Contacts of the helix formed by residues 78 - 90 (chain A) in PDB entry 3SJN
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 GLU 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A VAL* 5.0 4.3 - - - +
75A ASN* 3.0 47.5 + - + +
76A ALA 4.3 0.2 - - - -
77A LEU* 1.3 77.3 - - + +
79A ILE* 1.3 64.5 + - - +
80A GLU 3.5 1.8 - - - -
81A ARG* 2.9 40.0 + - + +
82A LEU* 3.1 24.3 + - - +
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Residues in contact with ILE 79 (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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76A ALA 3.7 14.8 - - - +
77A LEU* 3.0 13.6 + - - +
78A GLU* 1.3 71.0 - - - +
80A GLU* 1.3 57.2 + - - +
82A LEU* 3.2 7.9 + - - +
83A TRP* 2.8 25.8 + - - +
86A MET* 5.8 0.2 - - - +
107A ASP* 3.4 24.2 - - - +
110A LEU* 3.5 43.1 - - + +
111A TRP* 3.7 35.9 - - + +
114A ALA* 4.1 12.1 - - + -
282A THR* 3.5 9.4 - - - +
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Residues in contact with GLU 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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78A GLU 3.5 0.4 - - - -
79A ILE* 1.3 78.3 - - - +
81A ARG* 1.3 57.6 + - - +
83A TRP* 3.2 8.0 + - + +
84A ASN* 3.0 45.4 + - - +
282A THR* 4.1 14.8 - - + -
286A LYS* 2.7 35.4 + - - +
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Residues in contact with ARG 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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74A GLU* 2.7 42.6 + - - -
75A ASN* 4.3 7.5 - - - +
78A GLU* 2.9 47.3 + - + +
79A ILE 3.3 0.2 - - - -
80A GLU* 1.3 78.1 - - - +
82A LEU* 1.3 60.7 + - - +
84A ASN* 3.2 9.5 + - + +
85A LYS* 2.8 39.7 + - + +
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Residues in contact with LEU 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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4A ILE* 3.9 25.8 - - + -
71A LEU* 4.0 14.8 - - + -
74A GLU* 3.7 38.4 - - + +
75A ASN 3.4 20.9 - - - +
76A ALA* 4.1 5.2 - - - +
78A GLU 3.1 17.3 + - - +
79A ILE 3.6 6.5 - - - +
81A ARG* 1.3 84.9 - - - +
83A TRP* 1.3 64.0 + - - +
85A LYS* 3.6 6.1 - - + +
86A MET* 2.9 31.8 + - + +
110A LEU* 3.9 20.9 - - + -
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Residues in contact with TRP 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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79A ILE 2.8 16.4 + - - +
80A GLU* 3.4 14.1 - - + +
82A LEU* 1.3 72.0 - - - +
84A ASN* 1.3 75.3 + - - +
86A MET* 3.3 11.8 + - + +
87A TYR* 2.9 65.1 + + + +
100A ILE* 5.1 3.1 - - + -
103A ILE* 3.5 21.8 - - + +
107A ASP* 3.5 18.8 - - + +
255A THR* 4.7 8.1 - - + -
256A ARG* 3.5 16.4 - - - -
257A TYR* 6.2 1.3 - + - -
279A GLY* 2.7 34.0 + - - -
282A THR* 4.0 15.0 - - + -
283A GLU* 3.5 39.4 - - + +
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Residues in contact with ASN 84 (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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80A GLU* 3.0 30.9 + - - +
81A ARG* 3.2 10.3 + - + +
83A TRP* 1.3 97.8 - - - +
85A LYS* 1.3 56.3 + - - +
87A TYR* 4.2 3.9 - - - +
88A TRP* 3.0 48.3 + - + +
256A ARG* 4.5 10.3 - - - +
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Residues in contact with LYS 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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70A LEU* 2.8 51.8 + - + +
71A LEU* 4.9 1.8 - - + -
74A GLU* 2.8 34.9 + - + +
81A ARG* 2.8 27.2 + - + +
82A LEU* 3.3 12.5 + - + +
84A ASN* 1.3 70.5 - - - +
86A MET* 1.3 59.7 + - - +
88A TRP* 4.1 2.4 - - - +
89A GLY* 2.8 29.1 + - - -
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Residues in contact with MET 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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67A LEU* 3.9 11.9 - - + -
70A LEU* 4.1 10.5 - - + -
71A LEU* 3.9 24.9 - - + -
82A LEU 2.9 22.8 + - - +
83A TRP* 3.6 11.7 - - + +
85A LYS* 1.3 75.1 - - - +
87A TYR* 1.3 55.7 + - - +
90A SER* 2.6 40.7 + - - -
103A ILE* 3.9 38.8 - - + +
106A ILE* 3.8 47.6 - - + -
107A ASP* 4.7 4.9 - - + +
110A LEU* 4.7 7.0 - - + -
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Residues in contact with TYR 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 TRP* 2.9 48.5 + + + +
84A ASN* 3.7 6.5 - - - +
86A MET* 1.3 77.1 - - - +
88A TRP* 1.3 75.8 + + - +
90A SER* 4.0 0.9 + - - -
91A ASN* 3.2 45.8 + - - +
95A ARG* 3.6 26.2 + - + +
96A ARG* 3.0 19.8 + - - -
100A ILE* 3.9 15.0 - - + -
103A ILE* 3.9 7.6 - - + +
255A THR* 4.2 8.5 - - + -
257A TYR* 3.9 9.7 - + - -
229B LEU* 4.1 9.2 - - + -
231B ASP* 2.5 30.9 + - - -
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Residues in contact with TRP 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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63A TYR* 3.9 44.5 - + + +
84A ASN* 3.0 37.5 + - + +
85A LYS* 4.1 2.9 - - - +
87A TYR* 1.3 90.3 - + - +
89A GLY* 1.3 61.4 + - - +
91A ASN* 3.3 21.2 + - + +
200B ALA 4.8 0.9 - - - -
201B SER* 4.0 22.0 - - - -
202B LYS* 5.9 2.2 - - + -
204B HIS* 3.8 33.0 - + - -
229B LEU* 3.6 40.0 - - + +
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Residues in contact with GLY 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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62A PHE 4.8 4.0 - - - -
63A TYR* 3.2 7.1 - - - +
65A ASN* 2.9 37.5 + - - +
70A LEU* 3.8 16.8 - - - -
85A LYS 2.8 19.8 + - - -
88A TRP* 1.3 76.3 - - - +
90A SER* 1.3 57.7 + - - +
91A ASN 3.4 0.4 - - - -
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Residues in contact with SER 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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63A TYR 3.4 2.9 - - - -
64A CYS* 4.6 0.7 - - - +
65A ASN 3.5 20.9 - - - +
67A LEU* 3.6 19.9 - - - +
86A MET 2.6 23.9 + - - -
87A TYR* 4.1 1.4 + - - -
89A GLY* 1.3 76.3 - - - +
91A ASN* 1.3 53.6 + - - +
92A TYR 3.2 2.9 - - - -
93A MET* 3.1 18.6 + - - +
94A GLY* 2.7 38.2 + - - -
95A ARG 5.2 0.5 + - - -
99A GLY 5.2 1.2 + - - -
103A ILE* 4.1 9.4 - - - +
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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