Contacts of the helix formed by residues 65 - 76 (chain D) in PDB entry 3HR4
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 PHE 65 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D ILE* 3.9 15.0 - - + -
12D PHE 3.9 5.2 - - - -
13D LYS* 3.2 60.1 - - + -
16D PHE* 3.5 36.2 - + + -
25D GLY 4.0 2.0 + - - +
64D ASP* 1.3 72.8 - - - +
66D PRO* 1.3 65.8 - - + +
68D PHE* 2.9 11.6 + + - +
69D LEU* 2.7 68.1 + - + +
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Residues in contact with PRO 66 (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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64D ASP* 3.4 21.1 - - + +
65D PHE* 1.3 101.7 - - + +
67D GLU* 1.3 57.9 + - + +
69D LEU* 3.9 8.8 - - + +
70D THR* 2.9 30.0 + - - -
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Residues in contact with GLU 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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55D VAL* 3.6 27.9 - - + +
56D ASP* 3.5 4.9 - - - +
57D ALA* 3.4 21.6 - - + +
58D ASP* 2.8 36.1 + - - +
62D THR 3.3 9.7 - - - +
63D ILE* 3.7 2.2 - - + -
64D ASP* 2.7 32.0 + - - +
66D PRO* 1.3 77.0 - - + +
68D PHE* 1.3 62.2 + - - +
70D THR* 3.8 7.4 - - - +
71D MET* 3.5 15.6 + - - +
202D CA 2.7 24.4 - - - -
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Residues in contact with PHE 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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520C LYS 5.2 0.4 - - - -
524C PHE* 3.3 60.1 - + + -
12D PHE* 3.4 32.1 - + + -
15D ALA* 4.2 9.6 - - + -
16D PHE* 3.8 39.9 - + + -
19D PHE* 4.5 4.5 - + - -
27D ILE* 4.2 9.4 - - + -
55D VAL* 4.7 3.1 - - - -
63D ILE* 4.2 8.4 - - + +
64D ASP 3.0 10.5 + - - +
65D PHE* 2.9 15.2 + + - +
67D GLU* 1.3 76.0 - - - +
69D LEU* 1.3 66.8 + - - +
71D MET* 3.5 3.5 + - - +
72D MET* 3.2 37.8 + - + +
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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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3D GLN* 4.3 14.1 - - - +
9D ILE* 4.1 22.0 - - + -
12D PHE* 4.7 14.1 - - + -
65D PHE* 2.7 50.6 + - + +
66D PRO* 3.9 8.5 - - + +
68D PHE* 1.3 75.1 - - - +
70D THR* 1.3 66.8 + - - +
72D MET* 3.2 3.9 + - - -
73D ALA* 2.9 40.3 + - + +
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Residues in contact with THR 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 PRO 2.9 19.4 + - - -
67D GLU* 3.8 9.4 - - - +
69D LEU* 1.3 79.6 - - - +
71D MET* 1.3 66.1 + - - +
73D ALA* 3.5 4.4 + - - +
74D ARG* 3.3 36.6 + - + +
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Residues in contact with MET 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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524C PHE* 3.4 33.9 - - + +
527C MET* 3.4 38.8 - - + -
528C LEU* 4.5 7.9 - - + -
54D GLU 6.1 0.2 - - - +
55D VAL* 3.6 33.4 - - + -
67D GLU 3.5 11.2 + - - +
68D PHE 3.8 6.3 - - - +
69D LEU 3.3 0.6 - - - -
70D THR* 1.3 80.6 - - + +
72D MET* 1.3 72.5 + - - +
74D ARG* 3.1 37.3 + - - +
75D LYS* 3.2 23.1 + - + +
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Residues in contact with MET 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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520C LYS 3.2 27.4 - - - +
523C LEU* 4.3 15.7 - - + -
524C PHE* 3.8 22.0 - - + +
527C MET* 4.1 8.1 - - - +
12D PHE* 3.5 47.1 - - + -
68D PHE* 3.2 28.6 + - + +
69D LEU* 3.8 3.4 - - - +
71D MET* 1.3 100.7 - - - +
73D ALA* 1.3 58.2 + - - +
74D ARG 2.8 6.9 + - - -
76D MET* 3.0 29.9 + - - +
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Residues in contact with ALA 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 GLN* 3.4 41.0 - - + +
12D PHE* 5.0 3.5 - - + -
69D LEU* 2.9 28.1 + - + +
70D THR* 3.8 5.2 - - - +
72D MET* 1.3 70.3 - - - +
74D ARG* 1.3 56.1 + - - +
76D MET* 4.6 5.6 - - - -
77D LYS* 3.4 23.5 + - - +
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Residues in contact with ARG 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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54D GLU 5.3 6.9 + - - -
70D THR* 3.3 38.8 + - + +
71D MET* 3.1 33.7 + - - +
72D MET 2.8 4.4 + - - -
73D ALA* 1.3 78.5 - - - +
75D LYS* 1.3 77.2 + - + +
76D MET 3.0 3.8 - - - -
77D LYS* 3.1 34.1 + - - +
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Residues in contact with LYS 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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527C MET* 3.0 48.3 - - + +
531C LYS* 4.7 19.2 - - - +
71D MET* 3.2 11.5 + - + +
74D ARG* 1.3 106.5 - - + +
76D MET* 1.3 54.2 + - - +
77D LYS 2.8 6.8 + - - -
78D ASP* 2.6 29.2 + - - +
80D ASP* 5.9 0.2 + - - -
81D SER* 3.5 12.3 - - - -
84D GLU* 3.7 26.0 + - - +
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Residues in contact with MET 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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520C LYS* 4.8 4.5 - - + +
523C LEU* 3.8 28.7 - - + -
527C MET* 4.9 2.9 - - - +
8D GLN* 5.9 2.5 - - - +
12D PHE* 3.5 34.1 - - + -
72D MET* 3.0 21.7 + - - +
73D ALA* 4.6 6.3 - - - -
74D ARG 3.0 1.0 - - - -
75D LYS* 1.3 74.1 - - - +
77D LYS* 1.3 69.2 + - + +
81D SER* 4.7 10.6 + - - -
85D ILE* 5.7 4.3 - - + -
145D MET* 3.8 30.7 - - + +
146D THR* 4.8 14.4 - - + +
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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
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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