Contacts of the strand formed by residues 39 - 45 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73H GLY 3.4 25.4 - - - +
74H LEU* 5.0 1.6 - - + -
37P GLY 4.9 1.3 - - - +
38P TRP* 1.3 71.6 - - - +
40P PRO* 1.3 65.1 - - - +
79P PRO* 3.7 30.1 - - + -
80P MET 3.7 15.0 - - - +
81P PHE* 3.7 18.4 - - + +
109P ALA* 3.1 4.3 - - - -
110P PHE* 2.8 57.6 + - + +
112P ASN* 4.1 17.5 - - + +
1142P EDO 3.4 21.8 - - - +
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Residues in contact with PRO 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P ILE* 4.0 16.2 - - + -
34P VAL* 5.5 2.2 - - + -
38P TRP 3.3 8.7 - - - +
39P ILE* 1.3 86.2 - - - +
41P CYS* 1.3 58.3 + - - +
79P PRO* 3.5 0.5 - - - +
80P MET* 2.8 63.4 + - + +
83P CYS* 4.4 9.2 - - + +
89P VAL* 3.7 39.3 - - + -
107P LEU* 4.6 2.9 - - + -
108P VAL 3.5 8.3 - - - +
109P ALA* 4.2 3.8 - - + -
1142P EDO 4.6 1.1 - - - -
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Residues in contact with CYS 41 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40P PRO* 1.3 77.3 - - - +
42P LEU* 1.3 78.6 + - - +
43P GLU* 4.8 6.7 - - - -
75P MET* 4.0 19.5 - - - -
76P TRP 4.8 0.9 - - - -
78P LEU 4.4 3.4 - - - -
79P PRO* 3.8 28.0 - - + -
80P MET* 4.9 4.2 - - - +
107P LEU* 3.6 5.1 - - - +
108P VAL* 2.9 37.4 + - + +
110P PHE* 3.7 27.4 - - + -
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Residues in contact with LEU 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41P CYS* 1.3 82.9 - - - +
43P GLU* 1.3 65.1 + - - +
75P MET 3.8 0.2 - - - -
76P TRP* 2.9 47.8 + - + -
80P MET* 5.9 3.1 - - - -
89P VAL* 4.8 1.3 - - + +
92P GLU* 3.4 46.4 - - + +
93P ILE* 3.6 24.7 - - + +
96P CYS* 4.1 7.6 - - + -
105P VAL* 4.0 15.0 - - + -
106P ARG 3.5 14.1 - - - +
107P LEU* 3.9 19.7 - - + -
123P VAL* 4.5 1.3 - - + -
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Residues in contact with GLU 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41P CYS* 4.8 5.0 - - - -
42P LEU* 1.3 80.3 - - - +
44P PHE* 1.3 62.0 + - - +
72P TYR* 6.1 0.2 - - - -
73P TRP* 3.8 19.9 + - + +
74P THR 3.2 12.8 - - - +
75P MET* 4.6 7.6 - - - +
76P TRP 4.4 0.2 - - - +
105P VAL* 3.4 5.5 - - - +
106P ARG* 2.8 70.4 + - + +
108P VAL* 3.8 23.5 - - + +
110P PHE* 4.8 1.7 - - - -
117P GLN* 4.7 2.4 - - - +
187R ARG* 3.0 34.6 + - - -
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Residues in contact with PHE 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3M VAL* 4.0 9.9 - - + -
6M PRO* 3.5 26.0 - - + -
7M VAL* 5.7 0.9 - - + -
43P GLU* 1.3 78.8 - - - +
45P ALA* 1.3 67.0 + - - +
46P GLU 5.5 0.2 - - - -
73P TRP* 3.4 4.9 - - - +
74P THR* 2.9 63.0 + - + -
75P MET 3.7 16.6 - - - -
76P TRP* 3.9 20.9 - + + -
96P CYS* 4.3 7.0 - - - -
100P PHE* 3.5 46.9 - + + -
103P ALA* 4.4 6.7 - - + -
104P TYR 3.1 14.6 - - - +
105P VAL* 3.9 13.5 - - + -
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Residues in contact with ALA 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6M PRO* 6.0 1.8 - - - -
44P PHE* 1.3 80.4 - - - +
46P GLU* 1.3 65.3 + - - +
49P LYS* 3.7 22.4 - - + +
50P ALA* 4.4 0.9 - - + -
73P TRP* 3.6 34.0 - - + -
74P THR* 5.4 1.3 - - - -
103P ALA* 3.4 5.6 - - - +
104P TYR* 2.8 34.2 + - - +
227R LYS* 5.8 2.0 - - - +
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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