Contacts of the helix formed by residues 62 - 81 (chain D) in PDB entry 2YEV
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 THR 62 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D GLN* 4.3 2.7 - - - +
58D ASN 3.7 17.3 - - - +
59D GLN* 3.3 35.3 + - - +
61D LEU* 1.3 83.4 - - - +
63D GLY* 1.3 68.9 - - - +
64D GLU 3.4 0.3 + - - -
65D GLN* 3.1 26.2 + - - +
66D TYR* 3.2 4.8 + - - -
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Residues in contact with GLY 63 (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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62D THR* 1.3 73.8 - - - +
64D GLU* 1.3 63.3 + - - -
65D GLN* 5.1 0.2 - - - -
66D TYR* 3.1 7.0 + - - +
67D ASN* 3.0 30.8 + - - +
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Residues in contact with GLU 64 (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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62D THR 3.4 0.6 + - - -
63D GLY* 1.3 70.9 - - - -
65D GLN* 1.3 73.0 + - - +
67D ASN* 3.2 14.8 + - - +
68D GLN* 2.9 49.6 + - - +
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Residues in contact with GLN 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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61D LEU* 3.8 17.3 - - + -
62D THR* 3.1 16.0 + - - +
64D GLU* 1.3 92.5 + - - +
66D TYR* 1.3 62.4 + - - +
68D GLN* 3.3 20.8 + - - +
69D ILE* 3.1 27.0 + - - +
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Residues in contact with TYR 66 (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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49D ILE* 3.5 40.4 - - + +
52D GLN* 3.9 17.7 - - + -
53D LEU* 3.7 19.8 - - + +
61D LEU* 3.7 45.0 - - + +
62D THR* 3.2 7.8 + - - -
63D GLY 3.1 9.9 + - - +
65D GLN* 1.3 78.9 - - - +
67D ASN* 1.3 71.1 + - - +
69D ILE* 3.1 3.6 + - - +
70D LEU* 2.8 51.9 + - + +
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Residues in contact with ASN 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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63D GLY* 3.0 18.4 + - - +
64D GLU* 3.7 17.0 + - - +
66D TYR* 1.3 92.0 - - - +
68D GLN* 1.3 54.0 + - + +
70D LEU* 3.8 10.7 - - + +
71D THR* 2.7 36.7 + - - +
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Residues in contact with GLN 68 (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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64D GLU* 2.9 39.5 + - + +
65D GLN* 3.5 26.0 + - - +
66D TYR 3.1 0.4 - - - -
67D ASN* 1.3 75.4 - - + +
69D ILE* 1.3 69.1 + - + +
71D THR* 3.2 4.7 + - - -
72D LEU* 2.9 34.1 + - + +
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Residues in contact with ILE 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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45D PHE* 3.6 54.0 - - + +
48D LEU* 4.5 12.1 - - + -
49D ILE* 4.0 10.3 - - + -
61D LEU* 3.9 26.2 - - + -
65D GLN 3.1 14.9 + - - +
66D TYR 3.7 5.4 - - - +
68D GLN* 1.3 76.4 - - + +
70D LEU* 1.3 52.8 + - - +
72D LEU* 3.3 11.2 + - + +
73D HIS* 2.8 33.3 + - - +
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Residues in contact with LEU 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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49D ILE* 3.9 23.3 - - + +
66D TYR* 2.8 42.3 + - + +
67D ASN* 3.8 11.9 - - - +
69D ILE* 1.3 76.5 - - - +
71D THR* 1.3 64.6 + - - +
73D HIS* 3.2 10.3 + - + +
74D GLY* 3.1 20.0 + - - -
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Residues in contact with THR 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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67D ASN* 2.7 23.9 + - - +
68D GLN* 3.7 4.9 - - - -
70D LEU* 1.3 78.6 - - - +
72D LEU* 1.3 67.1 + - + +
74D GLY* 3.5 0.7 + - - -
75D ALA* 3.1 30.1 + - + +
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Residues in contact with LEU 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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45D PHE* 3.7 30.9 - - + -
68D GLN* 2.9 25.2 + - + +
69D ILE* 3.8 10.3 - - + +
71D THR* 1.3 75.8 - - + +
73D HIS* 1.3 66.6 + - - +
75D ALA* 4.8 4.0 - - + +
76D THR* 2.8 35.8 + - - +
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Residues in contact with HIS 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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42D ALA* 2.8 27.7 + - - +
45D PHE* 3.9 14.1 - - + -
46D SER* 3.5 21.2 - - - -
49D ILE* 4.0 22.0 - - + -
69D ILE 2.8 20.5 + - - +
70D LEU* 3.2 11.0 + - + +
72D LEU* 1.3 73.4 - - - +
74D GLY* 1.3 67.2 + - - +
77D MET* 3.1 55.9 + - + +
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Residues in contact with GLY 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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70D LEU 3.1 10.2 + - - -
71D THR* 4.0 1.6 - - - -
73D HIS* 1.3 88.4 - - - +
75D ALA* 1.3 56.3 + - - +
77D MET* 3.4 4.6 + - - +
78D LEU* 3.0 40.0 + - - +
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Residues in contact with ALA 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 THR* 3.1 23.8 + - + +
72D LEU* 4.5 4.5 - - + +
74D GLY* 1.3 76.5 - - - +
76D THR* 1.3 58.1 + - - +
78D LEU* 4.6 2.2 - - - +
79D PHE* 2.8 55.8 + - + +
80D PHE* 4.5 6.1 - - + -
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Residues in contact with THR 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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38D ALA* 3.6 36.1 - - + +
41D LEU* 4.9 11.5 - - + +
42D ALA* 3.7 12.1 - - + +
45D PHE* 4.7 4.7 - - - -
72D LEU* 2.8 31.8 + - - +
75D ALA* 1.3 76.2 - - - +
77D MET* 1.3 62.8 + - - +
80D PHE* 3.0 40.9 + - + +
81D PHE* 3.2 8.0 + - - +
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Residues in contact with MET 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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39D PHE* 3.5 54.3 - - + +
42D ALA* 3.6 17.9 - - + -
43D GLY* 3.6 11.4 - - - +
73D HIS* 3.1 41.7 + - + +
74D GLY* 3.8 4.7 - - - +
76D THR* 1.3 77.6 - - - +
78D LEU* 1.3 62.7 + - + +
81D PHE* 3.4 15.1 - - + +
82D ILE* 3.0 32.9 + - + +
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Residues in contact with LEU 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 GLY* 3.0 24.4 + - - +
75D ALA* 4.2 3.8 - - - +
77D MET* 1.3 83.8 - - + +
79D PHE* 1.3 72.1 + - + +
82D ILE* 3.8 15.0 - - + +
83D ILE* 3.2 29.3 + - - +
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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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75D ALA* 2.8 42.7 + - + +
78D LEU* 1.3 84.3 - - + +
80D PHE* 1.3 78.9 + + + +
81D PHE 3.7 0.2 - - - -
83D ILE* 3.7 9.7 - - + +
84D GLN* 2.9 27.9 + - - +
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Residues in contact with PHE 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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34D THR* 4.5 2.2 - - + +
35D ALA* 3.3 20.4 + - - -
38D ALA* 3.5 15.1 - - + +
75D ALA* 4.5 4.9 - - + -
76D THR* 3.0 38.9 + - + +
79D PHE* 1.3 98.6 - + + +
81D PHE* 1.3 59.5 + - - +
84D GLN* 3.6 13.4 - - - +
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Residues in contact with PHE 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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35D ALA* 3.3 24.6 - - - +
36D PHE* 3.9 28.3 - + - -
38D ALA* 4.2 0.2 - - + -
39D PHE* 3.3 52.0 - + + +
76D THR 3.2 7.9 + - - +
77D MET* 3.4 21.4 + - + +
79D PHE 3.7 0.8 - - - -
80D PHE* 1.3 78.8 - - - +
82D ILE* 1.3 91.9 + - + +
83D ILE 3.3 2.2 - - - -
84D GLN* 2.9 19.6 + - - +
85D ALA* 2.9 27.5 + - + +
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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