Contacts of the helix formed by residues 64 - 82 (chain D) in PDB entry 3ESF
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 GLY 64 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D LYS* 1.3 74.9 - - - +
65D PRO* 1.4 75.0 - - - +
67D PHE* 3.1 16.3 + - - +
68D ASN* 3.1 18.9 + - - +
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Residues in contact with PRO 65 (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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63D LYS 4.4 1.3 - - - +
64D GLY* 1.4 82.5 - - - +
66D ILE* 1.3 71.2 + - + +
68D ASN* 3.2 15.1 + - + +
69D LEU* 3.2 27.7 + - + +
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Residues in contact with ILE 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D LEU* 4.1 8.2 - - + +
43D ALA* 3.5 29.8 - - + -
50D LEU* 3.9 28.7 - - + -
58D ILE* 4.1 6.5 - - + -
62D GLU* 3.6 24.0 - - - +
63D LYS 4.2 4.4 + - - +
64D GLY 3.3 1.0 - - - -
65D PRO* 1.3 79.6 - - + +
67D PHE* 1.3 66.5 + - - +
69D LEU* 3.3 19.5 + - + +
70D ALA* 3.1 21.0 + - - +
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Residues in contact with PHE 67 (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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58D ILE* 4.4 9.4 - - - -
59D ILE* 3.3 41.1 - - + -
62D GLU* 3.6 25.8 - - - +
63D LYS* 3.8 12.8 + - + -
64D GLY 3.1 11.0 + - - +
66D ILE* 1.3 77.3 - - - +
68D ASN* 1.3 73.4 + - - +
69D LEU 3.3 0.2 + - - -
70D ALA* 3.3 1.9 + - - +
71D ALA* 2.8 49.3 + - + +
145D ALA 3.8 14.6 - - - -
146D GLY* 4.6 3.8 - - - -
147D CYS 4.5 6.7 - - - -
150D THR* 3.6 22.0 - - + -
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Residues in contact with ASN 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PHE* 3.7 47.4 - - + +
64D GLY* 3.1 13.5 + - - +
65D PRO* 3.2 15.3 + - + +
67D PHE* 1.3 93.1 - - - +
69D LEU* 1.3 57.6 + - + +
72D GLN* 2.9 37.6 + - - +
144D ASP* 5.8 0.3 - - - +
145D ALA* 3.5 14.8 + - - +
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Residues in contact with LEU 69 (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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121C PHE* 6.1 1.6 - - + -
36D TYR* 3.7 36.1 - - + +
39D LYS* 3.6 49.4 - - + +
40D LEU* 3.8 20.9 - - + +
65D PRO* 3.2 16.9 + - + +
66D ILE* 3.6 24.7 - - + +
67D PHE 3.2 0.2 - - - -
68D ASN* 1.3 77.0 - - + +
70D ALA* 1.3 62.3 + - - +
72D GLN* 3.5 2.3 + - - +
73D ILE* 3.1 30.2 + - - +
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Residues in contact with ALA 70 (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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40D LEU* 4.5 9.0 - - + +
55D VAL* 3.3 28.1 - - + +
58D ILE* 3.5 46.0 - - + -
59D ILE* 3.7 4.4 - - + +
66D ILE 3.1 5.9 + - - +
67D PHE 4.0 1.1 - - - +
69D LEU* 1.3 76.7 - - - +
71D ALA* 1.3 62.7 + - - +
73D ILE* 3.2 5.3 + - - +
74D PHE 3.0 18.9 + - - -
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Residues in contact with ALA 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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59D ILE* 3.7 12.9 - - + +
67D PHE* 2.8 42.0 + - + +
68D ASN 4.1 1.8 - - - +
70D ALA* 1.3 72.2 - - - +
72D GLN* 1.3 57.3 + - - +
74D PHE* 3.3 1.2 + - - +
75D ASN* 2.8 36.8 + - - +
145D ALA 3.1 24.9 - - - +
147D CYS* 4.1 9.2 - - + -
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Residues in contact with GLN 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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121C PHE* 3.8 5.8 - - + -
36D TYR* 3.2 51.0 + - + -
68D ASN 2.9 27.9 + - - +
69D LEU 3.9 0.2 - - - +
71D ALA* 1.3 72.5 - - - +
73D ILE* 1.3 57.8 + - - +
75D ASN* 3.4 2.9 + - - -
76D HIS* 2.6 50.7 + - - -
125D TRP* 3.2 26.7 + - - -
145D ALA* 3.4 24.0 - - + -
163D TRP* 3.4 27.0 - - - +
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Residues in contact with ILE 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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3D PHE* 5.4 1.8 - - + -
4D SER 5.1 3.4 - - - +
5D ILE* 3.6 20.9 - - + -
33D HIS* 3.2 10.5 + - + -
36D TYR* 3.8 12.8 - - + +
37D VAL* 3.6 42.0 - - + +
40D LEU* 3.8 25.1 - - + -
55D VAL* 4.1 19.5 - - + -
69D LEU 3.1 19.8 + - - +
70D ALA* 3.5 7.4 - - - +
72D GLN* 1.3 75.4 - - - +
74D PHE* 1.3 63.7 + - - +
77D ASN* 3.0 36.1 + - - +
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Residues in contact with PHE 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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55D VAL* 4.0 7.2 - - + +
56D GLU* 3.8 23.8 - - + -
59D ILE* 3.4 25.1 - - + -
70D ALA 3.0 5.6 + - - +
71D ALA 3.7 2.9 - - - +
73D ILE* 1.3 76.6 - - - +
75D ASN* 1.3 72.2 + - - +
77D ASN* 3.2 10.8 + - + +
78D PHE* 2.9 44.0 + + + +
127D TRP* 4.3 9.9 - + - -
147D CYS* 3.6 15.9 - - - -
149D LEU* 3.6 25.6 - - + -
156D PRO* 4.0 26.2 - - + -
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Residues in contact with ASN 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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71D ALA 2.8 25.0 + - - +
72D GLN* 3.4 13.1 + - - +
74D PHE* 1.3 74.1 - - - +
76D HIS* 1.3 56.1 - - - +
78D PHE* 3.4 2.8 + - - +
79D TYR* 2.9 27.9 + - - +
125D TRP* 3.5 33.6 - - + +
127D TRP* 3.3 21.4 - - + -
145D ALA 3.4 10.7 + - - -
146D GLY 3.1 22.8 + - - -
147D CYS* 3.3 24.8 - - - +
159D THR* 3.7 1.7 - - - +
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Residues in contact with HIS 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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28D HIS* 3.1 22.0 + + - -
32D HIS* 5.0 0.6 - - - +
33D HIS* 3.4 36.1 - + + +
36D TYR* 3.6 17.8 - + - -
72D GLN* 2.6 53.1 + - - +
75D ASN* 1.3 71.9 - - - +
77D ASN* 1.3 66.2 + - - +
79D TYR* 3.3 8.3 + + - +
80D TRP* 2.9 34.9 + + - +
125D TRP* 3.5 11.3 - + - -
161D ASP* 3.4 4.0 + - - -
165D HIS* 3.8 1.8 + - - -
198D FE 2.1 32.0 - - - -
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Residues in contact with ASN 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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4D SER 5.4 0.6 + - - -
5D ILE* 3.7 2.8 - - - +
6D PRO* 3.5 34.4 - - + +
33D HIS* 2.9 29.1 + - - -
55D VAL* 6.1 0.4 - - - +
73D ILE* 3.0 33.2 + - - +
74D PHE* 3.5 11.3 - - + +
76D HIS* 1.3 76.8 - - - +
78D PHE* 1.3 62.4 + - - +
80D TRP* 3.5 5.9 + - - +
81D GLU* 3.3 27.3 + - - +
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Residues in contact with PHE 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 PHE* 2.9 37.0 + + + +
75D ASN* 3.7 5.8 - - - +
77D ASN* 1.3 75.1 - - - +
79D TYR* 1.3 58.5 + - - +
81D GLU* 3.5 5.8 + - - +
82D SER* 2.9 36.4 + - - -
127D TRP* 3.7 17.0 - + + -
156D PRO* 3.3 39.9 - - + -
157D ILE 3.3 7.2 - - - -
158D LEU* 3.3 27.1 - - - -
159D THR* 4.0 5.6 - - + -
190D HIS* 3.3 30.2 + + - -
194D GLN* 3.7 14.4 - - + -
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Residues in contact with TYR 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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20D ILE* 4.5 4.2 - - - +
28D HIS* 3.5 28.2 + + - -
75D ASN 2.9 18.7 + - - +
76D HIS* 3.4 8.1 - + - +
78D PHE* 1.3 74.6 - - - +
80D TRP* 1.3 95.5 + + - +
82D SER* 3.0 16.3 + - - -
83D MET* 3.4 34.0 + - + +
125D TRP* 3.9 4.5 - - + -
159D THR* 3.5 23.0 - - + +
160D CYS* 4.1 5.2 - - - -
161D ASP* 3.4 35.9 - - + -
166D ALA* 4.2 8.0 + - - +
178D TYR* 2.8 30.7 + - - -
182D PHE* 4.8 0.4 - + - -
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Residues in contact with TRP 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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6D PRO 5.9 0.7 - - - -
7D PRO 6.3 0.2 - - - -
8D LEU* 3.4 17.7 - - + -
9D PRO* 3.7 22.7 - - + -
10D TRP* 3.1 39.6 + + + -
20D ILE* 5.9 0.9 - - + -
25D VAL* 4.4 16.8 - - + -
28D HIS* 3.5 44.9 - + + -
29D TYR* 3.5 25.4 - + + -
33D HIS* 3.0 31.0 + + - -
76D HIS* 2.9 30.3 + + + +
77D ASN* 4.0 5.6 - - - +
79D TYR* 1.3 93.8 - + - +
81D GLU* 1.3 58.2 + - - +
83D MET* 3.1 36.0 + - + +
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Residues in contact with GLU 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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9D PRO* 3.6 28.5 - - + +
77D ASN 3.3 16.6 + - - +
78D PHE* 3.7 2.9 - - - +
79D TYR 3.3 0.4 - - - -
80D TRP* 1.3 71.9 - - - +
82D SER* 1.3 55.6 + - - +
83D MET 3.1 6.4 + - - -
187D ASN* 3.0 34.3 + - - -
190D HIS* 3.2 35.9 + - + +
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Residues in contact with SER 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D PHE* 2.9 22.5 + - - -
79D TYR 3.0 8.8 + - - -
81D GLU* 1.3 75.9 - - - +
83D MET* 1.3 55.4 + - - +
158D LEU* 3.5 12.3 - - - -
159D THR 3.0 38.8 + - - -
182D PHE* 4.2 5.1 - - - -
186D VAL* 3.5 11.4 - - - +
187D ASN* 2.8 27.5 + - - -
190D HIS* 3.8 11.4 - - - -
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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
------------------------------------------------------------
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