92J GLU* 3.4 46.9 - - + +
93J ILE* 3.5 24.7 - - + +
96J CYS* 4.1 7.6 - - + -
105J VAL* 4.0 15.5 - - + -
106J ARG 3.6 14.6 - - - +
107J LEU* 3.9 19.5 - - + -
123J VAL* 4.4 1.3 - - + -
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Residues in contact with GLU 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E ARG* 3.0 35.5 + - - -
41J CYS* 4.9 5.0 - - - -
42J LEU* 1.3 79.7 - - - +
44J PHE* 1.3 63.3 + - - +
73J TRP* 3.8 19.9 + - + +
74J THR 3.2 12.3 - - - +
75J MET* 4.6 7.5 - - + +
76J TRP 4.4 0.2 - - - +
105J VAL* 3.4 5.8 - - - +
106J ARG* 2.9 75.3 + - + +
108J VAL* 3.8 22.9 - - + +
110J PHE* 4.7 1.7 - - - -
117J GLN* 4.6 2.6 - - - +
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Residues in contact with PHE 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F VAL* 4.1 7.2 - - + -
6F PRO* 3.5 27.1 - - + -
7F VAL* 5.3 1.3 - - + -
43J GLU* 1.3 78.6 - - - +
45J ALA* 1.3 65.9 + - - +
73J TRP* 3.4 5.1 - - - +
74J THR* 2.9 63.9 + - + -
75J MET 3.7 15.7 - - - -
76J TRP* 3.9 23.8 - + + -
96J CYS* 4.2 8.1 - - - -
100J PHE* 3.5 44.0 - + + -
103J ALA* 4.4 7.4 - - + -
104J TYR 3.1 14.1 - - - +
105J VAL* 3.9 13.2 - - + -
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Residues in contact with ALA 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E LYS* 5.7 1.8 - - - +
6F PRO* 6.1 1.3 - - - -
44J PHE* 1.3 79.7 - - - +
46J GLU* 1.3 66.6 + - - +
49J LYS* 3.7 21.3 - - + +
50J ALA* 4.4 0.9 - - - -
73J TRP* 3.6 34.3 - - + -
74J THR* 5.4 1.8 - - - -
103J ALA* 3.4 5.2 - - - +
104J TYR* 2.8 33.8 + - - +
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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