Contacts of the strand formed by residues 84 - 99 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26T PHE* 4.0 4.1 - - - -
72T ILE* 4.0 14.4 - - + -
75T ALA* 3.6 28.5 - - + -
76T ASN* 2.8 25.9 + - - +
79T PHE* 3.9 10.3 - + + -
80T GLY 3.1 24.0 - - - -
81T TYR 4.2 6.6 - - - +
82T ASN 4.7 0.5 - - - -
83T GLY* 1.3 81.7 + - - +
85T ALA* 1.3 72.5 + - - +
86T HIS* 4.4 4.5 - - + -
113T VAL* 3.9 15.9 - - + -
114T GLN 3.4 5.8 - - - +
115T LEU* 3.9 17.9 - - + -
151T LEU* 3.8 35.4 - - + -
155T LEU* 3.8 17.0 - - + -
119U SER* 4.7 3.1 - - - -
120U TYR 4.4 0.5 - - - +
121U HIS* 3.6 37.5 + + - -
157U SER* 3.8 15.3 - - - -
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Residues in contact with ALA 85 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26T PHE* 3.5 20.4 - - + -
84T TRP* 1.3 79.7 - - - +
86T HIS* 1.3 56.7 + - - +
113T VAL* 3.1 7.6 - - - +
114T GLN 2.6 36.3 + - - +
120U TYR* 3.1 50.0 - - + +
121U HIS* 3.9 2.5 - - - -
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Residues in contact with HIS 86 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84T TRP* 4.4 2.3 - - + -
85T ALA* 1.3 77.3 - - - +
87T SER* 1.3 60.0 + - - +
88T ILE* 5.6 0.4 - - + -
111T VAL* 3.9 15.7 - - + -
112T ARG 3.2 6.7 - - - +
113T VAL* 3.7 10.5 - - + -
147T VAL* 5.4 4.1 - - + +
151T LEU* 3.6 44.4 - - + +
120U TYR* 3.3 13.9 + - - -
121U HIS* 2.8 42.7 + - + -
122U GLU 2.9 44.2 + - - -
123U ASP* 4.3 7.4 + - + -
157U SER* 3.7 15.9 - - - -
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Residues in contact with SER 87 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86T HIS* 1.3 74.6 - - - +
88T ILE* 1.3 67.8 + - - +
89T THR* 3.6 2.1 + - - -
111T VAL* 3.3 6.9 - - - +
112T ARG* 2.8 45.9 + - - +
112U ARG* 5.0 6.3 - - - -
120U TYR* 3.5 24.0 + - - -
122U GLU* 3.6 17.3 - - - -
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Residues in contact with ILE 88 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86T HIS* 5.6 0.2 - - + -
87T SER* 1.3 72.9 - - - +
89T THR* 1.3 65.1 + - - +
90T GLN* 4.0 22.2 - - - +
91T GLN* 4.2 4.5 - - + +
109T ALA* 4.9 2.2 - - + -
110T PHE 3.5 8.5 - - - +
111T VAL* 4.5 6.7 - - + +
147T VAL* 3.7 33.9 - - + -
89U THR* 5.9 1.4 - - - +
110U PHE* 4.0 21.7 - - + -
122U GLU* 3.1 32.0 + - + +
123U ASP* 3.8 33.0 - - - +
124U VAL* 3.8 7.4 - - + -
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Residues in contact with THR 89 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88S ILE 5.7 2.5 - - - +
87T SER* 3.6 3.0 + - - -
88T ILE* 1.3 74.5 - - - +
90T GLN* 1.3 64.9 + - + +
110T PHE* 2.6 18.7 + - + -
112T ARG* 3.8 16.3 - - - +
122T GLU* 2.8 32.9 + - - +
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Residues in contact with GLN 90 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88T ILE* 3.3 6.2 - - - -
89T THR* 1.3 88.3 - - + +
91T GLN* 1.3 68.6 + - - +
92T ASN* 5.0 11.3 + - + +
110T PHE* 2.7 54.8 + - + +
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Residues in contact with GLN 91 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88T ILE* 4.2 5.9 - - + +
90T GLN* 1.3 79.9 - - - +
92T ASN* 1.3 63.8 + - - +
93T VAL 4.5 0.2 + - - -
107T VAL* 3.8 14.1 - - + +
108T CYS 3.4 8.7 - - - +
109T ALA* 3.7 10.0 - - + +
143T ARG* 2.6 72.1 + - - +
147T VAL* 3.3 17.4 - - - +
110U PHE* 3.5 33.8 - - + -
124U VAL* 3.8 4.0 - - - +
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Residues in contact with ASN 92 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143S ARG* 4.9 5.0 - - - +
90T GLN* 4.3 13.9 - - - +
91T GLN* 1.3 74.9 - - - +
93T VAL* 1.3 73.1 + - - +
94T ASP* 3.1 26.5 + - - +
107T VAL* 3.7 2.2 - - - -
108T CYS* 2.9 46.7 + - - -
110T PHE* 5.7 0.9 - - + -
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Residues in contact with VAL 93 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91T GLN 4.3 0.4 + - - -
92T ASN* 1.3 79.9 + - - +
94T ASP* 1.3 66.2 + - - +
95T PHE* 3.9 9.6 - - - +
96T VAL* 3.8 28.7 - - + -
106T GLY 3.9 2.9 - - - -
107T VAL* 3.7 22.7 - - + -
139T LEU* 4.2 7.4 - - + -
143T ARG* 3.2 39.4 - - - +
94U ASP* 5.1 0.2 - - - +
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Residues in contact with ASP 94 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93S VAL* 5.2 0.2 - - - +
139S LEU* 3.9 11.5 - - + +
143S ARG* 2.7 34.7 + - - -
92T ASN* 3.1 23.9 + - - +
93T VAL* 1.3 74.2 - - - +
95T PHE* 1.3 68.8 + - + +
106T GLY 2.8 16.5 + - - +
108T CYS* 3.9 1.8 - - - -
126T TYR* 2.9 34.8 + - - +
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Residues in contact with PHE 95 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135S LYS* 3.6 22.7 - - + +
136S ALA* 3.6 30.3 - - + -
139S LEU* 3.5 33.0 - - + -
93T VAL* 3.4 4.1 - - - +
94T ASP* 1.3 81.2 - - + +
96T VAL* 1.3 69.3 + - - +
97T ASP* 3.1 27.8 - - - +
104T TYR* 3.4 28.7 - - + -
105T VAL* 3.5 3.1 - - - +
106T GLY* 3.3 41.4 + - - +
126T TYR* 3.7 2.0 - - - -
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Residues in contact with VAL 96 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93T VAL* 3.8 18.4 - - + -
95T PHE* 1.3 79.6 - - - +
97T ASP* 1.3 65.6 + - - +
98T LEU 4.3 0.3 + - - -
103T PHE* 4.2 11.9 - - + -
104T TYR 3.7 3.6 - - - -
105T VAL* 3.9 15.9 - - + -
135T LYS* 3.8 29.2 - - + +
139T LEU* 3.9 21.1 - - + -
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Residues in contact with ASP 97 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135S LYS* 2.9 38.2 + - - -
95T PHE* 3.1 12.6 - - - +
96T VAL* 1.3 80.0 + - - +
98T LEU* 1.3 61.8 + - - +
99T ASN* 4.1 11.7 - - - +
102T LYS 3.7 0.5 - - - +
103T PHE* 3.3 9.2 - - - -
104T TYR* 2.9 44.1 + - + +
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Residues in contact with LEU 98 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96T VAL 4.3 0.4 + - - -
97T ASP* 1.3 73.0 - - - +
99T ASN* 1.3 63.7 + - - +
100T ASN 4.1 1.1 + - - +
101T GLY* 3.6 30.7 - - - +
102T LYS 3.4 16.4 - - - +
103T PHE* 3.7 35.9 - - + -
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Residues in contact with ASN 99 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97T ASP* 4.1 10.6 - - - +
98T LEU* 1.3 76.7 - - - +
100T ASN* 1.3 84.5 + - - +
101T GLY 3.2 0.9 - - - -
102T LYS* 2.9 24.6 + - - +
104T TYR* 3.7 33.6 + - + +
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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