Contacts of the strand formed by residues 39 - 45 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A GLY 3.4 25.8 - - - +
74A LEU* 4.9 1.3 - - - -
37F GLY 4.9 3.1 - - - +
38F TRP* 1.3 73.9 - - - +
40F PRO* 1.3 65.4 - - - +
41F CYS 3.7 0.2 + - - -
79F PRO* 3.6 29.4 - - + -
80F MET 3.7 10.3 - - - +
81F PHE* 3.7 30.3 - - + +
82F GLY 5.6 2.2 - - - +
109F ALA* 3.0 4.5 - - - -
110F PHE* 2.8 58.5 + - + +
112F ASN* 4.1 17.3 - - + +
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Residues in contact with PRO 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F ILE* 4.0 16.4 - - + -
34F VAL* 5.5 2.0 - - + -
38F TRP 3.3 10.0 - - - +
39F ILE* 1.3 85.0 - - - +
41F CYS* 1.3 58.0 + - - +
79F PRO* 3.5 0.7 - - - +
80F MET* 2.8 62.3 + - + +
83F CYS* 4.4 11.2 - - + +
89F VAL* 3.7 38.6 - - + -
107F LEU* 4.6 3.1 - - + -
108F VAL 3.4 8.5 - - - +
109F ALA* 4.3 2.9 - - + -
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Residues in contact with CYS 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F PRO* 1.3 77.1 - - - +
42F LEU* 1.3 76.5 + - - +
43F GLU* 4.8 4.5 - - - -
75F MET* 4.0 17.7 - - - -
76F TRP 4.8 0.7 - - - -
78F LEU 4.3 4.0 - - - -
79F PRO* 3.8 31.6 - - + -
80F MET* 5.3 3.8 - - - -
107F LEU* 3.7 5.1 - - - +
108F VAL* 2.9 40.2 + - + +
110F PHE* 3.6 27.4 - - + -
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Residues in contact with LEU 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F CYS* 1.3 81.5 - - - +
43F GLU* 1.3 65.6 + - - +
75F MET* 3.8 1.6 - - - -
76F TRP* 2.8 50.2 + - + +
78F LEU 5.6 0.2 + - - -
80F MET* 5.9 3.6 - - - -
89F VAL* 4.8 1.6 - - + +
92F GLU* 3.5 46.4 - - + +
93F ILE* 3.5 25.1 - - + +
96F CYS* 4.1 7.9 - - + -
105F VAL* 4.0 16.2 - - + -
106F ARG 3.6 14.6 - - - +
107F LEU* 3.9 19.1 - - + -
123F VAL* 4.4 1.3 - - + -
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Residues in contact with GLU 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B ARG* 3.0 33.8 + - - -
41F CYS* 4.8 4.8 - - - -
42F LEU* 1.3 81.6 - - - +
44F PHE* 1.3 62.7 + - - +
73F TRP* 3.7 19.1 + - + +
74F THR 3.2 11.2 - - - +
75F MET* 4.6 8.6 - - + +
76F TRP 4.4 0.2 - - - +
105F VAL* 3.4 5.4 - - - +
106F ARG* 2.8 70.3 + - + +
108F VAL* 3.8 24.2 - - + +
110F PHE* 4.7 1.9 - - - -
117F GLN* 4.7 2.4 - - - +
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Residues in contact with PHE 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C VAL* 4.1 7.0 - - + -
6C PRO* 3.5 25.8 - - + -
7C VAL* 5.4 1.6 - - + -
43F GLU* 1.3 78.4 - - - +
45F ALA* 1.3 65.3 + - - +
73F TRP* 3.4 5.5 - - - +
74F THR* 2.9 66.5 + - + -
75F MET 3.7 14.8 - - - -
76F TRP* 3.9 25.6 - + + -
96F CYS* 4.2 8.1 - - - -
100F PHE* 3.5 44.6 - + - -
103F ALA* 4.4 6.5 - - + -
104F TYR 3.1 13.9 - - - +
105F VAL* 4.0 14.1 - - + -
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Residues in contact with ALA 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B LYS* 5.7 1.6 - - - +
6C PRO* 6.1 2.0 - - - -
44F PHE* 1.3 80.5 - - - +
46F GLU* 1.3 65.1 + - - +
49F LYS* 3.7 25.6 - - + +
50F ALA* 4.4 0.7 - - - -
73F TRP* 3.6 31.2 - - + -
74F THR* 5.4 1.3 - - - -
103F ALA* 3.5 5.3 - - - +
104F TYR* 2.8 33.2 + - - +
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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