Contacts of the helix formed by residues 90 - 98 (chain A) in PDB entry 5TQB
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 ALA 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A GLY* 1.3 71.8 - - - -
91A PHE* 1.3 56.8 + - - +
93A ASN* 3.2 11.7 + - + +
94A MSE 2.8 35.0 + - + +
225B GLU* 4.8 13.5 - - - +
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Residues in contact with PHE 91 (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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89A GLY* 3.0 6.1 - - - +
90A ALA* 1.3 79.6 - - - +
92A GLY* 1.3 65.1 + - - +
94A MSE 3.2 3.5 + - - +
95A CYS* 3.1 30.0 + - - -
182B TYR 4.8 2.2 - - - -
183B MSE 4.0 35.4 - - + -
192B ALA* 4.3 11.4 - - + -
193B GLU* 3.6 58.3 - - + +
196B CYS* 4.2 13.5 - - - -
220B VAL* 4.0 11.2 - - + -
223B SER* 3.7 32.3 - - - -
224B GLN* 3.9 19.3 - - + -
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Residues in contact with GLY 92 (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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89A GLY 3.4 9.2 + - - +
91A PHE* 1.3 84.0 - - - +
93A ASN* 1.3 59.9 + - - +
95A CYS* 3.4 6.2 + - - +
96A ARG* 3.2 37.1 + - - +
187B SER* 3.4 30.9 - - - -
192B ALA* 5.9 0.2 - - - +
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Residues in contact with ASN 93 (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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89A GLY 3.1 26.1 + - - -
90A ALA* 3.2 10.8 + - - +
92A GLY* 1.3 74.3 - - - +
94A MSE 1.3 66.2 + - - +
96A ARG* 3.5 18.8 + - - +
97A SER* 3.0 34.9 + - - +
98A GLY* 3.3 1.9 + - - -
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Residues in contact with MSE 94 (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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77A ARG* 6.1 4.5 - - + -
90A ALA* 2.8 21.8 + - + +
91A PHE 3.5 2.0 - - - +
93A ASN* 1.3 75.6 - - - +
95A CYS* 1.3 59.6 + - - +
98A GLY* 2.9 59.4 + - - +
99A ARG* 3.5 18.6 + - + +
222B ILE* 4.0 19.7 - - + +
223B SER* 3.4 27.8 - - - +
225B GLU* 3.9 31.2 - - + +
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Residues in contact with CYS 95 (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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66A TRP* 5.2 0.8 + - - -
91A PHE* 3.1 27.6 + - - -
92A GLY* 3.5 11.0 - - - +
93A ASN 3.2 0.2 - - - -
94A MSE 1.3 79.6 - - - +
96A ARG* 1.3 60.8 + - + +
99A ARG* 4.4 1.7 - - - +
102A ALA* 3.6 10.4 - - - +
103A PRO* 3.3 22.8 - - + +
183B MSE 3.5 52.9 - - - +
187B SER* 4.7 3.4 - - - -
223B SER* 3.4 21.5 - - - -
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Residues in contact with ARG 96 (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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61A THR 5.2 0.2 - - - -
63A ALA* 3.5 37.9 - - + +
64A GLU* 4.4 6.1 + - - +
65A SER* 4.6 12.8 + - - -
66A TRP* 4.4 8.7 - - + +
72A VAL* 6.0 0.9 - - - +
92A GLY* 3.2 30.5 + - - +
93A ASN* 3.5 25.2 + - - +
95A CYS* 1.3 80.8 - - + +
97A SER* 1.3 63.0 + - - +
98A GLY 3.8 0.2 - - - -
99A ARG* 5.3 2.8 - - - +
102A ALA* 4.7 0.9 - - - +
187B SER* 3.1 42.2 + - - +
188B TRP* 3.1 59.2 - - - +
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Residues in contact with SER 97 (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 GLU* 6.0 5.2 - - - -
72A VAL* 6.4 1.1 - - - -
73A ALA 5.2 5.4 - - - +
74A ARG* 5.8 1.7 - - - -
75A ILE* 5.1 10.2 + - - +
93A ASN* 3.0 17.3 + - - +
96A ARG* 1.3 81.4 + - - +
98A GLY* 1.3 61.7 + - - +
99A ARG 3.4 5.1 - - - +
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Residues in contact with GLY 98 (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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74A ARG* 3.5 21.1 - - - +
75A ILE* 5.3 4.7 + - - +
77A ARG* 5.8 1.2 - - - +
93A ASN 3.3 3.0 + - - -
94A MSE 2.9 46.4 + - - +
97A SER* 1.3 78.5 - - - +
99A ARG* 1.3 63.3 + - - +
266B GLU* 4.7 0.2 - - - +
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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