Contacts of the helix formed by residues 98 - 107 (chain E) in PDB entry 3KZ1
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 98 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13E ASP* 5.3 2.9 - - - +
62E GLY 5.5 2.2 - - - -
64E GLU* 4.1 15.8 - - + +
67E ASP* 2.8 34.6 + - - -
70E ARG* 3.7 6.2 - - - +
94E ASN* 2.9 23.9 + - - +
97E GLU* 1.3 79.6 - - + +
99E TRP* 1.3 100.6 + - + +
101E PRO* 3.3 6.6 - - - +
102E GLU* 3.3 32.5 + - - +
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Residues in contact with TRP 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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11E VAL* 4.1 15.7 - - + -
12E GLY* 3.2 41.7 - - - -
13E ASP* 2.8 33.4 + - - +
61E ALA 4.4 2.2 - - - -
62E GLY 4.2 9.9 - - - -
70E ARG* 3.3 49.1 - - - -
74E TYR* 5.1 0.9 - - - -
82E MET* 4.0 19.5 - - + -
83E CYS 5.0 0.2 - - - -
91E SER 5.1 0.4 - - - -
94E ASN* 3.1 29.9 + - + +
95E ILE* 3.9 15.0 - - + +
98E LYS* 1.3 94.0 - - + +
100E THR* 1.3 60.9 + - - +
102E GLU* 3.1 11.3 + - - +
103E VAL* 2.8 37.1 + - + +
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Residues in contact with THR 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 MET* 3.4 24.8 - - + +
95E ILE 2.6 28.9 + - - -
96E PRO* 4.3 3.4 - - - -
99E TRP* 1.3 69.2 - - - +
101E PRO* 1.3 71.9 - - - +
103E VAL* 4.5 0.2 - - - -
104E LYS* 2.9 52.4 + - + +
112E ILE* 5.5 2.2 - - + -
151E ILE* 3.6 36.9 - - + +
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Residues in contact with PRO 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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96E PRO 3.4 25.1 - - - +
97E GLU 3.9 11.7 - - - +
98E LYS 3.3 16.2 - - - +
100E THR* 1.3 89.6 - - - +
102E GLU* 1.3 62.1 + - - +
104E LYS* 3.3 8.0 + - + +
105E HIS* 2.9 26.0 + - - +
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Residues in contact with GLU 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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67E ASP* 5.2 3.6 - - - +
70E ARG* 3.4 32.7 + - - +
71E PRO* 5.1 2.9 - - - +
74E TYR* 2.8 30.0 + - - +
98E LYS* 3.3 28.9 + - - +
99E TRP* 3.1 10.7 + - + +
101E PRO* 1.3 78.7 - - - +
103E VAL* 1.3 65.0 + - + +
105E HIS* 3.1 6.0 + - - +
106E PHE* 3.0 48.7 + - + +
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Residues in contact with VAL 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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11E VAL* 4.0 19.5 - - + -
74E TYR* 4.5 15.7 - - + +
80E ILE* 3.3 33.0 - - + -
82E MET* 3.5 26.5 - - + -
99E TRP* 2.8 21.7 + - + +
100E THR 3.9 1.8 - - - +
102E GLU* 1.3 76.7 - - + +
104E LYS* 1.3 55.8 + - - +
106E PHE* 5.2 0.2 - - - -
107E CYS* 2.6 40.4 + - + +
110E VAL 5.5 0.4 - - - +
112E ILE* 4.1 17.9 - - + -
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Residues in contact with LYS 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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100E THR* 2.9 41.5 + - + +
101E PRO* 3.9 5.6 - - - +
103E VAL* 1.3 75.4 - - - +
105E HIS* 1.3 58.8 + - - +
107E CYS 4.4 6.1 - - - -
108E PRO* 3.8 20.5 - - + +
112E ILE* 4.8 14.4 - - + -
151E ILE 4.8 9.5 + - - +
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Residues in contact with HIS 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 PRO 2.9 17.0 + - - +
102E GLU* 3.1 6.2 + - - +
104E LYS* 1.3 77.0 - - - +
106E PHE* 1.3 96.1 + + - +
108E PRO* 4.5 5.7 - - - +
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Residues in contact with PHE 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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71E PRO* 3.8 35.4 - - + -
74E TYR* 3.6 36.8 - + + +
75E PRO* 5.6 2.9 - - - +
102E GLU* 3.0 42.3 + - + +
103E VAL 4.3 0.4 - - - +
105E HIS* 1.3 104.4 - + - +
107E CYS* 1.3 65.6 + - - +
108E PRO* 3.4 8.6 - - - +
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Residues in contact with CYS 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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74E TYR* 3.7 48.5 - - - -
75E PRO 5.7 0.9 - - - -
77E THR* 4.0 7.0 - - - -
80E ILE* 3.8 20.4 - - + -
103E VAL* 2.6 25.7 + - - +
104E LYS* 4.4 1.6 - - - -
106E PHE* 1.3 79.1 - - - +
108E PRO* 1.4 69.3 - - - +
109E ASN 3.6 0.2 + - - -
110E VAL* 3.5 27.4 + - + +
112E ILE* 6.0 0.2 - - - +
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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