Contacts of the strand formed by residues 102 - 115 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97N ASP 3.7 0.3 - - - +
98N LEU* 3.6 3.3 - - - +
99N ASN 3.0 28.0 + - - +
100N ASN* 3.9 22.9 - - - +
101N GLY* 1.3 83.1 - - - +
103N PHE* 1.3 62.3 + - - +
104N TYR* 3.5 30.4 - - + +
131N GLY* 3.7 25.6 - - - +
132N LEU 3.4 4.3 - - - -
133N LYS* 4.9 10.8 - - + +
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Residues in contact with PHE 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96N VAL* 4.1 8.5 - - + -
97N ASP 3.4 13.5 - - - -
98N LEU* 3.7 37.5 - - + -
101N GLY 4.7 1.6 - - - -
102N LYS* 1.3 75.5 - - - +
104N TYR* 1.3 60.5 + - - +
105N VAL* 4.2 4.0 - - + -
129N SER 3.3 7.8 - - - +
131N GLY 3.2 20.4 + - - -
132N LEU 2.7 16.0 + - - +
133N LYS 3.3 29.2 - - - -
135N LYS* 3.4 54.3 - - + -
138N SER* 3.7 17.6 + - - +
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Residues in contact with TYR 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95N PHE* 3.4 18.9 - - + -
97N ASP* 3.1 37.5 + - + +
99N ASN* 3.4 45.1 + - + +
100N ASN* 4.9 2.3 + - - -
102N LYS* 3.5 32.6 - - + +
103N PHE* 1.3 80.0 - - - +
105N VAL* 1.3 61.0 + - - +
129N SER 3.4 3.4 - - - -
130N GLU* 3.4 25.8 - - + +
131N GLY* 3.2 27.4 - - - -
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Residues in contact with VAL 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136M ALA* 4.3 1.9 - - - +
93N VAL* 4.7 0.2 - - + -
95N PHE* 3.5 14.4 - - - +
96N VAL* 4.0 22.7 - - + -
103N PHE* 4.7 2.0 - - + -
104N TYR* 1.3 81.5 - - - +
106N GLY* 1.3 60.0 + - - +
107N VAL* 3.8 8.3 - - + -
127N GLY 3.8 0.5 - - - +
128N VAL* 3.5 9.5 - - - +
129N SER 3.0 29.0 + - - +
130N GLU* 5.3 0.8 - - - +
135N LYS 5.2 0.7 - - - +
138N SER* 3.8 28.0 - - - +
139N LEU* 3.8 24.9 - - + +
142N ALA* 3.7 23.6 - - + -
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Residues in contact with GLY 106 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136M ALA* 4.4 1.6 - - - -
94N ASP* 2.8 32.2 + - - +
95N PHE* 3.3 26.5 + - - +
105N VAL* 1.3 73.7 - - - +
107N VAL* 1.3 60.3 + - - +
126N TYR* 3.6 24.0 - - - -
127N GLY 3.6 3.8 - - - -
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Residues in contact with VAL 107 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91N GLN* 3.8 28.3 - - + +
92N ASN 3.6 9.4 - - - +
93N VAL* 3.7 22.7 - - + -
105N VAL* 3.8 9.6 - - + -
106N GLY* 1.3 79.0 - - - +
108N CYS* 1.3 71.2 + - - +
126N TYR* 3.4 8.0 - - - -
127N GLY 2.7 36.6 + - - -
139N LEU* 4.7 0.9 - - + -
142N ALA* 3.7 27.1 - - + +
143N ARG* 4.0 16.2 - - + -
146N ALA* 3.4 3.9 - - + +
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Residues in contact with CYS 108 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143M ARG* 3.5 40.2 - - - +
91N GLN* 3.4 6.6 - - - +
92N ASN* 2.9 55.7 + - - +
94N ASP* 4.1 0.9 + - - -
107N VAL* 1.3 74.3 - - - +
109N ALA* 1.3 63.2 + - - +
110N PHE* 3.7 15.9 - - + -
124N VAL* 4.9 1.8 - - + -
125N GLY 3.4 6.7 - - - +
126N TYR* 3.6 21.2 - - + -
146N ALA* 4.1 1.3 - - - -
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Residues in contact with ALA 109 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88N ILE* 5.0 2.2 - - + -
90N GLN 3.5 7.9 - - - +
91N GLN* 3.7 17.5 - - + +
108N CYS* 1.3 76.4 - - - +
110N PHE* 1.3 64.4 + - - +
111N VAL* 4.0 5.8 + - + -
124N VAL* 3.4 4.7 - - - +
125N GLY 2.7 36.1 + - - +
146N ALA 3.7 29.4 - - - +
147N VAL* 3.9 10.1 - - + +
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Residues in contact with PHE 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88M ILE* 3.9 23.1 - - + -
91M GLN* 3.7 45.5 - - + -
143M ARG* 4.2 5.8 - - - -
88N ILE* 3.5 3.8 - - - +
89N THR* 2.7 35.4 + - + -
90N GLN* 2.8 49.2 + - + +
92N ASN* 5.4 0.2 - - + -
108N CYS* 3.7 24.7 - - + -
109N ALA* 1.3 77.4 - - - +
111N VAL* 1.3 58.6 + - - +
122N GLU* 3.9 13.7 - - - +
123N ASP 3.6 5.2 - - - +
124N VAL* 3.5 22.2 - - + -
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Residues in contact with VAL 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86N HIS* 4.0 26.2 - - + -
87N SER 3.4 10.5 - - - +
88N ILE* 4.8 6.7 - - + -
109N ALA* 4.6 2.5 - - + -
110N PHE* 1.3 78.5 - - - +
112N ARG* 1.3 63.2 + - - +
113N VAL* 4.1 2.5 - - + -
122N GLU* 3.3 3.3 - - - -
123N ASP 3.1 30.6 + - - -
147N VAL* 3.6 35.7 - - + +
150N GLY* 3.6 20.0 - - - +
151N LEU* 3.8 19.3 - - + -
154N ALA* 3.6 5.0 - - - +
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Residues in contact with ARG 112 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87M SER* 4.7 5.9 - - - -
86N HIS* 3.3 1.8 - - - -
87N SER* 3.0 40.8 + - - +
89N THR* 3.9 16.8 - - - +
110N PHE 4.2 0.8 + - - -
111N VAL* 1.3 72.6 - - - +
113N VAL* 1.3 71.0 + - - +
114N GLN* 4.0 25.7 + - + +
118N GLY 4.8 1.0 + - - -
120N TYR* 3.8 50.5 - - + +
121N HIS 3.6 4.0 - - - +
122N GLU* 3.8 23.6 - - + -
120O TYR* 4.7 4.3 + - - +
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Residues in contact with VAL 113 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84N TRP* 3.8 11.4 - - + -
85N ALA 3.1 10.8 - - - +
86N HIS* 3.8 6.1 - - + -
111N VAL* 4.6 0.9 - - + -
112N ARG* 1.3 74.3 - - - +
114N GLN* 1.3 67.8 + - - +
115N LEU* 5.0 0.2 - - + -
120N TYR* 3.1 5.4 - - - +
121N HIS 2.9 36.3 + - - +
151N LEU* 3.6 30.3 - - + -
154N ALA* 3.7 20.2 - - + -
155N LEU* 3.6 28.3 - - + -
158N PHE* 4.0 16.4 - - + -
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Residues in contact with GLN 114 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N PHE* 3.6 10.2 - - + -
27N GLY* 4.1 12.8 - - - -
84N TRP* 3.4 1.7 - - - +
85N ALA* 2.6 41.3 + - - -
112N ARG* 4.0 19.0 + - - +
113N VAL* 1.3 74.5 - - - +
115N LEU* 1.3 74.1 + - - +
118N GLY* 3.5 24.4 - - - +
119N SER 3.2 12.3 - - - +
120N TYR* 4.4 6.1 - - + -
120O TYR* 2.9 33.9 + - - +
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Residues in contact with LEU 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81M TYR* 3.9 18.8 - - + -
82M ASN* 4.5 0.7 - - + -
26N PHE* 3.6 7.7 - - - -
27N GLY 4.5 0.2 + - - -
31N TYR* 4.1 5.4 - - - +
79N PHE* 3.5 50.0 - - + -
83N GLY 3.4 3.8 - - - +
84N TRP* 3.9 11.9 - - + -
113N VAL* 5.0 0.9 - - + -
114N GLN* 1.3 84.4 - - - +
116N LYS* 1.3 59.8 + - - +
117N ASP* 3.0 22.0 - - - +
118N GLY* 3.0 17.3 + - - -
119N SER* 2.7 16.9 + - - +
158N PHE* 3.5 39.5 - - + -
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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