Contacts of the strand formed by residues 108 - 115 (chain A) in PDB entry 5TX4
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 GLU 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ARG* 2.6 59.9 + - - +
67A LYS 3.4 14.1 - - - +
68A ASN* 4.2 12.7 + - + +
103A LYS 5.4 0.5 - - - +
105A LYS* 3.0 51.0 + - + +
106A PRO 3.9 5.2 - - - +
107A GLY* 1.3 80.1 - - - +
109A THR* 1.3 64.5 + - - +
110A PHE* 4.1 3.9 + - - -
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Residues in contact with THR 109 (chain A).
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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65A TRP* 3.8 15.1 - - + +
66A ARG* 3.2 6.8 - - - +
67A LYS* 2.8 40.6 + - - +
102A GLU* 4.0 13.2 - - - +
103A LYS 5.5 0.2 - - - -
108A GLU* 1.3 76.4 + - - +
110A PHE* 1.3 61.7 + - - +
111A PHE* 3.6 26.2 - - + -
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Residues in contact with PHE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL* 3.6 23.8 - - + -
65A TRP 3.5 2.7 - - - -
66A ARG* 3.7 30.3 - - + +
86A HIS* 3.8 26.5 - + + -
88A PHE* 3.5 26.2 - + - -
102A GLU* 3.5 6.5 - - - +
103A LYS* 2.9 54.9 + - + +
105A LYS* 4.1 22.9 - - + -
108A GLU* 4.1 7.4 + - - +
109A THR* 1.3 77.0 - - - +
111A PHE* 1.3 70.3 + - - +
112A MET* 3.8 27.8 - - + -
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Residues in contact with PHE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL* 3.3 6.8 - - - +
65A TRP* 2.8 51.9 + + + +
100A MET* 3.3 25.8 - - + -
101A LYS 3.4 7.6 - - - -
102A GLU* 3.5 45.5 - - + -
109A THR* 3.6 24.0 - - + -
110A PHE* 1.3 79.3 - - - +
112A MET* 1.3 62.0 + - - +
126A PHE* 3.8 30.3 - + + -
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Residues in contact with MET 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A VAL* 4.1 6.3 - - + -
63A ALA 3.2 14.1 - - - +
64A VAL* 3.7 19.3 - - + -
85A TYR* 4.0 15.9 - - - +
88A PHE* 3.6 44.0 - - + -
89A ILE 5.6 0.9 - - - +
90A LEU* 4.0 22.9 - - + -
99A ILE 3.9 0.3 - - - +
100A MET* 3.7 4.7 - - - -
101A LYS* 2.9 35.5 + - - +
103A LYS* 4.8 6.9 + - + -
110A PHE* 3.8 14.3 - - + -
111A PHE* 1.3 76.6 - - - +
113A CYS* 1.3 72.1 + - - +
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Residues in contact with CYS 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A VAL* 3.3 11.1 - - - +
63A ALA* 2.9 36.8 + - - -
90A LEU* 5.2 0.7 - - - -
92A ASP* 3.4 8.7 - - - +
98A CYS* 2.0 47.3 - - - -
99A ILE 3.3 31.6 - - - +
100A MET* 3.3 19.1 - - - -
112A MET* 1.3 75.7 - - - +
114A SER* 1.3 60.3 + - - +
124A ILE* 4.6 0.9 - - - -
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Residues in contact with SER 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL* 4.1 9.2 - - - -
61A CYS 3.1 15.9 - - - -
62A VAL* 4.0 11.9 - - - -
90A LEU* 3.7 16.3 - - - +
92A ASP* 2.7 49.5 + - - +
93A ALA* 3.3 15.6 + - - -
97A LYS 3.9 6.6 - - - +
98A CYS* 4.3 1.6 - - - -
113A CYS* 1.3 75.5 - - - +
115A CYS* 1.3 66.3 + - - +
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Residues in contact with CYS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL* 3.4 3.2 - - - +
61A CYS* 2.9 36.8 + - - +
93A ALA* 3.6 6.6 + - - +
95A SER 3.0 16.2 - - - +
96A PRO 4.0 0.4 - - - -
97A LYS 3.5 16.4 - - - +
98A CYS* 3.6 17.9 - - - -
114A SER* 1.3 77.4 - - - +
116A SER* 1.3 61.7 + - - +
120A CYS* 2.0 60.0 - - + -
121A ASN 3.7 1.6 - - - -
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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