Contacts of the strand formed by residues 39 - 45 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73E GLY 3.4 26.2 - - - +
74E LEU* 4.9 1.3 - - - -
37I GLY 4.9 3.1 - - - +
38I TRP* 1.3 73.9 - - - +
40I PRO* 1.3 64.7 - - - +
41I CYS 3.8 0.2 + - - -
79I PRO* 3.6 29.2 - - + -
80I MET 3.7 16.2 - - - +
81I PHE* 3.7 23.3 - - + -
82I GLY 5.6 1.1 - - - +
109I ALA* 3.1 4.2 - - - -
110I PHE* 2.8 59.9 + - + +
112I ASN* 4.1 17.0 - - + +
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Residues in contact with PRO 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I ILE* 4.0 16.6 - - + -
34I VAL* 5.5 2.5 - - + -
38I TRP 3.3 9.6 - - - +
39I ILE* 1.3 85.3 - - - +
41I CYS* 1.3 58.9 + - - +
79I PRO* 3.6 0.5 - - - +
80I MET* 2.8 56.6 + - + +
83I CYS* 4.4 11.4 - - + +
89I VAL* 3.7 40.2 - - + -
107I LEU* 4.6 2.9 - - + -
108I VAL 3.5 8.1 - - - +
109I ALA* 4.3 3.8 - - + -
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Residues in contact with CYS 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I PRO* 1.3 76.6 - - - +
42I LEU* 1.3 76.5 + - - +
43I GLU* 4.9 3.6 - - - -
75I MET* 4.0 18.4 - - - -
76I TRP 4.7 0.7 - - - -
78I LEU 4.3 3.4 - - - -
79I PRO* 3.8 32.3 - - + -
80I MET* 5.2 3.8 - - - -
107I LEU* 3.7 5.6 - - - +
108I VAL* 2.9 40.7 + - + +
110I PHE* 3.7 27.4 - - + -
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Residues in contact with LEU 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I CYS* 1.3 82.8 - - - +
43I GLU* 1.3 65.8 + - - +
75I MET 3.8 0.2 - - - -
76I TRP* 2.9 48.2 + - + +
80I MET* 5.9 3.5 - - - -
89I VAL* 4.8 1.6 - - + +
92I GLU* 3.4 46.7 - - + +
93I ILE* 3.6 25.1 - - + +
96I CYS* 4.1 7.4 - - + -
105I VAL* 4.0 15.5 - - + -
106I ARG 3.5 14.6 - - - +
107I LEU* 3.9 19.3 - - + +
123I VAL* 4.4 1.3 - - + -
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Residues in contact with GLU 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I CYS* 4.9 5.6 - - - -
42I LEU* 1.3 80.1 - - - +
44I PHE* 1.3 62.0 + - - +
72I TYR* 6.1 0.2 - - - -
73I TRP* 3.8 20.1 + - + +
74I THR 3.2 12.8 - - - +
75I MET* 4.6 7.4 - - - +
76I TRP 4.4 0.2 - - - +
105I VAL* 3.4 4.8 - - - +
106I ARG* 2.9 71.0 + - + +
108I VAL* 3.8 23.8 - - + +
110I PHE* 4.7 1.4 - - - -
117I GLN* 4.7 2.4 - - - +
187K ARG* 3.0 34.6 + - - -
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Residues in contact with PHE 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I GLU* 1.3 78.2 - - - +
45I ALA* 1.3 65.3 + - - +
46I GLU 5.5 0.2 - - - -
73I TRP* 3.4 4.9 - - - +
74I THR* 2.8 62.8 + - + -
75I MET 3.6 17.0 - - - -
76I TRP* 3.9 23.6 - + + -
96I CYS* 4.2 6.7 - - - -
100I PHE* 3.5 51.6 - + + -
103I ALA* 4.4 5.8 - - + -
104I TYR 3.1 14.4 - - - +
105I VAL* 4.0 13.9 - - + -
3P VAL* 4.0 6.7 - - + -
6P PRO* 3.6 22.4 - - + -
7P VAL* 5.6 0.9 - - + -
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Residues in contact with ALA 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I PHE* 1.3 79.5 - - - +
46I GLU* 1.3 65.3 + - - +
49I LYS* 3.8 24.5 - - + +
50I ALA* 4.4 0.9 - - - -
73I TRP* 3.6 31.8 - - + -
74I THR* 5.4 1.3 - - - -
103I ALA* 3.4 5.9 - - - +
104I TYR* 2.8 33.5 + - - +
227K LYS* 5.7 1.6 - - - +
6P PRO* 6.2 1.6 - - - -
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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