Contacts of the strand formed by residues 90 - 106 (chain F) in PDB entry 5HK5
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 ARG 90 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81F THR* 3.8 1.8 - - - +
82F VAL* 2.9 35.6 + - + +
88F ARG* 3.6 8.1 + - + +
89F SER* 1.3 77.4 - - - +
91F THR* 1.3 72.3 + - - +
92F ILE* 3.8 9.7 + - + +
133F VAL* 4.7 16.7 - - + +
134F GLU 3.9 22.0 - - - +
135F LEU* 5.2 4.0 - - + -
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Residues in contact with THR 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F ARG* 4.3 24.5 - - + +
80F GLN 3.4 9.9 - - - +
81F THR* 4.4 11.1 + - - +
89F SER 4.3 0.4 + - - -
90F ARG* 1.3 81.7 + - - +
92F ILE* 1.3 74.6 + - - +
93F LEU* 5.9 0.9 - - + -
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Residues in contact with ILE 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F ARG* 3.7 1.9 - - - -
80F GLN* 2.8 74.9 + - + +
82F VAL* 3.7 18.6 - - + -
90F ARG* 3.8 12.0 + - + +
91F THR* 1.3 82.5 - - - +
93F LEU* 1.3 62.2 + - - +
94F ASN* 4.0 12.8 - - + +
131F VAL* 6.3 1.1 - - + -
133F VAL* 3.8 29.4 - - + -
149F ILE* 4.0 15.0 - - + -
151F LYS* 5.2 4.5 - - + -
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Residues in contact with LEU 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F PRO* 4.8 14.4 - - + -
78F LEU 3.9 11.9 - - - +
79F ARG* 3.8 32.1 - - + +
91F THR* 5.9 1.3 - - + -
92F ILE* 1.3 75.8 - - - +
94F ASN* 1.3 66.8 + - - +
95F ARG* 5.8 7.9 - - - +
151F LYS* 3.6 21.0 + - - +
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Residues in contact with ASN 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E PRO* 3.9 14.8 - - - +
77F PRO* 4.0 2.9 - - - +
78F LEU* 2.8 34.8 + - + +
80F GLN* 2.7 31.4 + - + +
92F ILE* 3.8 5.4 - - + +
93F LEU* 1.3 77.8 - - - +
95F ARG* 1.3 87.5 + - - +
149F ILE* 4.0 4.9 - - - +
150F GLN 2.9 26.4 + - - -
151F LYS* 3.5 13.7 - - - +
152F VAL 3.3 22.9 + - - -
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Residues in contact with ARG 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E PRO* 3.3 24.9 - - - +
75F THR* 2.6 44.4 + - - +
76F GLN* 3.1 11.7 - - - +
77F PRO* 4.1 26.3 - - - +
78F LEU* 4.1 6.5 - - - -
93F LEU* 5.8 7.5 - - - +
94F ASN* 1.3 87.5 + - - +
96F PHE* 1.3 59.2 + - - +
151F LYS* 5.3 8.2 - - - +
152F VAL* 3.5 32.1 + - + +
153F LYS* 4.4 8.0 + - - +
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Residues in contact with PHE 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E VAL* 3.4 44.2 - - + -
63E THR* 3.7 21.8 - - + -
68E LEU* 6.1 0.2 - - + -
104E PHE* 4.3 14.4 - + - -
105E TYR 3.3 13.2 - - - +
106E ILE* 4.3 14.1 - - + -
75F THR* 3.5 3.5 - - - -
76F GLN* 2.8 62.7 + - + -
77F PRO* 3.5 12.3 - - + -
78F LEU* 4.1 13.0 - - + -
95F ARG* 1.3 74.1 - - - +
97F CYS* 1.3 75.0 + - - +
98F TYR* 3.8 22.7 - + + -
152F VAL* 5.1 0.9 - - - -
155F CYS* 4.6 0.7 - - - -
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Residues in contact with CYS 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E PHE* 3.2 7.3 - - - +
105E TYR* 2.8 34.2 + - + -
74F LYS 3.6 0.7 - - - -
96F PHE* 1.3 80.3 - - - +
98F TYR* 1.3 62.1 + - - +
123F CYS* 3.6 20.6 - - - +
125F PRO* 3.6 27.1 - - - -
152F VAL* 3.8 11.2 - - - -
155F CYS* 2.0 50.9 - - + -
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Residues in contact with TYR 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E TYR 3.9 22.0 - - - -
68E LEU* 3.7 8.9 - - + -
69E LYS* 2.8 31.3 + - + +
102E ASN* 2.6 38.7 + - + -
103E SER 3.5 6.5 - - - -
104E PHE* 3.3 29.2 - + + -
72F TRP* 3.4 32.3 - + - -
74F LYS* 3.0 29.7 + - - +
76F GLN* 4.4 15.9 + - + +
96F PHE* 3.8 19.2 + + + -
97F CYS* 1.3 75.4 - - - +
99F GLY* 1.3 66.4 + - - +
123F CYS* 3.5 3.6 - - - -
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Residues in contact with GLY 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E CYS 3.7 0.2 - - - +
102E ASN* 3.3 6.2 - - - +
103E SER* 3.0 33.1 + - - -
72F TRP* 3.2 22.4 - - - -
73F CYS* 3.7 5.4 - - - -
98F TYR* 1.3 76.1 - - - +
100F GLN* 1.3 64.0 + - - +
101F CYS* 4.0 0.9 - - - -
123F CYS* 3.5 12.2 - - - -
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Residues in contact with GLN 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E LYS* 3.4 28.5 + - - +
70E SER 3.0 33.0 + - - +
71E ASP* 3.5 6.7 - - - +
72E TRP* 4.7 3.5 + - - -
100E GLN* 4.0 29.7 - - + +
101E CYS 3.4 5.2 - - - -
102E ASN* 3.2 31.1 + - - +
71F ASP* 3.8 4.3 - - - -
72F TRP* 2.9 58.0 + - + +
99F GLY* 1.3 70.7 - - - +
101F CYS* 1.3 59.8 + - - +
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Residues in contact with CYS 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E GLN* 3.3 17.4 - - - -
101E CYS* 3.4 13.2 + - - +
103E SER* 5.1 2.0 - - - -
71F ASP* 3.6 1.6 - - - +
72F TRP 4.5 0.2 - - - -
99F GLY 4.7 0.7 - - - -
100F GLN* 1.3 76.3 - - - +
102F ASN* 1.3 65.0 - - - +
103F SER* 3.7 3.5 + - - -
121F ALA* 3.6 24.4 - - + +
122F PHE* 4.0 3.1 - - - +
123F CYS* 3.8 25.8 - - - -
157F CYS* 2.0 55.9 - - + -
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Residues in contact with ASN 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E TYR* 2.5 32.7 + - + -
99E GLY 3.4 3.6 - - - -
100E GLN* 2.9 19.6 + - - +
68F LEU* 5.4 6.7 - - - +
69F LYS 2.9 19.2 + - - -
70F SER* 4.8 0.2 - - - +
71F ASP* 2.8 33.5 + - - +
101F CYS* 1.3 74.5 - - - +
103F SER* 1.3 59.8 + - - +
104F PHE* 4.1 14.1 - - + -
119F SER* 4.5 1.6 + - - -
121F ALA* 3.3 18.4 - - - +
159F SER* 5.1 2.4 - - - -
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Residues in contact with SER 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E TYR* 3.3 7.8 - - - -
99E GLY 2.9 34.1 + - - -
101E CYS* 5.2 2.2 - - - -
121E ALA 4.5 5.2 - - - -
122E PHE* 3.4 6.2 - - - -
123E CYS* 3.2 29.7 + - - +
101F CYS 4.3 4.3 - - - -
102F ASN* 1.3 79.5 - - - +
104F PHE* 1.3 63.5 + - - +
118F GLN* 3.9 1.0 + - - -
119F SER* 2.8 31.8 + - - -
121F ALA* 4.8 1.6 - - - -
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Residues in contact with PHE 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E PHE* 4.4 13.5 - + + -
97E CYS 3.3 6.3 - - - +
98E TYR* 3.2 46.4 - + + -
123E CYS 4.3 1.3 - - - -
62F VAL* 5.6 4.5 - - + -
63F THR* 5.8 2.2 - - + -
68F LEU* 4.1 27.1 - - + -
102F ASN* 4.1 16.6 - - + -
103F SER* 1.3 74.1 + - - +
105F TYR* 1.3 62.4 + - - +
106F ILE* 5.1 7.4 - - + -
117F PHE* 3.7 17.7 - + + +
118F GLN* 3.3 10.2 + - - -
119F SER* 2.9 40.7 + - - +
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Residues in contact with TYR 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E PHE* 3.0 9.8 - - - +
97E CYS* 2.8 54.3 + - + +
123E CYS 4.0 2.2 - - - +
125E PRO* 3.9 24.1 - - + +
128E VAL* 6.0 1.7 - - - +
150E GLN* 4.5 11.8 + - - -
152E VAL* 3.7 29.6 - - + +
104F PHE* 1.3 73.5 - - - +
106F ILE* 1.3 62.1 + - - +
107F PRO* 3.8 17.8 - - + +
108F ARG 4.8 0.5 + - - -
116F SER* 3.6 34.9 + - - -
117F PHE 3.2 13.0 - - - -
118F GLN* 3.3 29.8 - - + +
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Residues in contact with ILE 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E LEU* 4.3 6.3 - - + -
96E PHE* 4.1 11.7 - - + -
60F LEU* 4.0 23.1 - - + -
62F VAL* 3.7 32.5 - - + -
104F PHE* 5.1 7.4 - - + -
105F TYR* 1.3 79.1 - - - +
107F PRO* 1.3 82.1 - - + +
110F VAL* 4.4 2.5 - - + -
114F GLU* 5.5 0.7 - - - +
116F SER* 3.4 3.6 - - - -
117F PHE* 3.0 52.8 + - + -
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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
------------------------------------------------------------
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