Contacts of the strand formed by residues 104 - 111 (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 TYR 104 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12P PHE* 3.4 33.4 - + - -
44P PHE* 3.1 8.3 - - - +
45P ALA 2.8 34.9 + - - +
47P ALA* 3.8 21.5 - - + -
50P ALA* 3.5 25.4 - - + -
51P TYR* 4.0 5.4 + + - -
73P TRP* 3.6 20.9 - - + -
103P ALA* 1.3 72.3 - - - +
105P VAL* 1.3 58.9 + - - +
122P LEU* 3.9 7.2 - - + -
124P GLN 3.3 4.7 - - - -
125P ARG* 3.5 30.1 + - + -
126P PRO* 3.6 21.5 - - + -
129P ALA* 3.7 19.6 - - - +
131P ASP* 3.7 18.7 + - - -
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Residues in contact with VAL 105 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P LEU* 4.0 12.6 - - + -
43P GLU 3.4 11.0 - - - +
44P PHE* 3.9 10.8 - - + -
73P TRP* 4.1 0.4 - - - -
93P ILE 5.7 0.2 - - - +
96P CYS* 3.8 26.5 - - + -
97P THR* 4.2 10.1 - - + -
100P PHE* 4.6 5.6 - - + +
103P ALA* 4.0 2.7 - - + +
104P TYR* 1.3 80.0 - - - +
106P ARG* 1.3 56.9 + - - +
122P LEU* 3.4 6.6 - - - +
123P VAL* 2.8 44.9 + - + -
124P GLN* 2.9 42.9 + - + +
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Residues in contact with ARG 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163K ASN* 4.0 22.1 + - - +
12P PHE* 5.3 4.8 - - + -
42P LEU* 3.5 8.5 - - - +
43P GLU* 2.8 61.2 + - + +
71P ARG 3.0 23.0 + - - -
72P TYR* 4.7 0.4 - - - +
73P TRP* 3.3 62.0 - - + +
105P VAL* 1.3 74.8 - - - +
107P LEU* 1.3 60.7 + - - +
108P VAL* 3.9 15.8 + - + +
117P GLN* 5.7 2.4 - - - +
121P PHE 3.4 20.9 - - - +
122P LEU* 4.1 4.7 - - + -
123P VAL* 4.1 0.9 - - - +
183R LYS* 5.9 0.6 - - - +
187R ARG* 5.9 0.6 - - - +
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Residues in contact with LEU 107 (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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26P ILE* 5.4 0.4 - - + -
30P VAL* 3.8 28.3 - - + -
33P ILE* 3.9 18.6 - - + -
40P PRO* 4.6 0.7 - - + -
41P CYS 3.6 20.4 - - - +
42P LEU* 3.9 17.3 - - + -
89P VAL* 3.8 21.3 - - + -
93P ILE* 4.4 8.5 - - + -
106P ARG* 1.3 72.1 - - - +
108P VAL* 1.3 68.9 + - - +
119P MET* 4.4 2.1 - - - +
120P GLY* 3.1 3.3 - - - -
121P PHE* 2.9 53.3 + - + +
123P VAL* 4.0 17.7 - - + +
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Residues in contact with VAL 108 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P ILE* 4.7 0.2 - - - +
40P PRO* 3.5 2.6 - - - +
41P CYS* 2.9 51.5 + - + +
43P GLU* 3.8 24.7 - - + +
106P ARG* 4.1 17.7 - - + +
107P LEU* 1.3 84.4 - - - +
109P ALA* 1.3 63.3 + - - +
110P PHE* 3.9 20.4 - - + -
117P GLN* 3.3 32.3 - - - +
119P MET* 3.4 9.2 - - - -
120P GLY* 4.1 2.0 - - - -
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Residues in contact with ALA 109 (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* 3.8 26.2 - - + -
38P TRP* 4.0 10.1 - - + -
39P ILE 3.1 11.2 - - - +
108P VAL* 1.3 75.8 - - - +
110P PHE* 1.3 60.1 + - - +
117P GLN* 3.4 4.9 - - - +
118P ILE* 2.8 32.3 + - + +
119P MET* 3.2 28.7 + - + -
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Residues in contact with PHE 110 (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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74H LEU* 4.0 24.0 - - + +
38P TRP* 3.5 5.7 - - - +
39P ILE* 2.8 57.1 + - + +
41P CYS* 3.7 29.8 - - + -
43P GLU* 4.8 1.8 - - - -
79P PRO* 4.4 13.2 - - + -
108P VAL* 3.9 13.2 - - + -
109P ALA* 1.3 72.6 - - - +
111P ASP* 1.3 61.4 + - - +
112P ASN* 5.8 0.4 - - - -
116P VAL 3.7 4.3 - - - +
117P GLN* 3.7 35.0 - - + -
118P ILE* 4.3 3.6 - - - -
184R ASN* 4.9 4.9 - - - -
187R ARG* 3.8 43.1 - - - -
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Residues in contact with ASP 111 (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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74H LEU 4.5 0.3 - - - +
38P TRP* 3.3 29.4 + - + -
110P PHE* 1.3 75.4 - - - +
112P ASN* 1.3 58.3 + - - +
113P GLN* 2.8 37.3 + - - +
114P LYS* 2.9 26.9 + - + +
115P GLN* 3.0 19.6 + - - -
116P VAL 2.9 21.6 + - - +
118P ILE* 4.0 20.5 - - + +
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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
------------------------------------------------------------
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