Contacts of the strand formed by residues 97 - 103 (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 TYR 97 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40V PHE 3.3 1.0 - - - +
41V ARG* 3.4 3.5 - - - +
42V MET* 2.7 47.3 + - + +
44V PRO* 3.9 28.7 - - + -
50V PRO* 3.8 36.9 - - + +
87V ILE* 3.9 19.1 - - + -
88V GLU 3.2 7.9 - - - +
89V PRO* 4.1 20.9 - - + -
90V VAL* 3.8 2.9 - - - -
94V ASP 4.0 14.8 + - - -
95V ASN* 4.0 20.8 + - - -
96V GLN* 1.3 80.2 - - - +
98V ILE* 1.3 63.0 + - - +
99V ALA 3.8 0.4 - - - -
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Residues in contact with ILE 98 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39V ALA* 4.1 18.4 - - + -
40V PHE 3.2 6.1 - - - +
41V ARG* 3.8 31.9 - - + +
87V ILE* 3.3 3.5 - - - -
88V GLU* 2.7 56.9 + - + +
89V PRO 5.4 0.7 - - - +
90V VAL* 3.9 20.6 - - + -
97V TYR* 1.3 71.4 - - - +
99V ALA* 1.3 60.8 + - - +
100V TYR* 3.6 31.3 - - + +
136V GLU* 4.9 1.1 - - + -
358V ARG* 4.3 6.3 - - - +
363V TYR* 4.1 24.9 - - + +
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Residues in contact with ALA 99 (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 2.4 - - - +
39V ALA* 3.7 0.2 - - - -
40V PHE* 2.8 44.9 + - + +
42V MET* 3.9 33.2 - - + -
54V GLY* 4.3 4.0 - - - -
57V VAL* 6.1 1.3 - - + -
84V CYS* 4.2 16.2 - - - -
86V ASP 3.6 4.5 - - - -
87V ILE* 4.5 3.4 - - + -
97V TYR 3.8 1.2 + - - -
98V ILE* 1.3 72.9 - - - +
100V TYR* 1.3 62.1 + - - +
101V VAL* 3.9 5.0 + - + -
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Residues in contact with TYR 100 (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 3.4 4.0 - - - -
39V ALA* 3.8 18.4 - - + -
84V CYS* 3.2 6.1 - - - -
85V TYR* 2.9 52.1 + + + +
86V ASP* 2.8 35.8 + - + +
88V GLU* 3.0 42.0 + - + -
98V ILE* 3.6 26.5 - - + +
99V ALA* 1.3 72.3 - - - +
101V VAL* 1.3 59.7 + - - +
356V LYS* 5.5 3.4 + - - -
358V ARG* 3.4 12.0 + - - -
363V TYR* 3.8 12.2 + + + +
364V PHE* 3.8 32.3 - + - -
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Residues in contact with VAL 101 (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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36V ILE 3.8 0.9 - - - +
37V LEU* 3.3 4.5 - - - -
38V ALA 2.9 35.1 + - - +
40V PHE* 3.9 26.2 - - + -
54V GLY 4.7 2.0 - - - +
57V VAL* 4.6 2.7 - - + -
58V ALA* 3.8 34.1 - - + +
83V ARG 3.2 15.0 - - - +
84V CYS* 4.4 6.1 - - + -
85V TYR* 3.6 3.7 - - - -
99V ALA* 4.5 4.7 - - + +
100V TYR* 1.3 79.2 - - - +
102V ALA* 1.3 63.1 + - - +
103V TYR* 3.4 36.8 - - + +
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Residues in contact with ALA 102 (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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29V TYR* 3.7 30.1 - - + -
31V VAL* 4.2 0.4 - - + -
35V ASP* 3.9 5.6 - - - +
36V ILE 3.5 4.0 - - - -
37V LEU* 3.7 16.8 - - + -
81V LYS 4.2 0.2 - - - +
82V GLY* 3.3 5.5 - - - -
83V ARG* 2.8 35.9 + - + +
85V TYR* 3.6 13.9 - - + -
101V VAL* 1.3 73.2 - - - +
103V TYR* 1.3 60.3 + - - +
104V HYP 4.0 3.1 - - - -
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Residues in contact with TYR 103 (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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35V ASP* 3.4 5.2 - - - -
36V ILE* 2.8 45.7 + - + +
38V ALA* 3.8 21.3 - - + -
40V PHE* 3.6 22.0 - - - -
58V ALA 4.6 0.2 - - - -
61V SER* 2.6 50.8 + - - -
62V SER* 4.3 6.3 - - - -
82V GLY* 4.5 0.2 - - - -
101V VAL* 3.4 25.2 - - + +
102V ALA* 1.3 75.9 - - - +
104V HYP 1.3 69.3 + - + +
107V LEU* 4.2 14.1 - - + -
108V PHE* 3.5 26.5 - + + -
119V SER* 5.6 0.2 - - - -
120V ILE* 4.0 25.8 - - + +
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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