Contacts of the helix formed by residues 71 - 83 (chain D) in PDB entry 1F9N
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 ASN 71 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69D ARG 4.0 0.8 + - - -
70D PHE* 1.3 101.0 - - + +
72D PRO* 1.3 74.5 - - - +
73D LEU* 3.4 3.8 - - - +
74D SER* 3.5 27.3 + - - +
75D LYS* 3.0 22.5 + - - +
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Residues in contact with PRO 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D GLN 3.4 24.0 - - - +
69D ARG* 4.2 10.3 - - - +
70D PHE 3.4 0.2 - - - -
71D ASN* 1.3 89.0 - - - +
73D LEU* 1.3 53.2 + - + +
75D LYS* 2.9 9.7 + - + +
76D LEU* 2.6 36.5 + - - +
109D LEU* 4.2 8.7 - - + +
112D ASN* 4.1 23.6 - - + +
113D LEU* 3.4 21.5 - - + -
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Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ASN* 3.4 2.0 - - - +
72D PRO* 1.3 79.7 - - + +
74D SER* 1.3 57.8 + - - +
76D LEU* 3.2 4.5 + - + +
77D LYS* 2.9 31.0 + - - +
113D LEU* 3.2 30.0 - - + +
115D TRP* 4.2 13.5 - - + -
144D ARG 5.7 0.4 - - - +
148D LEU* 3.8 38.8 - - + -
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Residues in contact with SER 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D ASN* 3.3 39.9 + - - +
72D PRO 3.2 0.4 - - - -
73D LEU* 1.3 79.8 - - - +
75D LYS* 1.3 60.8 + - - +
77D LYS* 3.7 7.8 + - - +
78D ARG* 3.5 19.6 + - - +
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Residues in contact with LYS 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D PRO 2.7 26.0 + - - -
66D ALA* 3.5 15.0 - - - +
67D ASP 3.0 19.5 + - - +
68D GLN* 4.3 12.6 - - + +
70D PHE* 2.8 30.2 + - - +
71D ASN* 3.0 11.3 + - + +
72D PRO 2.9 8.4 + - - +
74D SER* 1.3 76.2 - - - +
76D LEU* 1.3 64.1 + - - +
77D LYS 3.1 1.6 - - - -
78D ARG* 3.3 6.4 + - - +
79D ALA* 3.0 25.3 + - - +
109D LEU* 3.7 18.3 - - + +
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Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D PRO 2.6 19.3 + - - +
73D LEU* 3.6 7.0 - - + +
75D LYS* 1.3 73.1 - - - +
77D LYS* 1.3 62.5 + - - +
79D ALA* 3.9 1.8 - - + +
80D LEU* 3.1 40.9 + - + +
96D LEU* 6.2 0.2 - - + -
106D ILE* 4.0 24.2 - - + +
109D LEU* 3.4 16.5 - - + +
110D MET* 3.9 23.1 - - + -
113D LEU* 3.5 28.9 - - + -
115D TRP* 4.7 0.7 - - + -
145D LEU* 4.0 16.6 - - + -
148D LEU* 3.7 23.1 - - + -
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Residues in contact with LYS 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D LEU 2.9 16.6 + - - +
74D SER* 3.8 8.7 - - - +
76D LEU* 1.3 75.6 - - - +
78D ARG* 1.3 66.7 + - - +
80D LEU* 3.3 3.4 + - - +
81D MET* 3.1 45.2 + - + +
147D GLU 5.2 3.4 + - - -
148D LEU* 3.4 55.5 - - + +
149D LEU 5.6 1.1 - - - -
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Residues in contact with ARG 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D SER 3.5 10.3 + - - +
75D LYS* 3.3 9.5 + - - +
77D LYS* 1.3 78.9 - - - +
79D ALA* 1.3 62.9 + - - +
81D MET* 3.3 24.8 + - + +
82D ASP* 3.3 24.7 + - - +
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Residues in contact with ALA 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D LYS 3.0 16.9 + - - +
76D LEU* 3.9 6.7 - - + +
78D ARG* 1.3 77.7 - - - +
80D LEU* 1.3 57.8 + - - +
82D ASP* 3.1 7.5 + - - +
83D ALA* 2.9 31.5 + - + +
102D ASN* 5.4 1.0 + - - +
106D ILE* 4.4 20.9 - - + -
109D LEU* 4.7 7.4 - - + -
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Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D LEU* 3.1 37.1 + - + +
77D LYS* 3.8 4.7 - - - +
78D ARG 3.3 0.4 - - - -
79D ALA* 1.3 73.7 - - - +
81D MET* 1.3 59.3 + - - +
82D ASP 3.0 5.2 - - - -
83D ALA 5.0 0.2 - - - -
84D PHE* 2.8 54.4 + - + +
96D LEU* 4.1 26.0 - - + -
98D THR* 5.1 0.7 - - + -
106D ILE* 4.3 17.9 - - + -
145D LEU* 4.5 17.9 - - + +
148D LEU* 4.4 14.8 - - + +
149D LEU* 4.2 23.8 - - + -
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Residues in contact with MET 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ARG* 2.8 27.4 + - - +
47C GLU 5.0 12.1 - - - +
48C LEU* 6.2 3.8 - - - -
49C HIS* 5.1 14.6 - - + +
65C PRO* 6.1 0.2 - - - +
66C ALA* 4.0 10.6 + - - +
77D LYS* 3.1 32.2 + - + +
78D ARG* 3.3 25.3 + - + +
80D LEU* 1.3 75.7 - - + +
82D ASP* 1.3 65.0 + - - +
148D LEU 4.2 13.7 - - - +
149D LEU* 5.2 10.1 - - - -
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Residues in contact with ASP 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ARG* 5.5 0.4 - - - -
66C ALA* 4.1 13.7 - - - +
68C GLN* 3.4 42.7 + - - +
75C LYS* 4.8 10.7 + - - -
78D ARG* 3.3 15.8 + - - +
79D ALA* 3.1 9.4 + - - +
80D LEU 3.0 0.4 - - - -
81D MET* 1.3 90.9 - - - +
83D ALA* 1.3 60.1 + - + +
84D PHE 3.8 0.4 - - - -
99D MET* 4.3 6.9 - - - +
102D ASN* 6.0 1.3 - - - +
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Residues in contact with ALA 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D ALA 2.9 13.2 + - - +
82D ASP* 1.3 79.9 - - - +
84D PHE* 1.3 67.4 + - - +
85D VAL* 3.3 2.3 - - - +
98D THR* 3.2 9.4 - - - -
99D MET* 3.1 33.3 + - + +
102D ASN* 3.4 42.4 - - + +
106D ILE* 4.7 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