Contacts of the helix formed by residues 98 - 111 (chain X) in PDB entry 1SHU
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 ASP 98 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96X THR* 3.1 13.3 + - - +
97X GLY* 1.3 75.1 - - - +
99X ARG* 1.3 59.8 + - - +
100X GLY* 3.1 8.9 + - - -
101X LYS* 2.9 46.7 + - + +
102X ILE* 3.0 27.0 + - - +
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Residues in contact with ARG 99 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70X ALA 4.9 1.4 + - - -
73X PHE 2.7 27.7 + - - -
74X VAL* 3.2 40.7 + - + +
75X SER 2.9 21.4 + - - -
76X PRO* 4.0 0.2 - - - +
78X MET* 2.9 24.4 + - - +
80X LEU* 4.2 7.3 - - - +
97X GLY* 2.8 43.8 + - - -
98X ASP* 1.3 71.7 + - - +
100X GLY* 1.3 60.1 + - - +
102X ILE* 3.3 26.8 - - + +
103X SER* 2.9 28.1 + - - -
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Residues in contact with GLY 100 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98X ASP* 3.1 10.5 + - - -
99X ARG* 1.3 73.9 - - - +
101X LYS* 1.3 64.7 + - - +
103X SER* 3.3 9.0 + - - -
104X LYS* 3.1 21.5 + - - +
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Residues in contact with LYS 101 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93X LEU* 3.3 20.5 - - + +
96X THR* 4.1 22.5 + - + +
98X ASP* 2.9 28.2 + - + +
100X GLY* 1.3 72.1 - - - +
102X ILE* 1.3 61.2 + - - +
104X LYS* 3.2 7.8 + - - +
105X GLY 2.8 24.1 + - - -
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Residues in contact with ILE 102 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70X ALA* 4.5 5.2 - - + -
80X LEU* 4.0 23.6 - - + -
82X PHE* 4.0 6.0 - - + -
93X LEU* 3.9 21.5 - - + -
96X THR* 3.8 20.4 - - + +
98X ASP 3.0 20.2 + - - +
99X ARG* 3.3 52.3 - - + +
100X GLY 3.2 0.2 - - - -
101X LYS* 1.3 74.8 - - - +
103X SER* 1.3 64.2 + - - +
105X GLY* 3.1 1.7 + - - -
106X LEU* 2.9 37.8 + - + +
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Residues in contact with SER 103 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99X ARG 2.9 14.5 + - - -
100X GLY* 3.4 12.6 - - - -
102X ILE* 1.3 78.4 - - - +
104X LYS* 1.3 56.1 + - - +
106X LEU* 3.4 12.7 + - - +
107X GLU* 3.1 33.1 + - - +
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Residues in contact with LYS 104 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100X GLY 3.1 12.7 + - - +
101X LYS* 3.6 10.1 - - - +
103X SER* 1.3 74.0 - - - +
105X GLY* 1.3 61.0 + - - +
107X GLU* 3.2 26.0 + - + +
108X ASP* 2.9 57.7 + - - +
111X ARG* 4.4 9.6 - - - +
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Residues in contact with GLY 105 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82X PHE* 3.7 18.7 - - - -
92X ILE* 4.1 4.2 - - - +
93X LEU* 4.5 11.0 - - - -
101X LYS 2.8 14.3 + - - -
102X ILE 3.1 4.2 + - - -
104X LYS* 1.3 77.1 - - - +
106X LEU* 1.3 54.5 + - - +
108X ASP* 3.4 11.0 + - - +
109X LEU* 2.9 31.9 + - - +
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Residues in contact with LEU 106 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63X TYR* 3.1 35.1 - - + +
66X VAL* 4.2 7.4 - - + -
67X GLN* 3.8 40.8 - - + +
70X ALA* 4.4 9.4 - - + -
82X PHE* 3.9 19.5 - - + -
102X ILE* 2.9 31.1 + - + +
103X SER* 3.5 11.9 - - - +
104X LYS 3.2 0.2 - - - -
105X GLY* 1.3 73.7 - - - +
107X GLU* 1.3 65.0 + - - +
109X LEU* 3.2 3.3 + - + +
110X LYS* 2.9 19.4 + - - +
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Residues in contact with GLU 107 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103X SER* 3.1 19.9 + - - +
104X LYS* 3.2 35.5 + - + +
106X LEU* 1.3 75.6 - - - +
108X ASP* 1.3 62.0 + - - +
110X LYS* 3.3 21.4 + - - +
111X ARG* 3.5 28.5 + - - +
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Residues in contact with ASP 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92X ILE* 3.7 29.4 - - + +
104X LYS* 2.9 52.8 + - - +
105X GLY* 3.4 9.3 - - - +
106X LEU 3.3 0.2 - - - -
107X GLU* 1.3 73.7 - - - +
109X LEU* 1.3 65.1 + - - +
110X LYS 3.4 0.2 + - - -
111X ARG* 3.2 33.0 + - - +
112X VAL* 3.7 13.3 + - - +
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Residues in contact with LEU 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49X LEU* 3.7 26.5 - - + -
59X TRP* 2.9 35.0 + - + -
63X TYR* 3.9 12.1 - - + -
66X VAL* 4.0 15.3 - - + -
82X PHE* 3.5 36.8 - - + -
84X VAL* 3.8 28.7 - - + -
92X ILE* 4.3 10.5 - - + -
105X GLY 2.9 17.9 + - - +
106X LEU* 3.2 9.2 + - + +
108X ASP* 1.3 76.8 - - - +
110X LYS* 1.3 59.1 + - - +
112X VAL* 3.2 10.5 + - + -
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Residues in contact with LYS 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X TRP* 4.3 9.1 + - - +
60X ILE* 5.1 10.0 - - + +
63X TYR* 3.7 46.0 + - + +
64X ASN* 5.5 0.8 + - - -
106X LEU 2.9 16.0 + - - +
107X GLU* 3.4 11.2 - - - +
108X ASP 3.2 0.4 - - - -
109X LEU* 1.3 77.3 - - - +
111X ARG* 1.3 60.9 + - + +
112X VAL 3.4 1.8 + - - +
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Residues in contact with ARG 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104X LYS* 4.4 8.3 - - - +
107X GLU* 3.5 23.8 + - - +
108X ASP* 3.2 39.3 + - - +
109X LEU 3.2 0.8 - - - -
110X LYS* 1.3 78.7 - - + +
112X VAL* 1.3 65.2 + - - +
113X SER* 3.4 5.2 + - - -
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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