Contacts of the helix formed by residues 71 - 83 (chain A) in PDB entry 1S9D
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 GLN 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A GLY* 1.3 74.8 - - - -
72A ASP* 1.3 66.1 + - - +
73A LYS* 3.2 33.4 + - + +
74A ILE* 3.3 19.1 - - - +
75A ARG* 4.2 4.8 + - - +
161E ASP* 3.2 19.7 + - - +
162E ARG* 5.7 0.2 - - - -
165E GLU* 2.7 32.5 + - - +
186E TYR* 3.0 25.3 + - - +
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Residues in contact with ASP 72 (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 GLY 5.5 0.2 - - - +
71A GLN* 1.3 74.2 - - - +
73A LYS* 1.3 65.6 + - + +
74A ILE 3.1 1.4 + - - -
75A ARG* 3.1 37.2 + - - +
76A PRO* 3.8 4.0 - - - +
109A ARG* 3.9 24.5 + - - -
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Residues in contact with LYS 73 (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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71A GLN* 3.1 25.0 - - + +
72A ASP* 1.3 78.8 - - + +
74A ILE* 1.3 59.1 + - - +
76A PRO* 3.4 14.8 - - - +
165E GLU* 4.7 5.1 + - - -
183E ASP* 2.7 42.5 + - + +
186E TYR* 4.0 22.4 - - + +
187E VAL* 4.0 17.3 - - + +
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Residues in contact with ILE 74 (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 GLY* 4.4 7.9 - - - -
71A GLN 3.3 18.2 - - - +
73A LYS* 1.3 78.3 - - - +
75A ARG* 1.3 66.0 + - - +
76A PRO* 3.4 2.2 - - - -
77A LEU* 3.2 29.8 + - + +
78A TRP* 3.7 29.0 - - + +
403A AFB 3.9 1.8 - - - +
161E ASP* 3.7 15.0 - - - +
186E TYR* 3.6 24.2 - - + +
187E VAL* 4.4 9.4 - - + -
190E TYR* 3.8 52.3 - - + +
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Residues in contact with ARG 75 (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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68A VAL* 3.3 22.0 + - - +
70A GLY 4.6 4.9 + - - -
71A GLN 4.3 6.2 + - - +
72A ASP* 3.1 32.8 + - - +
74A ILE* 1.3 77.4 - - - +
76A PRO* 1.3 59.9 - - + +
78A TRP* 2.9 72.6 + - + +
79A ARG* 4.2 1.2 + - - -
106A GLU* 2.9 41.8 + - - -
109A ARG* 3.7 29.3 - - - +
110A MET* 4.2 3.8 - - - -
113A GLU* 4.3 20.1 + - - +
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Residues in contact with PRO 76 (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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72A ASP 3.8 5.4 - - - +
73A LYS* 3.4 17.9 - - - +
74A ILE 3.4 1.3 - - - -
75A ARG* 1.3 91.6 - - + +
77A LEU* 1.3 62.1 + - + +
78A TRP 3.2 0.7 + - - -
79A ARG* 3.0 43.5 + - + +
187E VAL* 6.4 1.1 - - + -
216E MET 4.8 0.7 - - - +
218E ARG 6.1 0.9 - - - +
220E ILE* 5.9 5.8 - - + -
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Residues in contact with LEU 77 (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 ILE* 3.3 16.8 - - + +
75A ARG 3.1 0.8 + - - -
76A PRO* 1.3 78.5 - - + +
78A TRP* 1.3 62.2 + - - +
79A ARG* 3.5 1.5 + - - +
80A HIS* 4.7 2.6 + - - -
81A TYR* 4.2 1.7 - - - -
187E VAL* 3.6 39.9 - - + +
190E TYR* 3.8 26.2 - - + -
191E SER* 4.0 4.9 - - - +
194E MET* 3.8 21.0 - - + +
216E MET* 3.3 54.9 - - + +
217E ASN* 3.6 19.5 - - - +
220E ILE* 4.4 4.7 - - + -
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Residues in contact with TRP 78 (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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66A TRP* 3.4 37.9 - + + -
67A ASP 4.2 4.7 - - - -
68A VAL* 4.1 16.8 - - + -
70A GLY 5.6 0.4 - - - -
74A ILE* 3.7 24.8 + - + +
75A ARG* 2.9 70.5 + - + +
77A LEU* 1.3 84.6 - - + +
79A ARG* 1.3 64.6 + - - +
80A HIS 3.3 0.9 - - - -
81A TYR* 2.9 30.2 + - - +
82A PHE* 3.6 27.8 + + + -
110A MET* 4.2 10.8 - - - -
113A GLU* 4.4 6.7 - - - +
403A AFB 3.1 33.6 + - + +
190E TYR* 4.9 0.2 - - - -
194E MET* 4.5 2.5 - - + -
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Residues in contact with ARG 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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75A ARG 4.2 1.0 + - - +
76A PRO* 3.0 32.7 + - + +
77A LEU* 3.3 1.0 - - - +
78A TRP* 1.3 78.8 - - - +
80A HIS* 1.3 66.6 + - + +
81A TYR 3.1 0.9 + - - -
82A PHE* 3.1 17.0 + - - +
83A GLN 3.9 0.3 + - - -
113A GLU* 5.2 6.3 - - - +
115A GLU* 3.6 29.9 - - + +
215E ALA* 2.9 24.0 + - - +
216E MET* 3.0 28.0 + - - +
218E ARG* 3.7 21.6 + - - +
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Residues in contact with HIS 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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77A LEU 4.7 2.0 + - - -
78A TRP 3.2 1.0 + - - -
79A ARG* 1.3 83.9 - - + +
81A TYR* 1.3 103.7 + + - +
83A GLN* 3.2 34.7 + - - +
84A ASN* 4.9 0.3 + - - -
208E MET* 3.8 28.5 - - + +
212E ARG* 3.4 58.3 + - + +
216E MET* 4.2 13.0 - - + +
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Residues in contact with TYR 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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18A MET* 3.3 22.8 - - + +
66A TRP* 3.8 24.0 - + + -
77A LEU 4.2 1.1 - - - -
78A TRP* 2.9 24.3 + - - +
80A HIS* 1.3 108.0 - + - +
82A PHE* 1.3 59.6 + - + +
83A GLN 3.3 0.6 + - - -
84A ASN* 4.5 5.8 + - - +
85A THR* 3.7 4.2 + - - -
403A AFB 3.5 41.7 - - + +
194E MET* 3.7 22.6 - - + +
198E ASP* 2.7 30.5 + - - -
206E ASP 5.9 0.9 - - - -
208E MET* 3.3 18.4 - - + +
216E MET* 3.7 4.2 - - + +
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Residues in contact with PHE 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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18A MET* 4.8 0.7 - - + -
21A LEU* 3.4 26.5 - - + -
66A TRP* 3.6 46.9 - + - -
78A TRP* 3.6 35.0 - + + -
79A ARG* 3.1 11.9 + - - +
81A TYR* 1.3 79.7 - - + +
83A GLN* 1.3 64.4 + - - +
84A ASN 3.2 3.1 - - - -
85A THR* 3.0 20.5 + - - +
110A MET* 4.1 10.5 - - + -
113A GLU* 4.0 26.0 - - + -
115A GLU* 3.6 26.9 - - + +
116A LEU* 3.9 20.9 - - + -
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Residues in contact with GLN 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 ARG 3.9 0.6 + - - -
80A HIS* 3.2 27.7 + - - +
82A PHE* 1.3 78.1 - - - +
84A ASN* 1.3 67.4 + - - +
85A THR 3.3 2.1 + - - +
115A GLU* 3.6 34.5 + - - +
212E ARG* 3.2 37.2 + - - +
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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