Contacts of the strand formed by residues 36 - 44 (chain V) 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 36 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34V THR 3.8 13.7 - - - +
35V ASP* 1.3 72.0 - - - +
37V LEU* 1.3 67.8 + - - +
102V ALA* 3.5 1.4 - - - -
103V TYR* 2.8 36.8 + - + -
105V ILE* 4.1 9.9 - - + -
108V PHE* 3.6 38.1 - - + -
116V MET* 4.9 3.4 - - - -
120V ILE* 3.8 29.6 - - + -
138V LEU* 4.7 3.4 - - + -
139V ARG 3.4 10.5 - - - +
140V ILE* 4.9 8.1 - - + -
141V PRO* 3.8 18.8 - - + -
144V TYR* 4.3 22.2 - - + -
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Residues in contact with LEU 37 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31V VAL* 3.9 23.8 - - + -
35V ASP* 3.9 12.8 - - + -
36V ILE* 1.3 76.9 - - - +
38V ALA* 1.3 60.1 + - - +
85V TYR* 3.7 16.8 - - - +
101V VAL 3.3 2.5 - - - +
102V ALA* 3.7 27.8 - - + -
138V LEU* 3.1 11.2 - - - +
139V ARG* 2.7 74.0 + - + +
364V PHE* 3.7 21.5 - - + -
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Residues in contact with ALA 38 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37V LEU* 1.3 74.9 - - - +
39V ALA* 1.3 60.0 + - - +
40V PHE* 3.6 26.7 - - + -
99V ALA 3.6 1.3 - - - +
100V TYR* 3.4 5.4 - - - -
101V VAL* 2.9 31.3 + - - +
103V TYR* 3.8 17.5 - - + -
120V ILE* 4.2 1.6 - - + -
135V LEU* 3.8 4.7 - - + -
137V ASP 3.5 4.7 - - - -
138V LEU* 3.7 16.4 - - + -
364V PHE* 3.7 4.8 - - - -
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Residues in contact with ALA 39 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38V ALA* 1.3 72.3 - - - +
40V PHE* 1.3 61.4 + - - +
98V ILE* 4.1 4.5 - - + -
99V ALA 3.7 3.6 - - - -
100V TYR* 3.8 10.3 - - + -
135V LEU* 3.7 2.8 - - - +
136V GLU* 2.8 29.0 + - - +
137V ASP 3.0 12.1 + - - +
363V TYR* 3.8 30.3 - - + -
364V PHE* 3.7 21.5 - - + -
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Residues in contact with PHE 40 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38V ALA* 3.6 17.7 - - + -
39V ALA* 1.3 72.8 - - - +
41V ARG* 1.3 58.4 + - - +
42V MET* 3.5 1.1 + - - -
57V VAL* 3.7 21.5 - - + -
61V SER* 5.2 0.2 - - - -
97V TYR 3.3 2.1 - - - +
98V ILE* 3.2 6.6 - - - -
99V ALA* 2.8 47.1 + - + +
101V VAL* 3.9 16.8 - - + -
103V TYR* 3.6 18.2 - - - -
120V ILE* 3.4 37.5 - - + -
124V VAL* 4.5 0.2 - - + -
125V PHE* 4.1 10.3 - + - -
133V LEU* 3.8 43.3 - - + -
134V ARG 3.4 2.0 - - - -
135V LEU* 4.1 18.6 - - + -
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Residues in contact with ARG 41 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39V ALA 4.0 1.2 + - - -
40V PHE* 1.3 67.9 - - - +
42V MET* 1.3 61.1 + - - +
43V THR* 5.1 0.8 + - - +
90V VAL* 3.8 12.9 - - + +
96V GLN* 3.0 43.6 + - + +
97V TYR 3.4 4.5 - - - +
98V ILE* 3.8 17.4 - - + +
132V ALA 4.1 0.3 - - - +
133V LEU* 3.3 5.8 - - - -
134V ARG* 2.7 46.3 + - + +
136V GLU* 2.9 34.7 + - + +
305V ARG* 3.2 50.3 + - - +
306V ASN* 4.3 6.7 - - - +
363V TYR* 3.6 15.0 + - - -
475V LEU* 3.2 24.5 + - - -
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Residues in contact with MET 42 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40V PHE* 4.1 5.8 - - - +
41V ARG* 1.3 74.6 - - - +
43V THR* 1.3 64.3 + - - +
44V PRO* 3.5 6.3 - - + +
50V PRO* 3.5 30.1 - - + +
53V CYS* 3.6 29.6 - - + +
54V GLY* 3.5 25.4 - - - -
57V VAL* 4.7 5.8 - - + -
87V ILE* 4.7 2.7 - - + -
96V GLN* 3.4 3.9 - - - -
97V TYR* 2.7 60.0 + - + +
99V ALA* 3.9 18.4 - - + -
130V LEU* 5.2 1.3 - - + -
132V ALA 3.9 3.6 - - - +
133V LEU* 3.8 15.9 - - + -
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Residues in contact with THR 43 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41V ARG 5.1 0.9 + - - -
42V MET* 1.3 72.6 - - - +
44V PRO* 1.3 55.7 - - - +
95V ASN* 3.3 28.5 - - + +
96V GLN* 3.6 22.1 + - + +
130V LEU* 3.6 3.1 - - - -
131V ARG* 2.7 47.4 + - + +
132V ALA* 3.0 34.2 + - + +
306V ASN* 4.8 3.6 + - - +
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Residues in contact with PRO 44 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42V MET* 3.5 10.5 - - + +
43V THR* 1.3 85.8 - - - +
45V GLN* 1.3 63.8 + - - +
48V VAL* 3.6 24.9 - - + +
50V PRO* 4.5 6.3 - - + -
53V CYS* 3.8 33.8 - - + -
95V ASN* 2.8 46.5 + - - +
97V TYR* 3.9 20.2 - - + -
129V ALA 4.0 1.1 - - - +
131V ARG* 3.9 4.3 - - - -
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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