Contacts of the helix formed by residues 70 - 85 (chain D) in PDB entry 2H8C
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 70 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C ASP* 5.7 4.4 + - - -
92C ALA* 6.2 2.2 - - - +
63D MET* 6.0 0.2 - - - -
68D ARG 5.9 0.6 - - - -
69D ARG* 1.3 75.2 + - - +
71D LEU* 1.3 67.9 + - - +
72D ASP* 2.9 20.7 - - - +
73D ASN* 2.9 39.6 + - - +
74D LEU* 3.8 5.7 + - - +
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Residues in contact with LEU 71 (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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94C VAL* 3.9 21.8 - - + +
95C VAL 4.3 3.8 - - - +
97C TYR* 4.1 16.2 - - + -
61D CYS* 3.9 24.7 - - + -
63D MET* 4.0 24.2 - - + -
69D ARG 3.5 5.6 + - - +
70D ASN* 1.3 68.0 - - - +
72D ASP* 1.3 56.6 + - - +
73D ASN 2.5 13.7 + - - -
74D LEU* 2.7 21.5 + - + +
75D GLN 3.3 6.9 + - - -
99D VAL* 3.7 27.4 - - + +
101D LYS* 4.1 28.3 - - + +
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Residues in contact with ASP 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ASP* 5.9 0.8 - - + +
75C GLN* 3.2 34.6 + - - +
76C LYS* 4.6 13.9 - - - +
97C TYR* 3.4 16.9 + - + +
70D ASN* 2.9 31.4 - - - +
71D LEU* 1.3 74.2 + - - +
73D ASN* 1.3 64.9 + - - -
74D LEU 3.5 0.2 - - - -
75D GLN* 3.6 8.1 - - - +
76D LYS* 3.1 28.2 + - - +
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Residues in contact with ASN 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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14D ASN* 3.1 45.6 + - + +
70D ASN* 2.9 30.0 + - - +
71D LEU 2.5 5.5 + - - -
72D ASP* 1.3 88.1 + - - +
74D LEU* 1.3 63.6 + - + +
76D LYS* 3.2 7.5 + - - +
77D ALA* 2.9 27.1 + - - +
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Residues in contact with LEU 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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10D TRP* 3.3 46.7 - - + +
11D PRO* 3.9 17.9 - - + -
12D PRO 5.8 0.2 - - - +
13D SER* 6.4 1.3 - - - -
59D ILE* 5.4 0.7 - - - -
61D CYS* 3.3 33.7 - - + -
63D MET* 4.6 2.2 - - + -
69D ARG* 5.8 3.8 - - + -
70D ASN 4.4 7.6 - - - +
71D LEU* 2.7 20.8 + - + +
73D ASN* 1.3 73.4 - - + +
75D GLN* 1.3 55.8 + - - +
77D ALA* 3.0 8.5 + - - +
78D ALA* 2.7 38.4 + - - +
110D LEU* 3.8 18.3 - - + +
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Residues in contact with GLN 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ASP* 3.5 27.9 + - - +
75C GLN* 4.3 1.0 - - - +
97C TYR* 3.7 8.4 + - - +
59D ILE* 4.0 12.3 - - - +
71D LEU 3.3 2.9 + - - +
72D ASP* 3.6 15.5 - - - +
73D ASN 3.3 0.2 - - - -
74D LEU* 1.3 77.2 - - - +
76D LYS* 1.3 66.0 + - - +
79D PHE* 3.0 68.8 + - + +
97D TYR* 3.3 41.0 + - + -
99D VAL* 3.6 20.2 - - + +
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Residues in contact with LYS 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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72C ASP* 5.7 4.5 - - + +
14D ASN* 6.0 2.9 - - - +
18D TYR* 4.2 13.9 + - + +
72D ASP 3.1 18.3 + - - +
73D ASN* 3.6 7.2 - - - +
74D LEU 3.2 0.2 - - - -
75D GLN* 1.3 86.6 - - - +
77D ALA* 1.3 64.8 + - - +
79D PHE* 4.3 2.5 - - - +
80D ASP* 3.1 23.4 + - - +
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Residues in contact with ALA 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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11D PRO* 3.5 35.0 - - + -
12D PRO 5.1 1.1 - - - +
17D TYR* 4.1 19.5 + - + -
18D TYR* 5.2 2.9 - - - -
34D TYR* 4.7 2.8 - - + -
73D ASN 2.9 13.6 + - - +
74D LEU 3.3 7.6 - - - +
76D LYS* 1.3 75.4 - - - +
78D ALA* 1.3 65.4 + - - +
80D ASP* 3.2 7.2 - - - +
81D ALA* 3.0 23.1 + - - +
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Residues in contact with ALA 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 5.6 7.4 - - + +
34D TYR* 5.7 2.2 - - - -
59D ILE* 4.1 20.2 - - + -
74D LEU 2.7 18.6 + - - +
75D GLN 3.8 2.9 - - - +
77D ALA* 1.3 69.3 - - - +
79D PHE* 1.3 70.0 + - + +
81D ALA* 2.8 18.5 + - - +
82D LEU* 2.9 21.0 + - + +
110D LEU* 4.8 15.9 - - + +
112D LEU* 4.9 10.3 - - + -
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Residues in contact with PHE 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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72C ASP* 5.2 3.6 - - - -
57D ILE* 3.6 34.1 - - + -
59D ILE* 3.8 22.0 - - + -
75D GLN* 3.0 44.7 + - + +
76D LYS* 4.3 2.9 - - - +
78D ALA* 1.3 78.5 - - + +
80D ASP* 1.3 63.6 + - - +
82D LEU* 3.3 3.6 + - + +
83D THR* 3.0 30.0 + - - -
88D TRP* 4.0 24.6 - + + -
91D ASP* 4.6 20.0 - - + +
94D VAL* 4.2 9.6 - - + -
97D TYR* 3.8 27.4 - + + -
112D LEU* 6.1 0.2 - - + -
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Residues in contact with ASP 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D TYR* 2.9 16.2 + - - +
18D TYR* 4.1 16.4 + - - +
35D ARG* 2.7 44.5 + - - +
76D LYS 3.1 19.1 + - - +
77D ALA* 3.2 7.4 - - - +
78D ALA 3.0 0.4 + - - -
79D PHE* 1.3 81.3 - - - +
81D ALA* 1.3 62.7 + - - +
83D THR* 3.6 5.4 + - - -
84D LYS* 3.2 23.9 + - - +
91D ASP* 5.4 2.7 + - - -
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Residues in contact with ALA 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 5.8 1.3 - - + -
17D TYR* 4.9 0.2 - - - +
34D TYR* 4.5 9.0 - - + -
35D ARG* 4.2 19.0 - - + +
38D VAL* 3.9 32.4 - - + +
77D ALA 3.0 11.6 + - - +
78D ALA* 2.8 14.8 + - - +
80D ASP* 1.3 77.3 - - - +
82D LEU* 1.3 50.5 + - + +
84D LYS* 3.0 4.2 + - - +
85D ALA* 2.6 38.7 + - - +
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Residues in contact with LEU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 5.2 7.0 - - + -
8D LEU* 4.4 20.9 - - + -
38D VAL* 4.9 6.7 - - + -
42D ILE* 6.1 1.8 - - + -
57D ILE* 5.3 5.2 - - + -
78D ALA* 2.9 21.5 + - + +
79D PHE* 3.8 5.8 - - + +
81D ALA* 1.3 73.1 - - - +
83D THR* 1.3 69.1 + - - +
85D ALA* 2.9 15.4 + - + +
86D GLY 3.2 6.6 + - - -
87D PHE* 3.2 49.6 + - + +
88D TRP* 3.7 34.1 - - + -
112D LEU* 5.1 17.3 - - + -
114D ILE* 5.4 2.0 - - + -
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Residues in contact with THR 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 PHE 3.0 14.6 + - - -
80D ASP* 3.7 5.6 - - - -
82D LEU* 1.3 77.7 - - - +
84D LYS* 1.3 76.9 + - - +
86D GLY* 3.3 11.6 + - - -
88D TRP* 2.8 32.4 + - - +
89D LEU 3.7 20.6 - - - +
90D ASP* 4.2 6.5 - - + +
91D ASP* 3.3 24.4 + - - +
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Residues in contact with LYS 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ARG* 3.4 53.8 - - + +
39D ALA* 5.3 1.2 - - - +
80D ASP* 3.2 11.9 + - - +
81D ALA 3.0 8.2 + - - +
82D LEU 3.0 1.0 - - - -
83D THR* 1.3 93.8 + - - +
85D ALA* 1.3 53.2 + - - +
86D GLY* 2.7 17.2 + - - -
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Residues in contact with ALA 85 (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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35D ARG 5.2 0.4 + - - +
38D VAL* 4.0 9.9 - - + -
39D ALA* 3.5 43.0 - - + +
42D ILE* 4.1 12.5 - - + +
43D LYS* 6.1 0.2 - - - +
48D ASP* 4.1 14.0 - - - +
81D ALA 2.6 19.9 + - - +
82D LEU* 2.9 6.4 + - - +
84D LYS* 1.3 69.4 - - - +
86D GLY* 1.3 62.5 + - - +
87D PHE* 3.1 7.7 + - + +
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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