Contacts of the helix formed by residues 95 - 108 (chain E) in PDB entry 6H7L
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 SER 95 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41E ILE* 4.6 3.1 - - - -
94E LEU* 1.3 76.6 - - - +
96E LYS* 1.3 65.3 + - - +
97E GLY* 4.0 3.1 + - - -
98E GLN* 3.2 29.1 + - - +
99E LEU* 3.1 22.7 + - - +
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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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41E ILE* 4.6 22.7 + - + +
44E GLU* 3.7 32.2 + - - +
45E ILE* 3.8 20.6 - - + +
48E GLU* 2.7 40.0 + - - -
95E SER* 1.3 74.3 - - - +
97E GLY* 1.3 56.6 + - - +
99E LEU* 3.3 6.3 + - - +
100E LYS* 2.9 46.7 + - + +
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Residues in contact with GLY 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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95E SER* 3.4 4.9 + - - -
96E LYS* 1.3 79.0 - - - +
98E GLN* 1.3 59.2 + - - +
100E LYS* 3.8 6.8 + - - +
101E GLU* 3.3 29.0 + - - +
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Residues in contact with GLN 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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94E LEU* 4.1 27.9 - - + +
95E SER* 3.2 26.5 + - - +
96E LYS 3.3 0.6 - - - -
97E GLY* 1.3 72.2 - - - +
99E LEU* 1.3 64.0 + - - +
101E GLU* 3.5 13.8 + - - +
102E PHE* 3.3 20.6 + - - +
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Residues in contact with LEU 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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24E LEU* 4.8 3.1 - - + -
38E ILE* 6.2 0.7 - - + -
41E ILE* 4.5 21.1 - - + -
42E LEU* 4.1 17.7 - - + -
45E ILE* 3.7 25.8 - - + -
78E LEU* 3.7 28.0 - - + -
94E LEU* 4.3 16.3 - - + +
95E SER 3.1 17.7 + - - +
96E LYS* 3.7 5.2 - - - +
98E GLN* 1.3 73.9 - - - +
100E LYS* 1.3 59.4 + - - +
102E PHE* 3.2 14.0 + - + +
103E LEU* 3.0 48.3 + - + +
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Residues in contact with LYS 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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45E ILE* 4.1 16.4 - - + -
48E GLU* 3.5 25.4 + - - +
49E TYR* 3.4 31.1 + - + +
96E LYS* 2.9 33.9 + - + +
97E GLY* 4.1 6.5 - - - +
99E LEU* 1.3 75.0 - - - +
101E GLU* 1.3 54.7 + - + +
103E LEU* 4.6 1.6 - - - -
104E ASP* 2.7 41.5 + - + +
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Residues in contact with GLU 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 GLY 3.3 17.3 + - - +
98E GLN* 3.7 12.7 - - - +
99E LEU 3.3 0.6 - - - -
100E LYS* 1.3 80.3 - - - +
102E PHE* 1.3 56.4 + - - +
104E ASP* 4.7 2.9 - - - -
105E ALA* 3.1 31.2 + - - +
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Residues in contact with PHE 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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24E LEU* 4.4 20.6 - - + -
78E LEU* 4.5 5.6 - - + -
80E LEU* 4.5 8.7 - - + -
88E ALA* 3.8 34.5 - - + -
89E THR 4.2 16.2 - - - -
90E LYS* 4.4 22.0 - - + -
94E LEU* 5.6 4.0 - - + -
98E GLN 3.3 9.8 + - - +
99E LEU* 3.2 19.8 + - + +
101E GLU* 1.3 79.6 - - - +
103E LEU* 1.3 71.2 + - + +
105E ALA* 4.8 0.2 - - - -
106E ASN* 2.9 48.3 + - - +
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Residues in contact with LEU 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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24E LEU* 3.8 28.5 - - + -
45E ILE* 3.5 32.5 - - + -
49E TYR* 4.0 24.2 - - + +
53E LEU* 3.7 25.6 - - + -
80E LEU* 4.6 7.2 - - + -
99E LEU* 3.0 34.1 + - + +
102E PHE* 1.3 84.9 - - + +
104E ASP* 1.3 61.1 + - - +
106E ASN* 4.8 2.0 - - - -
107E LEU* 2.9 37.3 + - - +
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Residues in contact with ASP 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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49E TYR* 3.6 19.5 + - - +
100E LYS* 2.7 25.7 + - + +
101E GLU* 4.5 2.9 - - - +
103E LEU* 1.3 72.9 - - - +
105E ALA* 1.3 60.7 + - - +
107E LEU* 4.8 2.1 - - - +
108E ALA* 3.6 21.9 + - - +
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Residues in contact with ALA 105 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ALA* 3.0 36.7 + - + +
101E GLU 3.1 21.8 + - - +
102E PHE* 4.0 3.1 - - - +
104E ASP* 1.3 79.3 - - - +
106E ASN* 1.3 65.7 + - - +
107E LEU 3.7 0.3 + - - -
108E ALA 3.8 4.5 + - - -
109E GLU 4.3 4.7 + - - -
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Residues in contact with ASN 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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80E LEU* 3.6 21.3 - - + +
82E LYS* 2.7 32.0 + - - +
87E ALA* 4.9 4.7 - - - +
88E ALA* 3.1 30.0 + - - +
102E PHE* 2.9 45.4 + - - +
103E LEU 4.2 0.4 - - - +
105E ALA* 1.3 81.5 - - - +
107E LEU* 1.3 58.1 + - - +
108E ALA 3.5 0.2 - - - -
109E GLU* 3.6 8.2 + - - +
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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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22E ALA* 3.8 23.6 - - + -
49E TYR* 3.7 32.3 - - + -
52E LYS* 3.6 32.5 - - + +
53E LEU* 3.8 20.6 - - + -
80E LEU* 4.9 6.5 - - + -
82E LYS* 4.5 7.4 + - - +
103E LEU* 2.9 21.0 + - - +
104E ASP* 4.8 2.2 - - - +
106E ASN* 1.3 74.1 - - - +
108E ALA* 1.3 56.4 + - - +
109E GLU* 2.9 21.7 + - - +
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Residues in contact with ALA 108 (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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40A ALA 3.0 24.1 + - - +
42A LYS* 3.6 15.3 - - - +
43A VAL* 6.0 1.3 - - + -
104E ASP* 3.6 19.4 + - - +
105E ALA 3.8 0.8 + - - -
106E ASN 3.5 0.8 - - - -
107E LEU* 1.3 73.8 - - - +
109E GLU* 1.3 71.4 + - - +
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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