Contacts of the strand formed by residues 102 - 115 (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 LYS 102 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98T LEU* 3.4 6.0 - - - +
99T ASN 2.9 32.0 + - - +
100T ASN* 4.5 9.9 - - - +
101T GLY* 1.3 81.9 - - - +
103T PHE* 1.3 59.7 + - - +
104T TYR* 3.2 27.6 - - + +
131T GLY* 3.3 34.3 + - - +
132T LEU 3.7 3.1 - - - -
133T LYS* 4.7 11.0 - - + +
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Residues in contact with PHE 103 (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* 4.2 8.3 - - + -
97T ASP 3.3 13.0 - - - -
98T LEU* 3.7 39.3 - - + -
101T GLY 4.9 1.3 - - - -
102T LYS* 1.3 70.5 - - - +
104T TYR* 1.3 63.1 + - - +
105T VAL* 4.8 3.8 - - + -
129T SER 3.3 12.2 - - - +
131T GLY 3.3 15.6 + - - -
132T LEU 2.9 14.1 + - - +
133T LYS* 3.3 29.8 - - - -
135T LYS* 3.7 53.4 - - + -
138T SER* 3.9 17.1 + - - +
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Residues in contact with TYR 104 (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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136S ALA* 6.5 0.4 - - + -
95T PHE* 3.4 18.8 - - + -
96T VAL* 3.7 0.2 - - - -
97T ASP* 2.9 41.8 + - + +
99T ASN* 3.7 35.6 + - + +
100T ASN* 5.2 1.6 + - - -
102T LYS* 3.2 44.1 - - + +
103T PHE* 1.3 74.7 - - - +
105T VAL* 1.3 60.7 + - - +
129T SER 3.4 4.7 - - - -
130T GLU* 3.4 38.8 - - + +
131T GLY* 4.6 4.2 - - - -
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Residues in contact with VAL 105 (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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136S ALA* 4.3 0.9 - - - +
93T VAL* 4.6 0.2 - - + -
95T PHE* 3.5 13.9 - - - +
96T VAL* 3.9 24.0 - - + -
103T PHE* 4.8 2.0 - - + -
104T TYR* 1.3 80.2 - - - +
106T GLY* 1.3 60.7 + - - +
107T VAL* 3.8 13.0 - - + -
127T GLY 3.7 0.3 - - - +
128T VAL* 3.5 9.9 - - - +
129T SER* 3.1 29.3 + - - +
130T GLU* 5.4 0.8 - - - +
135T LYS* 5.3 0.7 - - + +
138T SER* 3.8 27.1 - - - +
139T LEU* 3.8 18.8 - - + +
142T ALA* 3.7 24.0 - - + -
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Residues in contact with GLY 106 (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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136S ALA* 4.5 0.7 - - - -
93T VAL 3.7 0.3 - - - -
94T ASP* 2.8 32.1 + - - +
95T PHE* 3.3 24.3 + - - +
105T VAL* 1.3 74.4 - - - +
107T VAL* 1.3 59.8 + - - +
126T TYR* 3.4 24.9 - - - -
127T GLY 3.6 4.7 - - - -
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Residues in contact with VAL 107 (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* 3.8 28.5 - - + +
92T ASN 3.7 8.5 - - - +
93T VAL* 3.7 22.7 - - + -
105T VAL* 3.8 9.2 - - + -
106T GLY* 1.3 80.8 - - - +
108T CYS* 1.3 71.7 + - - +
126T TYR* 3.2 9.5 - - - -
127T GLY 2.7 34.6 + - - -
139T LEU* 4.7 0.7 - - + -
142T ALA* 3.6 26.9 - - + +
143T ARG* 3.9 15.7 - - + -
146T ALA* 3.3 3.9 - - + +
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Residues in contact with CYS 108 (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* 3.5 41.7 - - - +
91T GLN* 3.4 7.1 - - - +
92T ASN* 2.9 53.1 + - - +
94T ASP* 3.9 1.7 + - - -
107T VAL* 1.3 73.7 - - - +
109T ALA* 1.3 61.3 + - - +
110T PHE* 3.8 17.3 - - + -
124T VAL* 5.0 2.2 - - + -
125T GLY 3.3 7.4 - - - +
126T TYR* 3.6 19.6 - - + -
146T ALA* 4.1 0.7 - - - -
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Residues in contact with ALA 109 (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* 4.9 2.2 - - + -
90T GLN 3.4 8.1 - - - +
91T GLN* 3.7 22.2 - - + +
108T CYS* 1.3 76.2 - - - +
110T PHE* 1.3 65.7 + - - +
111T VAL* 4.0 5.8 + - + -
123T ASP 3.8 0.3 - - - +
124T VAL* 3.3 5.0 - - - +
125T GLY 2.7 35.5 + - - -
146T ALA 3.7 23.3 - - - +
147T VAL* 3.9 10.1 - - + +
150T GLY* 4.8 0.2 - - - -
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Residues in contact with PHE 110 (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* 3.8 24.9 - - + -
91S GLN* 3.6 46.7 - - + -
143S ARG* 4.4 5.4 - - - -
88T ILE* 3.4 3.1 - - - -
89T THR* 2.6 43.5 + - + -
90T GLN* 2.7 40.3 + - + +
92T ASN* 5.7 1.6 - - + -
108T CYS* 3.8 24.2 - - + -
109T ALA* 1.3 77.1 - - - +
111T VAL* 1.3 58.2 + - - +
122T GLU* 3.8 15.3 - - - +
123T ASP 3.5 4.9 - - - +
124T VAL* 3.5 21.5 - - + -
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Residues in contact with VAL 111 (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* 3.9 25.4 - - + -
87T SER 3.3 12.1 - - - +
88T ILE* 4.7 6.7 - - + -
109T ALA* 4.6 4.9 - - + -
110T PHE* 1.3 77.4 - - - +
112T ARG* 1.3 66.2 + - - +
113T VAL* 4.1 1.8 - - + -
122T GLU* 3.2 3.5 - - - +
123T ASP 3.0 30.3 + - - -
147T VAL* 3.5 36.6 - - + +
150T GLY* 3.6 16.8 - - - -
151T LEU* 3.7 22.7 - - + +
154T ALA* 3.8 4.0 - - - +
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Residues in contact with ARG 112 (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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87S SER* 4.8 5.6 - - - -
86T HIS* 3.2 2.1 - - - -
87T SER* 2.8 43.2 + - - +
89T THR* 3.8 16.8 - - - +
110T PHE 4.2 0.4 + - - -
111T VAL* 1.3 72.8 - - - +
113T VAL* 1.3 69.8 + - - +
114T GLN* 3.2 33.7 + - + +
120T TYR* 3.8 45.8 - - + +
121T HIS 3.5 3.4 - - - +
122T GLU* 3.9 21.3 - - + +
120U TYR* 4.7 7.2 + - - -
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Residues in contact with VAL 113 (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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84T TRP* 3.9 12.3 - - + -
85T ALA 3.1 10.3 - - - +
86T HIS* 3.7 5.4 - - + -
111T VAL* 4.6 0.7 - - + -
112T ARG* 1.3 73.9 - - - +
114T GLN* 1.3 67.5 + - - +
120T TYR* 3.0 6.1 - - - +
121T HIS 2.8 36.6 + - - +
151T LEU* 3.6 30.7 - - + -
154T ALA* 3.6 19.5 - - + -
155T LEU* 3.7 28.5 - - + -
158T PHE* 3.9 16.8 - - + -
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Residues in contact with GLN 114 (chain T).
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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26T PHE* 3.4 25.4 - - + -
27T GLY* 4.9 4.8 - - - -
84T TRP* 3.4 1.9 - - - +
85T ALA* 2.6 41.3 + - - +
112T ARG* 3.2 26.9 + - - +
113T VAL* 1.3 75.0 - - - +
115T LEU* 1.3 71.5 + - - +
118T GLY* 3.6 23.8 + - - +
119T SER 3.2 15.3 - - - +
120T TYR* 4.3 5.2 - - + -
120U TYR* 3.8 24.2 + - + +
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Residues in contact with LEU 115 (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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81S TYR* 4.0 19.3 - - + -
82S ASN* 4.6 0.9 - - + -
26T PHE* 3.7 7.4 - - - -
27T GLY* 4.5 0.2 - - - -
31T TYR* 4.3 6.3 - - + +
79T PHE* 3.7 47.8 - - + -
83T GLY 3.4 4.0 - - - +
84T TRP* 3.9 14.8 - - + -
113T VAL* 5.0 0.9 - - + -
114T GLN* 1.3 83.2 - - - +
116T LYS* 1.3 59.4 + - - +
117T ASP* 2.9 26.8 + - - +
118T GLY* 3.0 12.3 + - - -
119T SER* 2.7 18.3 + - - +
158T PHE* 3.6 37.7 - - + -
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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