Contacts of the strand formed by residues 79 - 87 (chain E) in PDB entry 4IHB
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 ARG 79 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14E THR* 4.1 3.4 - - - +
16E ASP* 2.8 40.4 + - - +
70E LYS* 3.1 5.1 - - - -
71E ASP* 2.6 50.6 + - + +
73E GLU* 2.2 34.6 + - + +
77E ARG* 3.6 41.8 + - - +
78E ASN* 1.3 70.7 - - - +
80E PHE* 1.3 73.6 + - - +
81E LEU* 3.6 11.8 - - + +
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Residues in contact with PHE 80 (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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108B THR* 5.9 0.9 - - - +
109B LYS* 3.4 33.2 - - + +
68E VAL* 3.6 30.7 - - + -
70E LYS* 4.1 12.5 - - + +
78E ASN 3.8 3.6 + - - -
79E ARG* 1.3 77.0 - - - +
81E LEU* 1.3 67.9 + - - +
82E GLY* 3.7 20.9 - - - -
83E GLU* 3.5 40.4 - - + -
106E LEU 3.8 6.5 - - - -
107E ASP* 4.0 4.9 - - + -
108E THR* 4.0 28.9 - - + -
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Residues in contact with LEU 81 (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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12E VAL* 3.6 27.4 - - + -
13E HIS 3.9 5.2 - - - +
14E THR* 3.5 31.0 - - + -
20E SER* 4.2 13.0 - - - +
22E ALA* 4.6 1.3 - - + -
69E VAL* 2.8 21.8 + - + +
70E LYS 4.0 4.0 - - - +
71E ASP* 3.5 33.0 - - + +
79E ARG* 3.8 8.7 - - + +
80E PHE* 1.3 86.9 - - - +
82E GLY* 1.3 60.3 + - - +
105E LEU* 5.6 1.8 - - + -
107E ASP* 5.0 1.0 - - - +
113E THR* 3.5 19.1 - - - +
205E FMT 4.3 14.8 + - - +
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Residues in contact with GLY 82 (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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68E VAL* 3.5 3.3 - - - +
69E VAL* 2.7 35.2 + - - +
80E PHE* 3.7 8.5 - - - -
81E LEU* 1.3 82.5 - - - +
83E GLU* 1.3 60.1 + - - -
105E LEU* 4.0 22.2 - - - -
106E LEU 3.3 12.3 - - - -
113E THR* 4.4 0.2 - - - -
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Residues in contact with GLU 83 (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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66E HIS* 2.5 38.1 + - - +
67E VAL 3.2 11.7 - - - +
68E VAL* 4.1 2.9 - - + +
80E PHE* 3.5 28.7 - - + -
82E GLY* 1.3 75.5 - - - +
84E ALA* 1.3 63.7 + - - +
85E LYS* 5.2 4.6 - - + -
104E PRO 4.3 0.2 - - - +
105E LEU* 3.7 4.5 - - - -
106E LEU* 2.9 46.8 + - + +
107E ASP 4.3 6.2 - - - +
108E THR* 5.1 2.8 - - - -
110E LYS* 3.7 23.1 + - - -
206E FMT 4.6 0.2 + - - -
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Residues in contact with ALA 84 (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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65E LEU 3.8 1.6 - - - +
66E HIS* 3.6 3.8 - - - -
67E VAL* 2.8 40.4 + - + +
83E GLU* 1.3 76.7 - - - +
85E LYS* 1.3 64.0 + - - +
86E VAL* 4.1 3.6 - - + -
103E ALA* 4.1 16.6 - - + -
104E PRO 4.5 0.9 - - - +
105E LEU* 4.0 16.4 - - + -
117E LEU* 5.0 4.5 - - + -
119E LEU* 6.0 0.7 - - + -
206E FMT 3.6 18.2 - - - +
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Residues in contact with LYS 85 (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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64E GLU* 3.8 33.1 + - + +
65E LEU 3.7 3.4 - - - +
66E HIS* 3.8 37.5 - - + -
83E GLU* 5.2 4.9 - - + -
84E ALA* 1.3 72.0 - - - +
86E VAL* 1.3 63.1 + - - +
87E PRO* 3.5 9.1 - - - +
110E LYS* 5.2 12.2 - - - +
206E FMT 3.0 25.9 + - - +
60F ASP* 5.4 4.9 - - - +
61F GLN* 5.4 3.3 - - - +
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Residues in contact with VAL 86 (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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64E GLU* 3.3 4.3 - - - -
65E LEU* 3.0 42.3 + - + +
67E VAL* 6.2 1.8 - - + -
84E ALA* 4.1 3.3 - - + -
85E LYS* 1.3 75.9 - - - +
87E PRO* 1.3 69.2 - - - +
88E LEU* 3.4 14.4 + - + +
101E PHE* 3.5 59.9 - - + -
103E ALA* 5.1 8.5 - - + -
119E LEU* 4.4 16.8 - - + -
121E VAL* 4.8 6.3 - - + -
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Residues in contact with PRO 87 (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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63E SER 3.9 0.9 - - - +
64E GLU* 3.7 21.5 - - + +
85E LYS 3.5 9.4 - - - +
86E VAL* 1.3 90.1 - - + +
88E LEU* 1.3 63.4 + - - +
89E ARG* 3.0 37.7 - - - +
90E GLU* 3.2 47.7 + - + +
91E VAL 4.2 0.7 + - - -
101E PHE* 4.5 0.6 - - + -
61F GLN* 4.8 15.5 - - + +
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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