Contacts of the helix formed by residues 96 - 105 (chain B) in PDB entry 4EMX
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 PRO 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ASP* 3.9 14.8 - - + +
75A CYS* 3.5 41.1 - - + +
76A THR* 3.8 2.2 - - - +
79A THR* 5.1 5.2 - - + +
91A CYS* 5.4 7.9 - - + +
98A ARG* 5.6 2.2 - - - +
67B HIS* 5.3 8.1 - - + -
95B GLU* 1.3 91.8 - - + +
97B GLU* 1.3 60.5 + - - +
98B ARG 3.4 1.8 - - - -
99B ASN* 3.5 5.8 + - + +
100B GLU* 2.9 37.1 + - - +
247B HIS* 6.3 1.6 - - + +
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A LEU 4.4 1.2 - - - +
72A ASP* 3.3 18.8 - - + +
73A LYS* 2.8 63.8 + - - +
76A THR* 4.0 11.6 - - + +
93B LYS* 4.1 22.5 - - + +
94B GLN 3.2 11.3 + - - +
96B PRO* 1.3 79.8 - - - +
98B ARG* 1.3 52.7 + - - +
100B GLU* 3.1 7.1 + - - +
101B CYS* 2.8 35.3 + - - +
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Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B HIS 3.4 1.0 + - - -
68B THR* 3.2 20.2 + - - +
71B GLY* 3.4 20.3 + - - -
72B ASP* 2.8 32.5 + - - +
75B CYS* 3.9 19.5 - - - +
90B CYS* 2.8 28.4 - - - +
91B CYS* 4.0 6.3 + - - +
93B LYS* 3.7 23.3 + - - +
94B GLN 3.1 7.4 + - - +
95B GLU* 2.8 35.8 + - - +
96B PRO 3.4 0.2 - - - -
97B GLU* 1.3 69.7 - - - +
99B ASN* 1.3 67.9 + - - +
101B CYS* 3.1 6.6 + - - +
102B PHE* 3.0 41.6 + - + -
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Residues in contact with ASN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B TYR* 3.0 29.8 + - - -
67B HIS* 3.2 43.2 + - + +
95B GLU* 3.0 25.1 + - - +
96B PRO* 3.8 6.1 - - + +
97B GLU 3.5 0.2 - - - -
98B ARG* 1.3 78.3 - - - +
100B GLU* 1.3 63.3 + - - +
102B PHE* 3.5 8.1 + - - +
103B LEU* 3.0 30.8 + - - +
247B HIS* 3.2 21.4 + - - -
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LYS* 5.6 3.8 - - - +
68A THR* 6.1 1.1 - - + -
72A ASP* 4.0 23.6 - - - +
94A GLN* 4.7 7.2 - - - +
96B PRO* 2.9 23.4 + - - +
97B GLU* 3.1 8.3 + - + +
99B ASN* 1.3 79.1 + - - +
101B CYS* 1.3 60.5 + - - +
103B LEU* 3.4 15.1 + - - +
104B GLN* 3.2 34.5 + - + +
247B HIS* 3.1 33.7 + - - -
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Residues in contact with CYS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLU* 5.7 1.1 - - - -
89B ASP* 4.1 6.5 - - - -
90B CYS* 2.1 57.6 - - + -
93B LYS* 3.5 25.1 - - + +
97B GLU 2.8 16.4 + - - +
98B ARG 3.4 7.0 - - - +
100B GLU* 1.3 68.3 - - - +
102B PHE* 1.3 62.1 + - - +
104B GLN* 3.0 23.1 + - - +
105B HIS* 3.3 29.7 + - - -
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Residues in contact with PHE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B TYR* 3.7 48.6 - + + +
31B LEU* 4.9 2.9 - - + -
71B GLY* 4.5 10.5 - - - -
74B LEU* 4.2 21.8 - - + -
75B CYS* 3.7 25.1 - - - -
78B ALA* 4.7 8.5 - - + -
87B MET* 4.1 16.6 - - - -
90B CYS* 3.3 20.3 - - + -
91B CYS* 4.2 0.4 - - - -
98B ARG* 3.0 55.8 + - + -
99B ASN* 3.8 9.4 - - - +
101B CYS* 1.3 66.5 - - - +
103B LEU* 1.3 67.5 + - - +
104B GLN 3.1 0.7 + - - -
105B HIS* 3.3 14.0 + - - +
106B LYS* 3.7 10.4 + - - +
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B TYR* 3.1 35.0 - - + +
99B ASN* 3.0 24.3 + - - +
100B GLU* 3.4 19.9 + - - +
102B PHE* 1.3 73.9 - - - +
104B GLN* 1.3 60.1 + - + +
105B HIS 3.5 0.5 + - - -
106B LYS* 3.5 32.2 + - + +
148B TYR* 4.2 6.5 + - + -
204B GLN* 5.4 10.5 + - - +
246B CYS 4.5 2.7 - - - +
247B HIS* 3.3 62.6 - - + +
248B GLY* 4.2 0.9 - - - +
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Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLU* 4.6 14.4 - - - +
61A ASN* 3.0 17.9 + - - +
64A LYS* 2.5 31.4 - - - +
100B GLU* 3.2 26.4 + - + +
101B CYS* 3.0 16.5 + - - +
103B LEU* 1.3 77.0 - - + +
105B HIS* 1.3 66.4 + - - +
106B LYS 3.3 6.9 + - - +
148B TYR* 5.9 0.2 - - - -
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Residues in contact with HIS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLU* 3.7 28.5 - - - -
30B TYR 6.1 0.4 - - - -
32B GLN* 3.9 3.3 - - - +
86B GLU* 3.3 51.0 + - + +
87B MET* 3.7 37.6 - - + +
89B ASP* 4.2 1.0 + - - -
90B CYS* 4.6 0.9 - - - -
101B CYS* 3.3 26.2 + - - +
102B PHE 3.3 4.4 + - - +
103B LEU 3.3 0.6 - - - -
104B GLN* 1.3 88.1 + - + +
106B LYS* 1.3 64.5 + - - +
107B ASP* 3.1 9.5 + - - +
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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