Contacts of the strand formed by residues 84 - 99 (chain B) in PDB entry 5XRZ
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B PHE* 3.7 2.0 - - - -
72B ILE* 4.4 7.9 - - + -
75B ALA* 3.8 22.7 - - + -
76B ASN* 3.0 31.4 + - - +
79B PHE* 3.9 22.2 - + + -
80B GLY 3.0 24.7 - - - -
81B TYR 4.3 1.4 - - - +
83B GLY* 1.3 77.9 + - - +
85B ALA* 1.3 68.5 + - - +
86B HIS* 4.0 9.9 - + + -
113B VAL* 3.6 20.0 - - + -
114B GLN 3.5 6.3 - - - +
115B LEU* 4.0 8.7 - - + -
151B LEU* 3.9 38.6 - - + -
155B LEU* 4.1 13.5 - - + -
119C SER* 3.4 15.4 + - - -
121C HIS* 3.6 28.9 + + - -
157C SER* 3.7 18.4 - - - -
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B PHE* 3.5 18.8 - - + -
84B TRP* 1.3 81.9 - - - +
86B HIS* 1.3 58.3 + - - +
112B ARG 3.9 0.2 - - - +
113B VAL* 3.2 3.5 - - - +
114B GLN* 2.5 42.1 + - - +
120C TYR* 3.1 49.4 - - + +
121C HIS* 4.0 3.6 - - - -
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Residues in contact with HIS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TRP* 4.0 6.1 - + + -
85B ALA* 1.3 74.8 - - - +
87B SER* 1.3 60.0 + - - +
88B ILE* 5.7 0.4 - - + -
111B VAL* 3.8 13.3 - - + +
112B ARG 3.2 9.4 - - - +
113B VAL* 4.2 2.9 - - + -
147B VAL* 5.2 4.7 - - + -
151B LEU* 3.4 48.8 - - + +
120C TYR* 3.3 21.5 + - - +
121C HIS* 3.2 33.9 - + - +
122C GLU 3.0 36.2 + - - -
123C ASP* 4.3 10.9 + - - +
154C ALA* 5.7 0.2 - - - -
157C SER* 3.8 12.0 + - - -
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Residues in contact with SER 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B HIS* 1.3 77.1 - - - +
88B ILE* 1.3 66.4 + - - +
89B THR* 3.5 2.1 + - - -
111B VAL* 3.3 6.4 - - - +
112B ARG* 2.8 49.5 + - - +
112C ARG* 5.2 3.4 - - - -
120C TYR* 3.5 22.8 + - - -
122C GLU* 3.6 15.7 - - - -
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B SER* 1.3 72.7 - - - +
89B THR* 1.3 66.5 + - - +
90B GLN* 4.1 19.0 - - - +
91B GLN* 4.3 4.5 - - + +
109B ALA* 4.8 2.5 - - + -
110B PHE 3.5 9.6 - - - +
111B VAL* 4.6 4.7 - - + +
147B VAL* 3.8 21.8 - - + -
89C THR* 6.0 0.9 - - - +
110C PHE* 3.6 36.6 - - + -
122C GLU* 2.6 38.7 + - + +
123C ASP* 3.8 19.1 - - - -
124C VAL* 3.7 17.7 - - + -
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Residues in contact with THR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ILE 5.7 2.0 - - - +
87B SER* 3.5 3.0 + - - -
88B ILE* 1.3 74.8 - - - +
90B GLN* 1.3 65.7 + - + +
110B PHE* 2.7 16.8 + - + -
112B ARG* 3.8 21.8 - - - +
122B GLU* 3.0 28.0 + - - +
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Residues in contact with GLN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLN 5.8 0.2 - - - +
88B ILE* 3.4 5.7 - - - -
89B THR* 1.3 87.5 - - + +
91B GLN* 1.3 69.6 + - - +
92B ASN* 4.8 10.9 - - + +
110B PHE* 2.7 55.9 + - + +
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Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ILE* 4.3 3.0 - - + +
90B GLN* 1.3 78.1 - - - +
92B ASN* 1.3 64.1 + - - +
107B VAL* 4.2 8.1 - - + +
108B CYS 3.4 11.7 - - - +
109B ALA* 3.9 8.2 - - + +
143B ARG* 2.4 66.7 + - - +
147B VAL* 3.2 30.7 - - - +
110C PHE* 3.3 28.3 - - + -
124C VAL* 3.7 5.8 - - - +
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Residues in contact with ASN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A ARG* 5.0 4.8 - - - +
90B GLN* 4.3 14.3 - - + +
91B GLN* 1.3 75.6 - - - +
93B VAL* 1.3 77.9 + - - +
94B ASP* 3.4 14.1 + - - +
107B VAL* 4.6 2.0 - - - -
108B CYS* 3.0 42.1 + - - +
110B PHE* 6.0 1.1 - - + -
143B ARG* 5.4 0.2 - - - +
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ASN* 1.3 82.3 + - - +
94B ASP* 1.3 66.3 + - - +
95B PHE* 3.8 15.5 - - - +
96B VAL* 4.0 16.4 - - + -
106B GLY 3.8 6.3 - - - +
107B VAL* 3.8 26.9 - - + -
139B LEU* 4.6 7.2 - - + -
143B ARG* 3.7 34.5 - - - +
94C ASP* 4.8 4.9 - - - +
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Residues in contact with ASP 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL* 4.8 6.4 - - - +
139A LEU* 3.9 10.9 - - + +
143A ARG* 2.8 33.5 + - - -
92B ASN* 3.4 13.0 + - - +
93B VAL* 1.3 74.3 - - - +
95B PHE* 1.3 71.7 + - + +
106B GLY 2.9 8.6 + - - +
108B CYS* 3.8 5.5 + - - +
126B TYR* 2.9 39.4 + - - +
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Residues in contact with PHE 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LYS* 3.6 30.3 - - + +
136A ALA* 3.4 30.3 - - + -
139A LEU* 3.5 33.2 - - + -
93B VAL* 3.5 3.1 - - - +
94B ASP* 1.3 83.1 - - + +
96B VAL* 1.3 71.1 + - - +
97B ASP* 3.1 25.4 - - - +
104B TYR* 3.5 22.0 - - + -
105B VAL* 3.7 1.5 - - - -
106B GLY* 3.2 50.9 + - - +
126B TYR* 3.7 1.3 - - - -
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B VAL* 4.0 17.9 - - + -
95B PHE* 1.3 80.6 - - - +
97B ASP* 1.3 69.1 + - - +
103B PHE* 4.6 7.0 - - + -
104B TYR 3.6 4.5 - - - -
105B VAL* 4.0 21.8 - - + -
135B LYS* 4.2 25.8 - - + +
139B LEU* 4.0 12.3 - - + -
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Residues in contact with ASP 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LYS* 3.3 24.4 + - - -
95B PHE* 3.1 27.1 - - - +
96B VAL* 1.3 83.2 + - - +
98B LEU* 1.3 62.5 + - - +
99B ASN* 4.3 8.5 - - - +
103B PHE* 3.4 11.2 - - - -
104B TYR* 3.0 42.2 + - + +
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ASP* 1.3 76.9 - - - +
99B ASN* 1.3 67.2 + - - +
100B ASN 4.1 1.7 + - - +
101B GLY* 3.7 17.3 - - - +
102B ALA 3.3 30.5 - - - +
103B PHE* 3.7 34.3 - - + -
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Residues in contact with ASN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ASP* 5.0 7.3 - - - +
98B LEU* 1.3 82.3 + - - +
100B ASN* 1.3 86.1 + - - +
101B GLY 3.3 0.7 - - - -
102B ALA* 3.0 23.2 + - - +
104B TYR* 3.2 36.0 + - + +
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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