Contacts of the helix formed by residues 104 - 114 (chain U) in PDB entry 5L4K
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 104 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456P GLN* 4.3 2.1 + - - +
60U GLU* 3.4 27.6 - - + +
65U ASP* 2.9 36.9 + - + +
68U TRP* 3.7 30.7 - - - +
102U HIS* 3.0 5.6 + - + +
103U LYS* 1.3 79.2 - - - +
105U ASP* 1.3 67.1 + - - +
107U ALA* 2.9 23.3 + - - +
108U ILE* 3.5 23.0 + - - +
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Residues in contact with ASP 105 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60U GLU* 5.3 0.7 - - - +
94U TRP* 4.2 2.4 - - + -
96U HIS* 3.8 25.8 + - - -
101U LEU* 3.5 20.5 - - + +
102U HIS* 2.9 42.8 + - - +
103U LYS 3.0 0.2 + - - -
104U ASN* 1.3 77.6 - - - +
106U ILE* 1.3 65.8 + - - +
108U ILE* 2.9 22.1 + - - +
109U ASN* 2.9 11.1 + - - +
121U LEU* 3.8 18.3 - - + +
123U ILE* 4.7 0.2 - - - +
155U PHE* 4.0 16.8 - - + -
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Residues in contact with ILE 106 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103U LYS* 3.6 17.4 + - + +
105U ASP* 1.3 77.5 - - - +
107U ALA* 1.3 69.9 + - + +
109U ASN* 2.9 18.2 + - + +
110U GLU* 3.4 15.8 + - + +
140U SER* 3.7 18.2 - - - +
153U LYS* 3.4 46.2 - - + +
154U THR 4.6 0.9 - - - +
155U PHE* 3.7 26.5 - - + -
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Residues in contact with ALA 107 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65U ASP 5.7 0.2 - - - +
68U TRP* 4.1 27.5 - - + -
104U ASN* 2.9 24.5 + - - +
106U ILE* 1.3 82.4 - - + +
108U ILE* 1.3 65.7 + - - +
110U GLU* 2.9 19.3 + - - +
111U LEU* 3.6 10.2 + - - +
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Residues in contact with ILE 108 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36U VAL* 4.4 4.9 - - + -
58U PHE* 3.4 31.6 - - + -
60U GLU* 4.9 0.9 - - - +
68U TRP* 3.7 21.3 - - + +
70U LEU* 5.5 5.6 - - + -
94U TRP* 3.3 45.8 - - + -
96U HIS* 4.6 7.0 - - + +
104U ASN* 3.5 21.9 + - - +
105U ASP* 2.9 11.9 + - - +
107U ALA* 1.3 78.0 - - - +
109U ASN* 1.3 59.9 + - - +
110U GLU 2.8 6.6 + - - -
111U LEU* 2.9 17.4 + - + +
112U MET* 3.1 21.7 + - + +
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Residues in contact with ASN 109 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94U TRP* 3.8 27.9 - - + +
105U ASP 2.9 9.9 + - - +
106U ILE* 2.9 20.1 + - + +
108U ILE* 1.3 74.7 - - - +
110U GLU* 1.3 61.8 + - - +
112U MET* 4.1 2.2 - - - +
113U LYS* 3.2 29.5 + - - +
119U SER* 3.9 20.1 + - - -
121U LEU* 3.8 11.9 - - - +
140U SER* 3.1 36.4 + - - +
155U PHE* 4.2 6.5 - - + -
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Residues in contact with GLU 110 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106U ILE* 3.7 20.2 - - + +
107U ALA* 2.9 8.5 + - - +
109U ASN* 1.3 90.2 - - - +
111U LEU* 1.3 66.6 + - + +
112U MET 3.3 1.6 - - - -
113U LYS* 3.3 26.9 - - - +
114U ARG* 3.6 23.7 + - - +
140U SER* 4.0 9.2 + - - -
153U LYS* 3.9 28.0 + - - -
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Residues in contact with LEU 111 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68U TRP* 3.5 42.2 - - + +
70U LEU* 5.3 20.4 - - + +
72U HIS* 5.0 9.2 - - + +
107U ALA 4.2 7.2 - - - +
108U ILE* 2.9 8.7 + - + +
110U GLU* 1.3 81.4 - - + +
112U MET* 1.3 63.5 + - + +
113U LYS 3.5 0.2 - - - -
114U ARG* 4.0 36.9 + - - +
115U TYR* 4.2 12.3 - - - -
59W GLU* 4.7 20.0 - - + +
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Residues in contact with MET 112 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36U VAL* 4.1 21.1 - - + -
37U GLY 4.4 4.3 - - - +
38U VAL* 4.6 13.9 - - + +
56U VAL* 5.1 1.6 - - + -
70U LEU* 4.1 20.0 - - + -
75U LEU* 3.7 31.2 - - + -
91U ILE* 5.4 5.8 - - + +
93U GLY 5.4 1.1 - - - +
94U TRP* 3.7 51.8 - - + +
108U ILE* 3.1 17.1 + - + +
109U ASN 4.4 1.8 - - - +
111U LEU* 1.3 78.4 - - + +
113U LYS* 1.3 61.7 + - - +
114U ARG 3.2 2.2 - - - -
115U TYR* 3.3 25.6 + - - +
116U CYS 3.9 2.6 + - - -
119U SER* 4.0 8.0 + - - +
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Residues in contact with LYS 113 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109U ASN* 3.2 31.8 + - - +
110U GLU* 3.3 29.1 + - - +
111U LEU 3.5 0.6 - - - -
112U MET* 1.3 72.7 - - - +
114U ARG* 1.3 56.8 + - - +
115U TYR 2.8 14.1 + - - -
116U CYS 3.4 24.0 + - - +
117U PRO* 4.2 11.0 - - + +
118U ASN* 3.8 23.4 - - - +
119U SER* 4.1 15.8 + - - +
139U ILE* 5.9 1.0 - - - +
140U SER* 4.4 15.6 + - - -
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Residues in contact with ARG 114 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72U HIS* 3.2 52.5 + - - +
76U GLU* 5.1 1.5 + - - -
110U GLU 3.6 14.0 + - - +
111U LEU* 4.0 33.9 + - - +
112U MET 3.2 0.8 - - - -
113U LYS* 1.3 75.8 - - - +
115U TYR* 1.3 73.3 + - + +
59W GLU* 5.8 2.4 + - - -
60W VAL 5.7 1.2 + - - -
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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