Contacts of the helix formed by residues 66 - 83 (chain F) in PDB entry 5N9G
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 66 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65F VAL* 1.4 79.1 - - - +
67F ARG* 1.4 59.0 + - - +
68F SER* 3.5 14.6 + - - -
69F GLN* 3.0 21.0 + - - +
70F GLN* 2.9 28.1 + - - +
101F TYR* 4.3 9.0 - - - -
107F ARG* 5.8 4.6 - - - +
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Residues in contact with ARG 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F VAL 3.6 2.3 + - - +
66F SER* 1.4 72.5 + - - +
68F SER* 1.3 56.1 + - - +
70F GLN* 3.7 15.5 + - - +
71F ARG* 3.1 45.5 + - - +
74F ARG* 4.7 2.5 + - - +
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Residues in contact with SER 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F SER* 3.2 8.2 + - - -
67F ARG* 1.3 76.3 - - - +
69F GLN* 1.4 59.3 + - - +
71F ARG* 3.1 28.2 + - - +
72F GLY* 3.1 21.7 + - - -
97F TYR* 4.1 2.4 + - - -
101F TYR* 3.3 22.5 + - - -
111F LEU* 3.5 15.8 - - - +
114F LYS* 3.8 12.8 + - - +
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Residues in contact with GLN 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F VAL 4.7 14.0 + - - +
66F SER* 3.0 24.7 + - - +
68F SER* 1.4 75.7 - - - +
70F GLN* 1.4 54.8 + - + +
72F GLY* 3.1 2.1 + - - -
73F LEU* 2.8 55.1 + - + +
97F TYR* 4.1 1.6 - - + -
98F GLN* 3.6 37.6 + - - +
101F TYR* 3.2 46.3 + - + +
107F ARG* 5.7 0.7 + - - -
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Residues in contact with GLN 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F VAL* 3.6 31.0 + - - +
66F SER 2.9 13.4 + - - +
67F ARG* 3.9 18.5 - - - +
69F GLN* 1.4 76.3 - - + +
71F ARG* 1.4 55.7 + - - +
73F LEU* 3.4 10.1 + - + +
74F ARG* 3.0 49.1 + - - +
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Residues in contact with ARG 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F ARG* 3.1 43.1 + - - +
68F SER* 3.1 34.7 + - - +
69F GLN 3.3 0.2 - - - -
70F GLN* 1.4 73.2 - - - +
72F GLY* 1.3 58.0 + - - +
74F ARG* 3.4 28.1 + - - +
75F ARG* 3.0 39.4 + - + +
111F LEU* 3.5 21.8 - - - +
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Residues in contact with GLY 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F SER 3.1 8.5 + - - -
69F GLN 3.1 7.2 + - - -
71F ARG* 1.3 73.9 - - - +
73F LEU* 1.4 51.8 + - - +
75F ARG* 3.1 7.3 + - - +
76F VAL* 2.9 36.3 + - - +
97F TYR* 3.5 30.3 - - - -
115F GLU* 5.9 0.2 - - - -
118F VAL* 3.6 7.1 - - - +
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Residues in contact with LEU 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F GLN* 2.8 41.3 + - + +
70F GLN* 3.8 9.0 - - + +
72F GLY* 1.4 68.0 - - - +
74F ARG* 1.3 63.2 + - - +
76F VAL* 3.7 4.3 - - + +
77F ARG* 3.2 33.8 + - - +
94F VAL* 3.7 37.3 - - + +
97F TYR* 3.6 24.2 - - + -
98F GLN* 3.8 29.2 - - + +
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Residues in contact with ARG 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F ARG 4.7 2.2 + - - -
70F GLN* 3.0 28.5 + - - +
71F ARG* 3.6 45.1 + - - +
72F GLY 3.3 0.2 - - - -
73F LEU* 1.3 75.1 - - - +
75F ARG* 1.4 51.9 + - + +
77F ARG* 3.3 7.2 + - - +
78F ASP* 2.8 44.4 + - - +
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Residues in contact with ARG 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F ARG* 3.0 26.1 + - + +
72F GLY* 3.1 10.3 + - - +
74F ARG* 1.4 73.8 - - + +
76F VAL* 1.4 54.9 + - - +
78F ASP* 3.3 28.1 + - - +
79F LEU* 2.9 38.3 + - - +
115F GLU* 3.1 37.4 + - - +
118F VAL* 3.8 19.2 - - + +
141F LEU 5.0 7.1 + - - -
142F LEU* 4.6 11.1 - - - +
143F TYR* 6.4 0.4 - - - -
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Residues in contact with VAL 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F GLY 2.9 20.0 + - - +
73F LEU* 3.7 6.7 - - - +
74F ARG 3.3 0.2 - - - -
75F ARG* 1.4 72.1 - - - +
77F ARG* 1.4 62.3 + - - +
79F LEU* 3.3 4.3 + - - +
80F CYS* 3.1 29.1 + - - -
90F GLU 4.4 1.8 - - - +
93F ALA* 3.7 28.7 - - + +
94F VAL* 3.7 23.6 - - + +
97F TYR* 3.7 33.4 - - + -
118F VAL* 3.7 22.2 - - + +
121F CYS* 5.2 0.4 - - + -
122F VAL* 3.9 5.7 - - + +
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Residues in contact with ARG 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ASP* 5.8 1.6 + - - -
73F LEU* 3.2 20.9 + - - +
74F ARG* 3.7 7.9 - - - +
76F VAL* 1.4 71.3 - - - +
78F ASP* 1.3 66.5 + - - +
80F CYS* 3.5 1.0 + - - +
81F ARG* 3.2 33.3 + - - +
90F GLU* 2.8 42.3 + - + +
91F ASP* 3.0 28.3 + - - +
94F VAL* 3.6 39.2 - - + +
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Residues in contact with ASP 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F ARG* 2.8 29.0 + - - +
75F ARG* 3.4 36.8 + - - +
76F VAL 3.3 0.2 - - - -
77F ARG* 1.3 75.7 - - - +
79F LEU* 1.4 57.0 + - - +
81F ARG* 2.9 28.8 + - - +
82F VAL* 2.9 33.7 + - + +
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Residues in contact with LEU 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F ARG* 2.9 25.0 + - - +
76F VAL 3.3 4.7 + - - +
78F ASP* 1.4 70.6 - - - +
80F CYS* 1.3 57.3 + - - +
82F VAL* 3.3 10.3 + - + +
83F LEU* 2.9 44.1 + - + +
118F VAL* 4.1 10.1 - - + -
119F GLY* 4.1 12.8 - - - -
122F VAL* 3.7 28.9 - - + -
138F ILE* 3.9 13.9 - - + -
141F LEU* 3.9 36.6 - - + -
142F LEU* 4.6 11.9 - - + -
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Residues in contact with CYS 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F VAL* 3.1 21.1 + - - -
77F ARG 3.7 7.4 - - - +
79F LEU* 1.3 75.3 - - - +
81F ARG* 1.4 58.0 + - - +
83F LEU 3.5 0.5 + - - -
84F GLN 3.1 5.9 + - - -
85F LEU* 3.1 62.9 + - + +
86F PRO 5.9 0.4 - - - +
89F PHE 4.6 0.4 - - - -
90F GLU* 3.8 37.7 - - + +
93F ALA* 4.4 6.5 - - - -
122F VAL* 3.7 15.9 - - - -
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Residues in contact with ARG 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F ARG* 3.2 20.6 + - - +
78F ASP* 2.9 35.3 + - - +
80F CYS* 1.4 74.0 - - - +
82F VAL* 1.3 64.8 + - + +
84F GLN* 3.2 19.8 + - - +
90F GLU* 3.7 16.8 - - - +
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Residues in contact with VAL 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F ASP* 2.9 21.1 + - + +
79F LEU* 3.3 10.5 + - + +
81F ARG* 1.3 76.8 - - + +
83F LEU* 1.3 61.9 + - + +
84F GLN* 3.4 13.7 + - - +
141F LEU* 4.2 30.3 - - + -
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Residues in contact with LEU 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F LEU* 2.9 29.4 + - + +
80F CYS 4.0 4.5 - - - +
81F ARG 3.3 0.2 - - - -
82F VAL* 1.3 73.5 - - + +
84F GLN* 1.4 69.9 + - - +
85F LEU* 3.3 15.7 + - + +
122F VAL* 3.8 18.6 - - + -
131F TRP* 4.8 10.2 + - - +
133F LEU* 3.7 37.9 - - + -
138F ILE* 4.2 2.2 - - + -
141F LEU* 3.8 23.6 - - + -
287H SER 5.1 0.4 - - - +
288H THR* 3.8 36.5 - - + +
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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