Contacts of the strand formed by residues 84 - 99 (chain Q) in PDB entry 5XS0
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 TRP 84 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26Q PHE* 3.6 3.6 - - - -
72Q ILE* 4.3 11.7 - - + -
75Q ALA* 3.5 35.0 - - + -
76Q ASN* 3.1 21.5 + - - -
79Q PHE* 3.8 10.3 - + + -
80Q GLY 3.1 23.6 - - - -
81Q TYR* 4.0 2.8 - - - +
82Q ASN 3.6 0.2 - - - -
83Q GLY* 1.3 80.1 - - - +
85Q ALA* 1.3 68.8 + - - +
86Q HIS* 4.4 2.9 - - + -
113Q VAL* 4.0 7.6 - - + -
114Q GLN 3.2 6.5 - - - +
115Q LEU* 3.8 19.1 - - + -
151Q LEU* 4.0 24.2 - - + -
155Q LEU* 3.9 32.1 - - + -
119R SER* 3.7 13.3 + - - -
121R HIS* 3.5 36.8 + + - -
157R SER* 3.8 18.8 - - - -
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Residues in contact with ALA 85 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Q PHE* 3.4 19.1 - - + -
84Q TRP* 1.3 79.5 - - - +
86Q HIS* 1.3 57.4 + - - +
113Q VAL* 3.2 5.0 - - - +
114Q GLN 2.5 41.2 + - - +
120R TYR* 3.1 51.6 - - + +
121R HIS* 4.0 3.4 - - - -
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Residues in contact with HIS 86 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84Q TRP* 4.4 1.9 - - + -
85Q ALA* 1.3 76.8 - - - +
87Q SER* 1.3 62.3 + - - +
88Q ILE* 5.4 1.3 - - + -
111Q VAL* 3.7 16.6 - - + -
112Q ARG 3.1 12.8 - - - +
113Q VAL* 3.9 6.7 - - + -
147Q VAL* 5.2 3.5 - - + +
151Q LEU* 3.6 43.8 - - + +
120R TYR* 3.3 15.4 + - - -
121R HIS* 2.9 32.3 + - + -
122R GLU 2.9 49.6 + - - -
123R ASP* 4.5 6.0 + - - -
157R SER* 3.8 18.6 - - - -
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Residues in contact with SER 87 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86Q HIS* 1.3 76.0 - - - +
88Q ILE* 1.3 65.9 + - - +
89Q THR* 3.5 3.1 + - - -
111Q VAL* 3.5 5.8 - - - +
112Q ARG* 3.0 43.3 + - - +
112R ARG* 5.0 4.3 - - - -
120R TYR* 3.6 22.2 + - - -
122R GLU* 3.5 18.2 - - - -
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Residues in contact with ILE 88 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86Q HIS* 5.4 1.1 - - + -
87Q SER* 1.3 72.9 - - - +
89Q THR* 1.3 65.0 + - - +
90Q GLN* 4.0 21.5 - - - +
91Q GLN* 4.4 3.8 - - + +
109Q ALA* 4.9 4.5 - - + -
110Q PHE 3.6 7.4 - - - +
111Q VAL* 4.7 6.1 - - + +
147Q VAL* 3.7 30.7 - - + -
89R THR* 5.8 1.7 - - - +
110R PHE* 3.8 27.6 - - + -
122R GLU* 3.0 35.2 + - + +
123R ASP* 3.6 37.5 - - - +
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Residues in contact with THR 89 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88P ILE 5.9 1.1 - - - +
87Q SER* 3.5 3.7 + - - -
88Q ILE* 1.3 74.8 - - - +
90Q GLN* 1.3 64.8 + - + +
110Q PHE* 2.7 17.4 + - + -
112Q ARG* 4.0 15.9 - - - +
122Q GLU* 3.1 30.4 + - - +
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Residues in contact with GLN 90 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88Q ILE* 3.4 5.5 - - - +
89Q THR* 1.3 87.7 - - + +
91Q GLN* 1.3 68.8 + - - +
92Q ASN* 4.1 19.2 + - + +
109Q ALA* 3.4 0.7 - - - -
110Q PHE* 2.7 55.8 + - + +
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Residues in contact with GLN 91 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88Q ILE* 4.4 2.8 - - + +
90Q GLN* 1.3 80.8 - - - +
92Q ASN* 1.3 63.0 + - - +
93Q VAL 4.4 0.2 + - - -
107Q VAL* 3.7 19.6 - - + +
108Q CYS 3.3 8.3 - - - +
109Q ALA* 3.8 11.2 - - + +
143Q ARG* 2.6 71.0 + - - +
147Q VAL* 3.5 16.0 - - - +
110R PHE* 3.4 32.5 - - + -
124R VAL* 4.1 1.6 - - - +
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Residues in contact with ASN 92 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143P ARG* 5.0 3.5 + - - +
90Q GLN* 4.1 17.5 + - - +
91Q GLN* 1.3 74.5 + - - +
93Q VAL* 1.3 72.9 + - - +
94Q ASP* 3.2 22.9 + - - +
107Q VAL* 4.3 1.8 - - - -
108Q CYS* 2.9 48.2 + - - -
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Residues in contact with VAL 93 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91Q GLN 4.3 0.4 + - - -
92Q ASN* 1.3 78.4 + - - +
94Q ASP* 1.3 65.4 + - - +
95Q PHE* 3.8 10.7 - - - +
96Q VAL* 3.8 28.9 - - + -
106Q GLY 3.9 2.9 - - - -
107Q VAL* 3.7 23.3 - - + -
139Q LEU* 4.2 5.8 - - + -
143Q ARG* 3.3 40.1 - - - +
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Residues in contact with ASP 94 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93P VAL* 5.2 0.7 - - - +
139P LEU* 3.7 20.2 - - + +
143P ARG* 2.8 34.9 + - - -
92Q ASN* 3.2 22.6 + - - +
93Q VAL* 1.3 73.6 - - - +
95Q PHE* 1.3 62.6 + - + +
106Q GLY 2.7 16.8 + - - +
108Q CYS* 4.0 0.6 - - - -
126Q TYR* 2.6 35.1 + - - +
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Residues in contact with PHE 95 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135P LYS* 3.7 32.1 - - + +
136P ALA* 3.4 33.9 - - + -
139P LEU* 3.7 18.4 - - + -
93Q VAL* 3.4 3.8 - - - +
94Q ASP* 1.3 84.7 - - + +
96Q VAL* 1.3 69.5 + - - +
97Q ASP* 3.1 28.9 - - - +
104Q TYR* 3.2 31.6 - - + -
105Q VAL* 3.5 4.0 - - - +
106Q GLY* 3.3 43.6 + - - +
130Q GLU* 5.7 0.4 - - - -
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Residues in contact with VAL 96 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93Q VAL* 3.8 9.4 - - + -
95Q PHE* 1.3 79.1 - - - +
97Q ASP* 1.3 66.0 + - - +
103Q PHE* 4.2 11.2 - - + -
104Q TYR 3.8 3.6 - - - -
105Q VAL* 4.0 15.0 - - + -
135Q LYS* 3.8 29.4 - - + +
139Q LEU* 3.8 31.0 - - + -
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Residues in contact with ASP 97 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135P LYS* 3.1 25.1 + - - -
95Q PHE* 3.1 26.3 - - + +
96Q VAL* 1.3 79.7 - - - +
98Q LEU* 1.3 61.6 + - - +
99Q ASN* 4.0 14.6 - - - +
102Q LYS 3.7 0.3 - - - +
103Q PHE* 3.3 10.2 - - - -
104Q TYR* 3.0 39.2 + - + +
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Residues in contact with LEU 98 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97Q ASP* 1.3 73.4 - - - +
99Q ASN* 1.3 64.5 + - - +
100Q ASN 4.2 1.7 + - - +
101Q GLY* 3.7 30.7 - - - +
102Q LYS 3.5 13.9 - - - +
103Q PHE* 3.6 35.0 - - + -
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Residues in contact with ASN 99 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97Q ASP* 4.0 11.3 - - - +
98Q LEU* 1.3 77.0 - - - +
100Q ASN* 1.3 83.2 + - - +
101Q GLY 3.2 0.9 - - - -
102Q LYS* 2.8 27.7 + - - +
104Q TYR* 3.6 37.1 + - + +
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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