Contacts of the helix formed by residues 99 - 107 (chain B) in PDB entry 3EKR
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 THR 99 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS* 5.8 0.4 - - - +
199A GLU* 4.6 21.5 - - - +
201A ARG* 5.0 7.3 + - - +
98B MET* 1.3 75.0 - - - +
100B LYS* 1.3 65.9 + - - +
101B ALA* 3.5 8.2 + - - +
102B ASP* 3.0 33.8 + - - +
103B LEU* 2.9 20.8 + - - +
154B HIS* 3.7 32.9 - - + +
155B ASN 5.2 0.2 - - - +
157B ASP* 3.3 20.2 - - + +
160B TYR* 4.4 1.1 - - - -
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Residues in contact with LYS 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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16B GLU* 6.1 2.4 - - - +
18B GLU* 2.7 31.8 + - - -
99B THR* 1.3 73.6 - - - +
101B ALA* 1.3 62.1 + - - +
103B LEU* 3.3 7.7 + - - +
104B ILE* 3.1 43.2 + - + +
157B ASP* 3.2 7.7 + - - +
160B TYR* 3.5 46.8 - - + +
172B VAL* 4.4 14.8 - - + -
173B ARG* 6.2 1.1 - - - +
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Residues in contact with ALA 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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195A THR* 6.0 1.6 - - - +
99B THR* 3.1 8.0 + - - +
100B LYS* 1.3 75.1 - - - +
102B ASP* 1.3 64.0 + - - +
104B ILE* 4.0 6.7 - - - +
105B ASN* 2.8 48.9 + - - +
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Residues in contact with ASP 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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201A ARG* 4.8 12.2 + - - -
97B GLY 4.5 1.7 - - - +
98B MET* 3.7 18.2 - - + +
99B THR* 3.0 47.1 + - - +
101B ALA* 1.3 78.1 - - - +
103B LEU* 1.3 57.2 + - - +
105B ASN* 4.6 2.0 + - - +
106B ASN* 2.7 57.1 + - - +
154B HIS* 4.3 7.6 + - - -
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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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98B MET* 3.6 29.8 - - + +
99B THR 2.9 10.9 + - - +
100B LYS* 3.3 10.1 - - - +
102B ASP* 1.3 77.3 - - - +
104B ILE* 1.3 59.6 + - + +
107B LEU* 2.9 42.0 + - + +
150B VAL* 4.9 0.9 - - + -
152B THR* 3.9 15.7 - - + -
160B TYR* 3.8 29.4 - - + -
162B TRP* 3.8 45.4 - - + +
170B PHE* 5.3 0.2 - - - -
172B VAL* 3.9 17.5 - - + -
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Residues in contact with ILE 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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20B PHE* 3.3 53.2 - - + -
100B LYS* 3.1 40.8 + - + +
101B ALA* 4.0 4.9 - - - +
103B LEU* 1.3 76.5 - - - +
105B ASN* 1.3 61.4 - - - +
108B GLY 4.0 1.6 + - - -
109B THR* 2.6 48.8 + - + +
170B PHE* 4.2 6.6 - - - -
172B VAL* 4.2 12.6 - - + -
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Residues in contact with ASN 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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101B ALA* 2.8 40.9 + - - +
102B ASP* 4.1 2.3 + - - +
104B ILE* 1.3 78.5 - - - +
106B ASN* 1.3 68.9 + - - +
108B GLY 4.4 0.2 + - - -
109B THR* 3.6 7.9 + - - -
110B ILE* 3.1 57.3 + - + +
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Residues in contact with ASN 106 (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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102B ASP* 2.7 42.8 + - - +
105B ASN* 1.3 83.1 - - - +
107B LEU* 1.3 60.3 + - - +
108B GLY 3.6 1.9 + - - -
110B ILE* 5.2 7.5 - - - +
139B TYR* 4.5 3.3 + - - -
901B PY9 3.6 39.1 - - + +
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Residues in contact with LEU 107 (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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22B PHE* 3.9 0.9 - - - -
98B MET* 4.3 20.2 - - + -
103B LEU* 2.9 37.7 + - + +
104B ILE 4.4 0.4 - - - -
106B ASN* 1.3 85.3 - - - +
108B GLY* 1.3 54.9 + - - +
138B PHE* 3.6 47.8 - - + -
139B TYR* 3.3 12.8 + - + +
150B VAL* 4.3 8.5 - - + -
162B TRP* 2.9 51.5 + - + +
170B PHE* 4.0 2.0 - - - -
901B PY9 4.5 13.5 - - + -
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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