Contacts of the helix formed by residues 66 - 78 (chain D) in PDB entry 1H69
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 GLN 66 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193B GLY* 6.1 1.2 - - - -
1274B FAD 2.8 48.1 + - - +
64D ASN* 3.4 28.3 + - - +
65D PHE* 1.3 80.1 - - - +
67D TYR* 1.3 66.6 + - - +
68D PRO* 3.3 9.9 - - + -
69D ALA* 3.6 13.2 + - + +
70D GLU* 3.2 26.7 + - + +
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Residues in contact with TYR 67 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1274B FAD 3.6 25.1 - - + -
50D ILE* 3.7 36.6 - - + +
51D SER* 3.5 13.7 - - - -
54D ASP* 2.6 38.5 + - + +
55D ILE* 4.7 2.5 - - + -
65D PHE* 3.7 34.6 - + + -
66D GLN* 1.3 70.6 - - - +
68D PRO* 1.3 64.4 - - + +
71D SER* 2.6 59.2 + - - -
80D LEU* 5.7 0.2 - - - +
84D ILE* 4.2 1.6 - - - +
117D GLU 4.0 10.3 - - - -
118D ARG* 4.0 5.5 - - - -
121D ILE* 3.8 15.5 - - + +
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Residues in contact with PRO 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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1274B FAD 3.8 43.7 - - + +
1275B ARH 3.7 24.0 - - + +
66D GLN* 3.3 10.1 - - + -
67D TYR* 1.3 93.2 - - + +
69D ALA* 1.3 62.7 + - - +
71D SER* 2.8 19.6 + - - +
72D VAL* 3.0 19.8 + - + +
126D TYR* 5.4 5.6 - - - +
128D TYR* 5.1 1.1 - - - +
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Residues in contact with ALA 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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60D LYS* 6.5 1.1 - - + -
66D GLN* 3.6 15.7 + - + +
67D TYR 3.5 0.2 - - - -
68D PRO* 1.3 79.5 - - - +
70D GLU* 1.3 59.3 + - + +
72D VAL* 3.3 6.5 + - - +
73D LEU* 3.0 29.7 + - - +
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Residues in contact with GLU 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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55D ILE* 3.9 10.6 - - + +
59D LEU* 3.6 18.4 - - - +
60D LYS* 3.0 28.7 + - - +
61D ASP* 2.9 37.0 + - - +
64D ASN 5.1 0.2 - - - +
65D PHE* 3.6 29.5 - - + -
66D GLN* 3.2 21.1 + - + +
67D TYR 4.1 0.9 - - - +
69D ALA* 1.3 77.2 - - + +
71D SER* 1.3 59.2 + - - +
73D LEU* 3.4 7.6 + - - +
74D ALA* 2.9 29.1 + - - +
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Residues in contact with SER 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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54D ASP* 6.1 0.2 - - - -
55D ILE* 4.6 5.3 - - - +
67D TYR* 2.6 53.7 + - - -
68D PRO* 2.8 13.9 + - - +
70D GLU* 1.3 74.7 - - - +
72D VAL* 1.3 60.5 + - - +
74D ALA* 3.4 7.8 + - - +
75D TYR* 2.9 26.7 + - - +
80D LEU* 3.8 7.5 - - - +
121D ILE* 3.5 25.8 - - - +
122D GLY 5.1 0.9 + - - -
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Residues in contact with VAL 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 PRO* 3.0 20.9 + - + +
69D ALA* 3.7 6.7 - - - +
71D SER* 1.3 76.1 + - - +
73D LEU* 1.3 59.5 + - - +
75D TYR* 3.1 4.8 + - - +
76D LYS* 2.9 55.5 + - - +
121D ILE* 4.1 5.8 - - - -
122D GLY* 3.7 30.5 - - - +
123D GLU* 3.5 16.2 - - + -
126D TYR* 5.5 1.8 - - - +
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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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58D LYS 6.2 0.2 - - - +
60D LYS* 3.4 57.7 - - + +
69D ALA 3.0 17.4 + - - +
70D GLU* 3.7 9.4 - - - +
72D VAL* 1.3 76.1 - - - +
74D ALA* 1.3 65.6 - - - +
76D LYS* 3.1 14.3 + - + +
77D GLU* 2.9 64.2 + - + +
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Residues in contact with ALA 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 ILE* 3.7 28.0 - - + -
70D GLU 2.9 18.1 + - - +
71D SER 3.6 5.2 - - - +
73D LEU* 1.3 75.7 - - - +
75D TYR* 1.3 57.9 + - - +
77D GLU* 3.6 3.8 - - - +
78D GLY 2.8 9.0 + - - -
79D HIS* 2.6 47.1 + - - +
80D LEU* 3.9 13.7 - - + -
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Residues in contact with TYR 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 SER 2.9 15.1 + - - +
72D VAL* 3.1 12.1 + - - +
74D ALA* 1.3 77.0 - - - +
76D LYS* 1.3 68.6 + - + +
78D GLY* 3.1 12.7 + - - -
80D LEU* 3.7 27.6 - - + +
85D VAL* 6.3 0.2 - - + -
88D GLN* 3.7 12.6 - - - -
92D GLU* 4.0 7.8 + - - -
121D ILE* 4.2 4.3 - - + -
122D GLY 4.1 1.6 - - - -
123D GLU* 3.8 24.4 + - + -
124D PHE* 3.4 50.9 - + + +
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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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72D VAL* 2.9 30.7 + - + +
73D LEU* 3.6 14.6 - - + +
75D TYR* 1.3 83.6 - - + +
77D GLU* 1.3 63.7 + - + +
78D GLY 3.4 0.7 + - - -
123D GLU* 3.1 42.9 + - + +
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Residues in contact with GLU 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 50.8 + - + +
74D ALA* 4.6 0.5 + - - -
76D LYS* 1.3 77.3 - - + +
78D GLY* 1.3 62.9 + - - +
79D HIS* 3.4 37.9 + - + +
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Residues in contact with GLY 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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56D THR* 5.0 0.2 + - - -
74D ALA 2.8 8.6 + - - -
75D TYR* 3.1 12.1 + - - -
76D LYS 3.2 1.4 + - - -
77D GLU* 1.3 79.6 - - - +
79D HIS* 1.3 60.6 + - - -
80D LEU* 3.5 4.8 + - - +
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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