Contacts of the helix formed by residues 90 - 107 (chain E) in PDB entry 2HAK
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 ASN 90 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88E GLN 4.4 0.8 + - - -
89E LEU* 1.3 77.6 - - - +
91E PRO* 1.4 77.3 - - + +
92E THR* 3.0 28.6 + - - -
93E SER* 3.3 20.6 + - - -
94E LEU* 3.2 15.1 + - - +
268F ARG* 5.9 2.2 - - - +
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Residues in contact with PRO 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E LEU 4.5 1.3 - - - +
90E ASN* 1.4 84.2 - - + +
92E THR* 1.3 65.9 + - + +
94E LEU* 3.5 14.6 + - + +
95E GLN* 3.2 19.9 + - - +
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Residues in contact with THR 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E ASN* 3.0 19.2 + - - -
91E PRO* 1.3 73.8 - - + +
93E SER* 1.3 54.2 + - - +
95E GLN* 2.8 13.0 + - + +
96E LYS* 2.7 34.9 + - - +
99E ARG* 3.8 6.9 + - - +
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Residues in contact with SER 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E LEU* 4.1 11.6 - - - +
90E ASN* 3.3 36.3 + - - -
92E THR* 1.3 74.0 + - - +
94E LEU* 1.3 66.8 + - - -
96E LYS* 3.0 6.5 + - - +
97E LEU* 2.8 24.3 + - - +
199E GLU* 2.2 41.2 + - - -
200E PHE* 3.7 5.8 - - - -
268F ARG* 5.1 0.9 + - - -
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Residues in contact with LEU 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E LYS* 3.7 26.7 - - + +
89E LEU* 3.4 51.6 - - + +
90E ASN 3.2 11.5 + - - +
91E PRO* 3.5 13.0 - - + +
93E SER* 1.3 76.3 - - - +
95E GLN* 1.3 54.9 + - - +
97E LEU* 3.4 5.0 - - + +
98E PHE* 2.9 59.3 + - + -
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Residues in contact with GLN 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E PRO 3.2 8.8 + - - +
92E THR* 2.8 13.5 + - + +
94E LEU* 1.3 71.2 - - - +
96E LYS* 1.3 60.5 + - - +
98E PHE* 3.9 6.0 - - - +
99E ARG* 2.9 54.6 + - - +
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Residues in contact with LYS 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E THR 2.7 15.4 + - - +
93E SER* 3.4 10.1 - - - +
95E GLN* 1.3 73.7 - - - +
97E LEU* 1.3 62.4 + - - +
99E ARG* 2.8 36.0 + - + +
100E GLU* 3.0 25.1 + - + +
174E ARG* 4.9 7.2 - - - +
197E SER* 2.9 37.5 + - - +
199E GLU* 2.7 31.0 + - - +
200E PHE* 4.3 6.1 - - + -
268F ARG* 4.5 6.1 - - - +
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Residues in contact with LEU 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E ILE* 3.9 40.4 - - + -
86E LYS* 5.2 2.0 - - + -
89E LEU* 4.3 14.8 - - + -
93E SER 2.8 14.2 + - - +
94E LEU* 3.4 11.9 - - + +
96E LYS* 1.3 71.3 - - - +
98E PHE* 1.3 70.2 + - + +
100E GLU* 3.3 9.7 + - + +
101E VAL* 3.0 32.0 + - + +
104E MET* 5.9 0.7 - - + -
125E LEU* 3.6 30.3 - - + -
127E LEU* 5.1 1.8 - - + -
200E PHE* 3.6 28.6 - - + -
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Residues in contact with PHE 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E LYS* 3.9 14.6 - - + -
94E LEU* 2.9 52.1 + - + +
95E GLN* 4.4 5.4 - - - +
97E LEU* 1.3 79.3 - - + +
99E ARG* 1.3 57.3 + - - +
101E VAL* 3.3 14.2 + - + +
102E ARG* 2.9 28.9 + - - +
120E GLU* 3.5 33.0 - - - -
125E LEU* 4.3 18.6 - - + -
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Residues in contact with ARG 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E THR* 3.8 9.3 + - - +
95E GLN* 2.9 55.0 + - - +
96E LYS* 2.8 32.9 + - + +
98E PHE* 1.3 71.4 - - - +
100E GLU* 1.3 61.7 + - + +
102E ARG* 3.3 16.8 + - - +
103E ILE* 3.2 30.1 + - + +
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Residues in contact with GLU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E LYS* 5.3 3.8 + - - -
96E LYS* 3.0 21.1 + - + +
97E LEU* 3.5 12.2 - - + +
99E ARG* 1.3 75.9 - - + +
101E VAL* 1.3 55.6 + - - +
103E ILE* 2.9 20.3 + - + +
104E MET* 3.0 27.4 + - + +
196E PHE* 3.6 44.5 - - + +
197E SER* 3.4 35.4 + - - +
200E PHE* 3.8 28.4 - - - +
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Residues in contact with VAL 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E LEU* 3.0 22.3 + - + +
98E PHE* 3.3 15.2 + - + +
100E GLU* 1.3 71.0 - - - +
102E ARG* 1.3 67.4 + - - +
104E MET* 3.4 15.9 + - + +
105E LYS* 3.0 47.5 + - + +
115E LEU* 5.1 1.3 - - + -
118E VAL* 4.3 16.8 - - + -
125E LEU* 4.1 15.9 - - + -
127E LEU* 3.8 25.1 - - + -
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Residues in contact with ARG 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E PHE 2.9 14.1 + - - +
99E ARG* 3.3 18.7 + - - +
101E VAL* 1.3 79.0 - - - +
103E ILE* 1.3 69.5 + - + +
105E LYS* 3.3 19.6 + - - +
106E ILE* 3.7 16.7 + - + +
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Residues in contact with ILE 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E ARG* 3.2 19.6 + - + +
100E GLU* 2.9 9.1 + - + +
102E ARG* 1.3 80.0 - - + +
104E MET* 1.3 69.1 + - - +
106E ILE* 2.8 29.9 + - + +
107E LEU* 3.4 11.2 + - + +
170E TYR* 3.6 59.9 - - + -
171E ILE 5.3 1.6 - - - +
173E HIS* 6.3 1.3 - - + +
196E PHE* 3.7 26.7 - - + -
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Residues in contact with MET 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E LYS* 5.4 6.1 - - - +
97E LEU* 5.9 1.3 - - + -
100E GLU* 3.0 27.3 + - + +
101E VAL* 3.5 20.9 - - + +
103E ILE* 1.3 75.7 - - - +
105E LYS* 1.3 64.1 + - - +
106E ILE 3.0 0.9 + - - -
107E LEU* 3.2 25.7 + - + +
113E VAL* 6.4 0.7 - - - -
114E LYS* 5.2 0.2 + - - -
115E LEU* 4.0 36.4 + - + +
127E LEU* 3.5 31.4 - - + -
129E MET* 5.0 15.3 - - - +
193E ASP* 5.2 6.5 - - - +
196E PHE* 4.1 17.5 - - + -
351E TYR* 4.5 0.5 + - - -
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Residues in contact with LYS 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E VAL* 3.0 39.0 + - - +
102E ARG* 3.7 13.5 - - - +
103E ILE 3.1 0.8 - - - -
104E MET* 1.3 75.9 - - - +
106E ILE* 1.3 64.0 + - + +
107E LEU 3.7 0.5 + - - -
114E LYS* 4.4 1.9 + - - -
115E LEU* 3.6 12.8 - - + -
118E VAL* 4.4 15.1 - - - +
349E GLN* 4.4 11.0 + - + +
350E LYS 5.4 2.6 + - - -
351E TYR* 2.6 54.8 + - + +
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Residues in contact with ILE 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E ARG* 3.8 20.2 - - + +
103E ILE* 2.8 25.9 + - + +
105E LYS* 1.3 84.3 - - + +
107E LEU* 1.3 65.5 + - + +
108E ASN* 3.2 8.1 + - - +
165E TYR* 3.5 7.6 + - - -
169E LYS* 3.6 49.1 + - + +
170E TYR* 5.0 4.3 - - + -
318E GLU* 4.0 1.4 - - - +
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Residues in contact with LEU 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E ILE* 3.4 31.6 - - + +
104E MET* 3.2 17.9 + - + +
105E LYS 3.5 0.9 - - - -
106E ILE* 1.3 79.3 - - + +
108E ASN* 1.3 56.6 + - - +
109E HIS 3.9 3.0 + - - -
112E ILE* 4.0 28.7 - - + +
113E VAL 4.8 3.5 - - - +
114E LYS* 4.4 20.9 + - - +
165E TYR* 3.7 20.9 - - + -
166E CYS* 4.6 7.2 - - - -
169E LYS* 4.1 11.4 - - + -
170E TYR* 3.5 36.3 - - + +
193E ASP 6.3 1.3 - - - +
196E PHE* 5.3 3.8 - - + -
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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
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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