Contacts of the strand formed by residues 73 - 80 (chain C) in PDB entry 1XRG
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 VAL 73 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A ILE* 4.6 5.4 - - - +
22A ILE* 5.4 1.2 - - - +
63C LEU* 3.3 34.8 - - + -
69C SER 3.7 2.0 - - - +
70C LEU* 3.3 19.1 + - - +
71C ASN 4.8 1.4 - - - +
72C LYS* 1.3 79.0 - - - +
74C VAL* 1.3 64.1 + - - +
75C LYS 3.8 3.4 - - - +
76C THR* 3.7 22.9 - - + -
97C PHE* 3.9 9.2 - - + -
100C PRO 5.1 3.6 - - - +
102C PRO* 3.6 32.1 - - + +
122C ALA* 4.1 7.6 - - + -
123C VAL 3.6 11.2 - - - +
124C ALA* 3.7 8.5 - - + -
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Residues in contact with VAL 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 4.1 16.6 - - + -
22A ILE* 3.4 36.4 - - + +
24A THR* 4.1 17.3 - - + -
29A TYR* 3.9 29.3 - - + +
27C PHE* 5.1 1.8 - - + -
72C LYS 3.5 10.3 + - - +
73C VAL* 1.3 77.2 - - - +
75C LYS* 1.3 57.8 + - + +
102C PRO* 4.0 1.1 - - - -
103C ALA* 3.0 24.4 + - - +
123C VAL* 2.8 33.1 + - + +
124C ALA* 4.4 2.5 - - - +
125C ILE* 4.3 7.0 - - + -
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Residues in contact with LYS 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A TYR* 3.8 31.2 - - + -
30A THR 3.5 22.2 - - - +
121A GLU* 3.0 30.5 + - - -
73C VAL* 3.7 2.2 - - - +
74C VAL* 1.3 81.9 - - + +
76C THR* 1.3 87.8 + - - +
77C THR* 3.0 19.4 + - - -
102C PRO* 4.3 0.2 - - - -
103C ALA* 3.2 20.0 - - + +
104C ARG 4.4 0.4 - - - -
105C SER* 3.7 7.8 + - - +
122C ALA* 3.3 3.1 - - - -
123C VAL* 2.7 43.9 + - + +
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Residues in contact with THR 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C LEU* 5.0 0.4 - - + -
73C VAL* 3.7 20.0 - - + -
75C LYS* 1.3 95.2 + - - +
77C THR* 1.3 63.6 + - - +
78C VAL* 4.1 0.9 - - - +
93C TYR* 2.8 31.2 + - + +
97C PHE* 4.5 8.3 - - + -
102C PRO* 4.4 2.0 - - + -
103C ALA 2.9 7.1 + - - -
104C ARG* 3.3 18.0 - - - +
105C SER 3.1 14.7 + - - -
120C ILE* 4.1 16.6 - - + -
121C GLU 3.2 13.7 - - - +
122C ALA* 4.3 5.2 - - + -
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Residues in contact with THR 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PHE* 4.9 2.7 - - + -
505A UNX 3.1 20.4 - - - -
75C LYS* 3.0 18.4 + - - +
76C THR* 1.3 71.8 - - - +
78C VAL* 1.3 64.5 + - - +
79C PHE* 3.6 30.7 + - + -
105C SER* 3.4 16.4 - - - +
107C VAL* 5.2 2.5 - - + -
119C GLU 3.8 0.9 - - - +
120C ILE* 3.4 6.6 - - - +
121C GLU* 3.0 54.1 + - - +
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Residues in contact with VAL 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C THR* 4.2 2.5 - - - +
77C THR* 1.3 74.8 - - - +
79C PHE* 1.3 61.0 + - - +
80C ILE* 3.7 24.2 + - + +
86C PHE* 4.4 13.9 - - + -
89C VAL* 4.5 4.0 - - + -
93C TYR* 4.0 20.2 - - + -
104C ARG* 3.8 28.9 - - + +
105C SER 2.8 11.7 + - - +
106C CYS* 3.4 8.1 - - - +
107C VAL* 3.1 25.5 + - - +
118C ILE* 4.3 7.4 - - + -
119C GLU 3.7 2.9 - - - -
120C ILE* 4.2 18.2 - - + -
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Residues in contact with PHE 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PHE* 5.0 2.9 - + - -
77B THR* 4.8 9.4 - - + -
79B PHE* 4.8 5.2 - + - -
105B SER* 4.3 17.7 - - - -
107B VAL* 3.6 29.8 - - + -
77C THR* 3.6 35.0 - - + -
78C VAL* 1.3 71.9 - - - +
80C ILE* 1.3 60.3 + - - +
107C VAL* 3.5 25.8 - - + -
109C VAL* 3.9 13.2 - - + -
112C LEU* 3.8 21.0 - - + +
118C ILE* 3.3 3.3 - - - +
119C GLU* 2.8 54.2 + - + +
120C ILE* 5.3 0.2 - - - -
121C GLU* 4.3 9.0 - - + -
506C UNX 3.7 16.6 - - - -
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Residues in contact with ILE 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ILE* 5.3 0.7 - - + -
78C VAL* 3.7 20.6 - - + +
79C PHE* 1.3 79.7 - - - +
81C LYS* 1.3 59.9 + - - +
82C ASP 3.6 24.7 - - - +
83C MSE 3.7 22.7 - - + -
86C PHE* 3.8 28.3 - - + -
89C VAL* 4.3 12.1 - - + -
106C CYS* 5.6 0.7 - - + -
107C VAL 2.9 22.4 + - - +
108C GLU* 3.1 9.0 - - - -
109C VAL* 2.9 27.6 + - - +
112C LEU* 4.7 0.2 - - - -
117C LEU 3.4 7.4 - - - +
118C ILE* 3.9 17.0 - - + -
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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