Contacts of the helix formed by residues 79 - 92 (chain A) in PDB entry 5E6J
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 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A LEU* 4.8 7.9 - - - -
77A ASP* 2.8 28.0 + - - -
78A GLU* 1.3 76.9 - - - +
80A PHE* 1.3 65.4 + - - +
81A LEU 3.3 1.8 - - - -
82A GLY* 3.3 12.0 + - - -
83A ARG* 3.1 22.0 + - - +
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Residues in contact with PHE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A TYR* 3.4 40.4 - + + -
75A THR* 4.0 19.5 - - + -
77A ASP* 3.5 17.3 + - - +
78A GLU 3.2 2.2 - - - -
79A SER* 1.3 77.5 + - - +
81A LEU* 1.3 60.5 + - - +
82A GLY 3.2 0.3 + - - -
83A ARG* 3.2 27.1 + - - +
84A TYR* 2.9 32.7 + - + +
151A LEU* 3.7 12.3 - - + -
154A ALA* 3.4 28.7 - - + +
155A TYR* 3.5 52.3 - + - -
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 5.3 1.6 - - + +
36A TYR* 4.2 8.7 - - + -
57A PHE* 3.9 17.5 - - + -
58A VAL 3.1 44.0 - - - +
59A LEU* 3.7 16.4 - - + -
60A PRO* 6.0 1.6 - - + -
73A TYR* 3.5 28.2 - - + +
78A GLU 4.6 1.4 + - - +
79A SER 3.3 0.4 - - - -
80A PHE* 1.3 81.2 - - - +
82A GLY* 1.3 56.7 + - - +
84A TYR* 3.3 9.7 - - + +
85A MET* 2.8 59.4 + - + +
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Residues in contact with GLY 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A TYR* 3.6 22.6 + - - -
59A LEU* 4.4 6.7 - - - +
79A SER* 3.3 8.6 + - - -
80A PHE 3.1 1.2 - - - -
81A LEU* 1.3 79.1 - - - +
83A ARG* 1.3 55.2 + - - +
85A MET* 3.4 1.7 + - - +
86A SER* 2.8 36.2 + - - -
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Residues in contact with ARG 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASP* 2.7 30.5 + - - +
79A SER* 3.1 23.7 + - - +
80A PHE* 3.2 26.5 + - - +
82A GLY* 1.3 71.7 - - - +
84A TYR* 1.3 61.0 + - - +
86A SER* 3.2 7.3 + - - -
87A ALA* 2.8 33.5 + - - +
154A ALA* 3.2 34.8 + - - +
157A ASN* 3.8 32.0 + - - +
158A LYS 6.2 0.2 - - - +
159A THR* 6.4 2.5 - - - -
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 6.3 1.1 - + - -
72A TYR* 5.5 5.5 + + - -
73A TYR* 3.7 30.7 - + - -
80A PHE* 2.9 20.9 + - + +
81A LEU* 3.3 17.7 - - + +
83A ARG* 1.3 77.5 - - - +
85A MET* 1.3 63.5 + - + +
87A ALA* 3.2 2.4 + - - +
88A LEU* 2.8 40.4 + - + +
132A ALA* 5.8 1.0 - - + +
136A ALA* 5.5 0.2 - - - +
147A ASN* 3.5 25.1 - - - +
150A ALA* 3.6 27.1 - - + -
151A LEU* 3.5 40.5 - - + +
154A ALA* 4.1 8.4 - - + +
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Residues in contact with MET 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A TYR* 3.8 39.5 - - + -
39A GLY* 3.8 31.9 - - - +
57A PHE* 3.8 33.9 - - + -
81A LEU* 2.8 44.6 + - + +
82A GLY 3.9 0.7 - - - +
84A TYR* 1.3 76.6 - - + +
86A SER* 1.3 60.6 + - - +
88A LEU* 3.5 21.3 - - + +
89A ASN* 2.9 33.3 + - - +
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Residues in contact with SER 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A TYR* 5.1 4.0 + - - -
82A GLY 2.8 24.8 + - - -
83A ARG* 3.5 9.1 - - - -
85A MET* 1.3 77.9 - - - +
87A ALA* 1.3 61.3 + - - +
89A ASN* 3.8 7.2 - - - +
90A HIS* 3.3 23.2 + - - -
160A VAL* 4.9 2.3 - - - +
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ARG 2.8 16.4 + - - +
84A TYR 3.6 3.8 - - - +
86A SER* 1.3 75.6 - - - +
88A LEU* 1.3 60.6 + - - +
90A HIS* 2.9 8.8 + - - +
91A THR* 2.9 27.5 + - - +
150A ALA* 3.8 19.1 - - - +
153A LEU* 3.8 29.4 - - + -
154A ALA 5.3 0.4 - - - +
158A LYS 5.7 0.2 - - - +
159A THR* 6.2 0.7 - - - -
160A VAL* 3.8 11.4 - - + +
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Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLY* 5.9 3.1 - - - -
84A TYR* 2.8 35.4 + - + +
85A MET* 3.1 25.5 + - + +
87A ALA* 1.3 76.5 - - - +
89A ASN* 1.3 63.7 + - - +
91A THR* 3.3 12.1 - - - +
92A LYS* 2.9 39.3 + - + +
146A ALA* 4.6 2.9 - - + -
147A ASN* 3.4 32.5 - - - +
150A ALA* 3.6 12.1 - - + +
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Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLY* 5.0 12.5 - - - +
85A MET 2.9 16.5 + - - +
86A SER* 3.8 9.6 + - - +
88A LEU* 1.3 75.0 - - - +
90A HIS* 1.3 71.7 + - - +
92A LYS* 3.3 31.9 + - - +
93A LYS* 3.0 25.8 + - - +
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Residues in contact with HIS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A SER 3.3 17.4 + - - -
87A ALA 2.9 8.0 + - - +
89A ASN* 1.3 93.4 - - - +
91A THR* 1.3 66.4 + - - +
92A LYS 3.1 1.8 - - - -
93A LYS* 3.0 26.9 + - + +
94A TRP* 3.5 11.5 + - - +
109A ASP* 4.6 15.3 - - - +
160A VAL* 3.8 34.5 - - + +
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Residues in contact with THR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA 2.9 17.2 + - - +
88A LEU* 3.3 15.8 + - - +
90A HIS* 1.3 76.1 - - - +
92A LYS* 1.3 63.2 + - - +
93A LYS 3.0 1.9 + - - -
94A TRP* 3.1 43.5 + - + +
96A PHE* 3.6 4.2 - - - -
146A ALA* 2.8 37.3 + - - +
149A CYS* 3.7 14.1 - - + -
150A ALA* 3.7 22.2 - - - +
153A LEU* 4.4 5.8 - - + -
160A VAL* 4.8 0.2 - - + -
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Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASP 5.6 4.2 + - - -
88A LEU* 2.9 26.1 + - + +
89A ASN* 3.3 39.8 + - - +
91A THR* 1.3 78.2 + - - +
93A LYS* 1.3 78.4 + - + +
94A TRP 4.3 3.8 - - - +
96A PHE* 5.6 0.4 - - - -
146A ALA* 3.8 11.8 - - + +
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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