Contacts of the helix formed by residues 62 - 84 (chain D) in PDB entry 2X2D
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 HIS 62 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D VAL* 4.3 13.3 + - + +
31D ALA* 3.8 21.4 - - + +
32D PHE* 3.8 27.6 - + + -
59D VAL* 4.5 2.9 - - + -
60D GLY 3.6 16.4 - - - -
61D GLY* 1.3 70.2 - - - +
63D GLN* 1.3 60.9 + - - +
64D ALA* 3.2 3.1 - - - -
65D ALA* 3.2 3.2 + - + -
66D MET* 2.9 28.6 + - - +
145D TYR* 2.7 45.5 + + - +
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Residues in contact with GLN 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D GLY* 3.2 30.7 - - - +
62D HIS* 1.3 78.2 + - - +
64D ALA* 1.3 64.0 + - - +
66D MET* 3.2 6.7 + - - +
67D GLN* 3.0 31.8 + - + +
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Residues in contact with ALA 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D HIS* 5.9 0.2 - - - -
63D GLN* 1.3 79.3 - - - +
65D ALA* 1.3 63.9 + - - +
67D GLN* 3.4 6.3 + - - +
68D MET* 3.0 26.0 + - + +
144D MET* 4.5 14.4 - - - -
145D TYR* 6.0 0.4 - - - +
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Residues in contact with ALA 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D PHE* 4.3 3.8 - - + -
62D HIS* 3.2 12.0 + - + +
64D ALA* 1.3 81.1 - - - +
66D MET* 1.3 58.9 + - + +
68D MET* 3.2 4.3 + - - +
69D LEU* 2.9 25.1 + - - +
141D ILE* 3.3 17.8 - - + +
144D MET* 3.6 25.3 - - + -
145D TYR* 3.4 29.1 + - + +
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Residues in contact with MET 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D PHE* 3.3 38.4 - - + -
56D LEU* 4.4 14.4 - - + +
59D VAL* 4.3 22.9 - - + +
61D GLY 4.3 7.2 - - - +
62D HIS 2.9 24.7 + - - +
63D GLN* 3.2 7.4 + - - +
65D ALA* 1.3 68.9 - - - +
67D GLN* 1.3 64.2 + - - +
69D LEU* 3.3 21.6 + - + +
70D LYS* 2.9 28.9 + - - +
141D ILE* 3.9 16.4 - - + -
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Residues in contact with GLN 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D GLN* 3.0 19.6 + - + +
64D ALA* 3.7 8.5 - - - +
66D MET* 1.3 76.3 - - - +
68D MET* 1.3 67.3 - - - +
70D LYS* 2.9 45.3 + - - +
71D GLU* 2.9 25.3 + - - +
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Residues in contact with MET 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ALA* 3.0 14.7 + - + +
65D ALA 3.2 9.4 + - - +
67D GLN* 1.3 75.9 - - - +
69D LEU* 1.3 61.8 + - - +
71D GLU* 3.3 6.4 + - - +
72D THR* 3.0 26.3 + - - +
140D LYS* 4.2 30.5 - - + +
141D ILE* 3.4 18.4 - - + -
143D ARG* 6.4 0.4 - - - -
144D MET* 3.1 41.1 - - + -
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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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56D LEU* 3.8 34.8 - - + -
65D ALA 2.9 12.4 + - - +
66D MET* 3.4 32.5 - - + +
68D MET* 1.3 76.4 - - - +
70D LYS* 1.3 63.8 + - - +
72D THR* 3.2 7.0 + - - -
73D ILE* 2.9 37.1 + - + +
134D ILE* 3.8 11.7 - - + +
137D GLY* 3.4 35.9 - - - +
138D LEU* 3.6 17.0 - - + +
141D ILE* 3.8 6.0 - - + +
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Residues in contact with LYS 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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66D MET 2.9 17.4 + - - +
67D GLN* 2.9 35.9 + - - +
69D LEU* 1.3 75.3 - - - +
71D GLU* 1.3 61.6 + - - +
73D ILE* 3.2 12.0 + - - +
74D ASN* 2.8 52.9 + - - +
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Residues in contact with GLU 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 GLN 2.9 17.2 + - - +
68D MET* 3.6 7.4 - - - +
69D LEU 3.2 0.2 - - - -
70D LYS* 1.3 80.7 - - - +
72D THR* 1.3 56.2 + - - +
74D ASN* 3.2 12.5 + - - +
75D GLU* 3.0 60.3 + - - +
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Residues in contact with THR 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 MET 3.0 15.1 + - - -
69D LEU 3.5 7.6 - - - -
71D GLU* 1.3 74.7 - - - +
73D ILE* 1.3 64.9 + - - +
75D GLU* 3.5 16.3 + - + +
76D GLU* 3.2 25.9 + - + +
133D TRP 4.3 5.4 - - - +
136D LEU* 4.3 9.2 - - + +
137D GLY* 3.5 32.9 - - - +
140D LYS* 3.7 26.8 - - + +
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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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56D LEU* 4.2 7.9 - - + -
69D LEU* 2.9 34.9 + - + +
70D LYS* 3.2 11.4 + - + +
72D THR* 1.3 74.4 - - - +
74D ASN* 1.3 65.2 + - - +
76D GLU* 3.2 6.7 + - - +
77D ALA* 2.9 27.6 + - + +
105D ALA* 4.1 14.8 - - + -
130D TYR* 3.5 33.2 - - + +
133D TRP* 4.1 12.1 - - + +
134D ILE* 3.9 37.7 - - + +
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Residues in contact with ASN 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 LYS* 2.8 40.4 + - - +
71D GLU* 3.6 15.3 - - - +
72D THR 3.1 0.4 - - - -
73D ILE* 1.3 86.5 - - - +
75D GLU* 1.3 61.3 - - - +
77D ALA* 3.4 9.3 + - - +
78D ALA* 3.1 23.4 + - - +
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Residues in contact with GLU 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D GLU* 3.0 43.3 + - - +
72D THR* 3.7 19.0 + - - +
74D ASN* 1.3 76.8 - - - +
76D GLU* 1.3 60.7 + - + +
78D ALA* 3.4 6.1 + - - +
79D GLU* 3.0 29.7 + - - +
140D LYS* 4.8 12.6 + - - -
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Residues in contact with GLU 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 THR* 3.2 16.5 + - + +
73D ILE 3.2 6.0 + - - +
75D GLU* 1.3 77.3 - - + +
77D ALA* 1.3 61.0 + - - +
79D GLU* 3.4 13.0 + - - +
80D TRP* 2.8 29.8 + - - +
133D TRP* 3.5 47.8 + - + -
136D LEU* 3.6 28.0 - - + +
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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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73D ILE 2.9 16.8 + - - +
74D ASN* 3.6 12.3 - - - +
76D GLU* 1.3 77.1 - - - +
78D ALA* 1.3 60.5 + - - +
80D TRP* 3.2 5.2 + - - +
81D ASP* 3.1 20.9 + - - -
101D GLY* 3.7 31.2 - - - +
102D SER* 4.5 2.0 - - - +
105D ALA* 5.2 4.3 - - + -
133D TRP* 3.7 16.3 - - + -
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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
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74D ASN 3.1 16.3 + - - +
75D GLU* 3.7 7.0 - - - +
77D ALA* 1.3 76.3 - - - +
79D GLU* 1.3 58.1 + - - +
81D ASP* 3.3 10.0 + - - +
82D ARG* 3.0 27.6 + - - +
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Residues in contact with GLU 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 GLU 3.0 17.6 + - - +
76D GLU* 3.8 16.2 - - - +
78D ALA* 1.3 75.7 - - - +
80D TRP* 1.3 63.8 + - - +
82D ARG* 2.4 53.1 + - - +
83D LEU* 3.1 38.1 + - + +
45E GLU* 5.7 0.2 - - - +
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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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76D GLU 2.8 18.0 + - - +
77D ALA 3.2 8.9 + - - +
79D GLU* 1.3 72.8 - - - +
81D ASP* 1.3 62.3 + - - +
83D LEU* 3.3 1.8 + - - -
84D HIS* 2.7 85.0 + + + +
99D PRO* 3.4 30.4 + - + -
100D ARG* 4.9 0.6 - - - +
101D GLY* 3.5 20.6 - - - -
104D ILE* 3.5 20.7 - - + +
124D ILE* 5.7 3.6 - - + -
129D ILE* 3.8 35.2 - - + -
132D ARG* 5.1 5.4 - - - -
133D TRP* 3.9 16.6 - + + -
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Residues in contact with ASP 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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77D ALA 3.1 10.9 + - - +
78D ALA* 3.6 11.0 - - - +
80D TRP* 1.3 78.4 - - - +
82D ARG* 1.3 63.6 + - - +
84D HIS 3.3 17.5 + - - +
85D PRO* 4.0 3.5 - - - +
100D ARG* 3.2 43.0 + - - +
101D GLY* 2.7 32.6 + - - -
102D SER 5.0 1.7 + - - -
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Residues in contact with ARG 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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78D ALA 3.0 16.7 + - - +
79D GLU* 2.4 47.9 + - - +
81D ASP* 1.3 77.3 - - - +
83D LEU* 1.3 77.7 + - - +
84D HIS 3.8 0.2 + - - -
85D PRO* 4.5 6.2 - - - +
45E GLU* 4.8 12.1 + - - -
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Residues in contact with LEU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D GLU* 3.1 33.0 + - + +
80D TRP* 5.5 0.9 - - - -
82D ARG* 1.3 105.0 - - - +
84D HIS* 1.3 77.9 + - + +
85D PRO* 3.5 9.5 - - - +
128E GLU* 5.5 7.2 - - - +
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Residues in contact with HIS 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D TRP* 2.7 84.3 + + - +
81D ASP 3.3 2.9 + - - -
83D LEU* 1.3 95.6 + - + +
85D PRO* 1.4 63.2 - - - +
86D VAL* 4.4 0.2 - - - -
99D PRO 5.6 0.9 - - - +
100D ARG* 2.5 31.4 + - - +
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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
------------------------------------------------------------
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